Synthetic cancer-specific promoters

Described herein are synthetic promoters and/or enhancers that are specific for cancer cells and methods of engineering synthetic cancer-specific promoters.

1. 11. A method for increasing expression of a gene in a cancer cell as compared with a non-cancer cell, the method comprising, administering a recombinant polynucleotide to a subject with cancer, wherein said recombinant polynucleotide comprises: a) one or more synthetic response elements comprising one or more enhancers and a plurality of transcription factor binding sites; b) a core promoter operably linked to an open reading frame (ORF) comprising said gene, wherein said core promoter comprises a promoter element obtained from one or more cancer-responsive genes; and c) a transcription start site (TSS) upstream of said ORF, wherein said one or more synthetic response elements and said core promoter increase transcription of said gene in said cancer cell of said subject as compared with a non-cancer cell.
2. 22. The method of claim 1, wherein said one or more cancer-responsive genes has at least a 10-fold increase in expression in cancer cells compared to non-cancer cells.
3. 33. The method of claim 1, wherein said gene encodes a therapeutic protein.
4. 44. The method of claim 1, wherein said gene encodes a biomarker protein.
5. 55. The method of claim 1, wherein said gene is transcribed at a higher level in said cancer cell compared to said non-cancer cell as determined by chromatin immunoprecipitation (ChIP).
6. 66. The method of claim 1, wherein said one or more cancer-responsive genes is a Homo sapiens cancer-responsive gene.
7. 77. The method of claim 1, wherein said recombinant polynucleotide further comprises a spacer element disposed between two enhancers of said one or more enhancers, wherein said spacer element comprises 1-20 contiguous nucleotides.
8. 88. The method of claim 1, wherein said one or more cancer-responsive genes comprises FAM111B or KIF20A.

CROSS REFERENCE
This application claims the benefit of U.S. Provisional Application No. 63/834,389, filed on Jan. 22, 2025, and is a Continuation in-part of U.S. Nonprovisional Application No. 18/455,209, filed on Aug. 24, 2023, which is a Continuation of U.S. Nonprovisional Application No. 17/219,666, filed Mar. 31, 2021, now U.S. Pat. No. 12,060,613, issued Aug. 13, 2024, which is a Continuation in-part of International Application No. PCT/US2020/026758, filed Apr. 4, 2020, which claims benefit of U.S. patent application No. 62/955,925, filed Dec. 31, 2019, and U.S. Provisional Application No. 62/830,279, filed Apr. 5, 2019, each of which are incorporated by reference herein in their entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML format sequence listing, created on May 22, 2025, is named 53531-724_201_SL.xml, and is 704,717 bytes in size.
BACKGROUND
Endogenous cancer-activated promoters are controlled by a wide network of transcription factors (TFs), which can lead to non-ideal basal activity in non-target cells. It is also difficult to reliably predict the activity in a wide variety of cancer models.
SUMMARY
There is a need to develop synthetic cancer-specific promoters with high specificity and sensitivity, for use in delivering polypeptides to cancer cells.
In some aspects, provided herein is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells. In some embodiments, the recombinant polynucleotide further comprises a plurality of enhancers. In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some aspects, provided herein is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS) and two or more promoter elements derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells. In some embodiments, the recombinant polynucleotide further comprises a plurality of enhancers. In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some aspects, provided herein is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and (b) a plurality of enhancers. In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some aspects, provided herein, is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF), (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells, and (c) a plurality of enhancers. In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some aspects, provided herein is a recombinant polynucleotide comprising any of the sequences from Table 1A, Table 1B, or Table 1C. In some aspects, provided herein is a recombinant polynucleotide comprising a human alpha-fetoprotein (AFP) promoter sequence comprising a plurality of HNF-1A TF binding sites, wherein each HNF-1A binding site comprises the sequence 5′-GTTAATTATTAAC-3.′
In some aspects, provided herein is a vector comprising any of the recombinant polynucleotide described herein. In some aspects, provided herein is a pharmaceutical composition comprising any of the recombinant polynucleotide described herein or any the vector described herein and a pharmaceutically acceptable excipient, carrier, or diluents. In some aspects, provided herein is a lipid nanoparticle (LNP) comprising any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the pharmaceutical composition described herein. In some aspects, provided herein is a cell comprising any the recombinant polynucleotide described herein, any of the vector described herein, any of the pharmaceutical composition described herein, or any of the LNP described herein.
In some aspects, provided herein is a method of selectively expressing a reporter protein in a cancer or tumor cell, comprising contacting said tumor cell with any of the recombinant polynucleotide described herein, any of the vector described herein, any of the pharmaceutical composition described herein, or any of the LNP described herein, wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding said reporter protein, wherein said ORF is operatively linked to said synthetic promoter.
In some aspects, provided herein is a method comprising: (a) administering to a subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) detecting said reporter protein, wherein said pharmaceutical composition or said composition induces expression of said reporter protein preferentially in diseased cells in said subject compared to in non-disease cells, and wherein a relative ratio of said reporter protein expressed in said diseased cells over said non-diseased cells is greater than 1.0.
In some aspects, provided herein is a method for treating a subject having or suspected of having a disease, comprising administering to said subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a therapeutic protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, wherein said pharmaceutical composition or said composition induces expression of said therapeutic protein preferentially in diseased cells in said subject compared to in non-disease cells, and wherein a relative ratio of said therapeutic protein expressed in said diseased cells over said non-diseased cells is greater than 1.0.
In some aspects, provided herein is a method comprising: (a) administering to a subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) localizing a tumor or an absence thereof in a body of said subject via expression of said reporter protein using an imaging technique performed on said body of said subject.
In some aspects, provided herein is a method comprising: (a) introducing to a subject suspected of having a cancer via intravenous administration any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein said recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) detecting said reporter protein from said subject.
In some aspects, provided herein is a method comprising: (a) introducing to a subject suspected of having a cancer via intravenous administration a plurality of recombinant polynucleotides, wherein: said plurality of recombinant polynucleotides comprises a plurality of different promoters of genes overexpressed in a tumor cell versus a normal tissue or functional fragments thereof operably linked to genes encoding reporter proteins, wherein said plurality of different promoters of genes overexpressed in said tumor cell versus said normal tissue drive expression of said corresponding reporter proteins in a cell affected by said cancer, wherein said DNA molecules are selected from the group consisting of nanoplasmids and linear double-stranded DNA molecules; and (b) detecting said reporter proteins from said subject.
INCORPORATION BY REFERENCE
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.



BRIEF DESCRIPTION OF THE DRAWINGS
The features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:
FIG. 1 shows a schematic of synthetic promoter architecture and design including, for example, a fragment of SEQ ID NO: 378.
FIG. 2 describes coreCEACAM5 design, including, for example, a fragment of SEQ ID NO: 121.
FIG. 3 describes coreCEP55 design.
FIG. 4 describes coreFAM111B design.
FIG. 5 describes coreAGR2 design.
FIG. 6 shows the comparison of the reporter gene expression by endogenous promoter and synthetic promoter in H1299 cells.
FIG. 7 shows the reporter gene expression performance by synthetic promoters in human PDX models. Bar graphs from left to right: BIRC5, FOSL1-coreBIRC5, FOSL1-CEACAM5, FOSL1-FAM111B, FOSL1-KIF20A, FOSL1-AGR2, and FOSL1-TATA, respectively.
FIG. 8 shows signal-to-noise profiles of the reporter gene expression by synthetic promoters. Bar graphs from left to right: BIRC5, FOSL1-coreBIRC5, FOSL1-FAM111B, FOSL1-KIF20A, FOSL1-AGR2, FOSL1-CST1, and FOSL1-TATA, respectively.
FIG. 9 shows the reporter gene expression by synthetic promoters in H1299 cells.
FIG. 10 describes the workflow of synthetic promoter design and construction.
FIG. 11 describes the workflow of synthetic promoter design and construction with coreAGR2.
FIG. 12 describes the synthetic promoter architecture, design, discovery and validation pipeline.
FIG. 13 describes Transcription Factor Tile Design (top) and how to measure synthetic element expression (bottom). Each synthetic DNA sequence was designed as a series of repeated transcription factor (TF) binding sites derived from the consensus binding motif for the TF of interest (blue). To test the impact of the different relative positioning of these sites around the helical nature of the double stranded DNA (one helical turn is equivalent to ˜10.5 base pairs), the repeated binding sites are separated by a variable length of nucleic acid spacer sequences (yellow). Lastly, the synthetic DNA sequence contains a short filler sequence (grey) to maintain consistent total length of the candidate enhancer sequence block.
FIG. 14 shows Expression Score Distribution Across Lung Cancer Models. The expression score distribution varies across different lung cancer models. The PDX cell line LXFL430 had the widest distribution and outliers with the highest expression scores.
FIG. 15 shows the reporter gene expression by HOXC10 tiles. Using a luciferase reporter assay lead candidates representing the MNX1, HOXC10 and CREB3L1 transcription factors were tested across seven lung cancer cell line models (H1299, PDX430, PDX1121, PDX629, PDX529, PDX586, and PDX2184) and one lung normal cell line (IMR90). Higher expression compared to FOSL-coreBIRC5 lead synthetic promoter with up to 50-80 fold improvement was observed.
FIG. 16 shows the reporter gene expression by TCF7L1 TF tiles in PDX430 cell line.
FIG. 17 shows Wnt-driven cell lines identified by PCA (LK2 and NCI-H520) driving the expression by TCF7 and TCF7L1 promoters. In a transient transfection of two TCF7 variant promoters across five cell lines, H520 and LK-2 show the same high levels of activation as PDX430, which was predicted by the PCA analysis. As expected, H1299 and A549 cell lines do not show substantial expression by the TCF7 promoters, and are much better represented by the FOS-coreBIRC5 promoter.
FIG. 18 shows the expression of the reporter gene by TP53 elements. Addition of TP53 elements to TATA-TSS core results in significantly increased expression of the reporter gene in PDX586 as predicted by HTS-002.
FIG. 19 shows the expression of the reporter gene by TP53 variants in A549 cells.
FIG. 20 shows PCA analysis in H1944 and H2023 cells.
FIG. 21A shows a table comparing mutation status of P53, key gene set expression, and TP63 expression in different cancer cell lines.
FIGS. 21B and 21C show mutation profile in Clinical Proteomic Tumor Analysis Consortium (CPTAC) Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), respectively.
FIG. 22 shows the reporter gene expression by p53 in A549, H1944, and H358 cell lines.
FIG. 23 shows a table comparing TP53 status and reporter gene expression in different cell lines.
FIG. 24 shows the reporter gene expression by TP53 and TCF7. Pathway specific TP53 and TCF7 response elements pair well and get higher signal using new non-coreBIRC5 cores. As observed with the FOS response element, TP53 and TCF7 response elements combined with coreCST1, coreAGR2, and coreFAM111B show up to a 10-fold signal increase compared to the same promoters constructed with coreBIRC5.
FIG. 25 shows the reporter gene expression by coreBIRC5 and coreAGR2 combined with different response elements in H1299, PDX430, and PDX586 cell lines.
FIG. 26 shows the reporter gene expression by coreBIRC5, coreAGR2, coreFAM111B combined with different response elements in different cell lines.
FIG. 27 shows fold change in expression of reporter genes from constructs comprising combination of FOSL and CREB3L1.
FIG. 28 shows fold change in expression of reporter genes from constructs comprising combination of TCF7 and TP53.
FIG. 29 shows validation of top ranked TF tiles with the coreBIRC5 promoter. Using a luciferase reporter assay various TF tiles that were highly ranked in the MPRA screens for H1299 and LXFL430 were tested. Many of the TF tiles showed stronger expression than the base expression of the coreBIRC5 and the FOSL-coreBIRC5. The TCF7L1 TF tiles showed specific expression in the LXFL430 cell line.
FIGS. 30A and 30B show expression of synthetic promoter FOS-coreBIRC5 in PDX cell lines and normal lung cell lines. Compared to endogenous promoters, including the Survivin (BIRC5) promoter and other first-generation endogenous promoters used in multiplexes, the synthetic promoter FOS-coreBIRC5 outperformed in terms of strength and sensitivity in 8 PDX cell lines that represent different patients' genomic profiles (FIG. 30A). FIG. 30B shows that the synthetic promoter also demonstrates lack of expression in normal human fibroblast cell line (IMR-90), small airway epithelial cells (SAEC) and normal human bronchial epithelial cells (NHBE).
FIG. 31 shows the top 30 contributing features that make up a factor of MOFA analysis.
FIG. 32 shows comparison of reporter gene expression by FOSL2 in Normal Adjacent Tissues (NAT) and tumor.
FIG. 33 shows the binding of FOSL2 and C-Jun TFs to the FOS element in the FOS-coreBIRC5 promoter. Chromatin immunoprecipitation (ChIP) was performed on two different cell lines transfected with the FOS-coreBIRC5 promoter construct (e.g., SEQ ID NO: 169). Pulldowns for FOSL2 and c-Jun showed significant enrichment of the coreBIRC5 element compared to nonspecific pulldown, by 14× for FOSL2 in H1299 and 5× for FOSL2 in A549. With the comparison to the control construct of solely coreBIRC5, this makes it clear that the FOS response element is responsible for the association of FOSL2 and C-Jun with the synthetic promoter.
FIG. 34 shows demonstration of high sensitivity and specificity in primary-derived and commercial cell lines by chimeric promoters using core-BIRC5. Response elements for different TFs (FOSL2, TWIST1, ETV4) in combination with the coreBIRC5 promoter showed variable sensitivity across different PDX cell lines, H1299 NSCLC cell line, and a lack of expression in IMR-90 (normal human fibroblast) cell line.
FIG. 35 shows the activity of TCF7 & TCFL1 variants in different cell lines. TCF7 & TCFL1 variants were only active in PDX LXFL430 among cell lines tested. Two variants of the TCF7-response element promoter, as compared to the minimal coreBIRC5 and positive control FOS-coreBIRC5 promoter, demonstrated extremely high levels of expression in the large cell lung cancer PDX430.
FIG. 36 shows that alternative core promoters to coreBIRC5 demonstrate high utility in synthetic promoter constructs. The full-length endogenous promoters, core promoters, and FOS-core promoters using BIRC5, FAM111B, AGR2 and CST1 were tested in two lung cancer cell lines—H1299 and PDX629. The use of the new cores with FOS demonstrated up to 20-fold improvement in signal compared to the original FOS-coreBIRC5 promoter described previously. On the bottom, experiments using three primary normal lung cell lines (small airway epithelial cells from two donors and normal human lung fibroblasts) demonstrated the FOS-coreAGR2 and FOS-coreCST1 constructs still maintain high specificity for cancer, while FOS-coreFAM111B appears to have significant noise in lung fibroblasts.
FIG. 37 shows reporter gene expression derived by different synthetic promoters in cancer epithelial cells, cancer associated fibroblast cells, and normal adjacent tissue (NAT) cells from patient derived cell lines (LU057: 63/F/White, Stage IIIB Adeno-squamous pT4, N2). *: not tested. dotted line: CAG, constitutive promoter.
FIGS. 38A and 38B show AFP-3, an engineered variant of the human alpha-fetoprotein (AFP) promoter that can drive strong and highly specific expression in HCC. In FIG. 38A, the primary changes to the AFP promoter sequence are shown, changing the HNF-1A sites to the consensus sequence for the transcription factor binding site. FIG. 38A discloses SEQ ID NOs: 553-554 and 128, respectively, in order of appearance. FIG. 38B shows that engineered AFP-3 (SEQ ID NO: 554) drives up to 200-fold higher expression in liver cancer cell lines than the wildtype AFP promoter (SEQ ID NOs: 553), while still maintaining high specificity against lung normal (IMR-90, MRC-9), lung cancer (H1299) and melanoma (MeWo) cell lines, as compared to the Survivin (BIRC5) promoter which shows some cancer-activated activity in both liver and non-liver cancer cell lines.
FIG. 39 shows signal-to-noise ratio of SEAP in Hep3B orthotopic tumor model. Secreted alkaline phosphatase (SEAP) was measured from the serum of tumor-bearing and normal animals dosed with the BIRC5-SEAP construct versus the AFP-3-SEAP construct. At the day 0 bleed (pre-dosing), background levels of SEAP in all mice were below the lower limit of quantification (LLOQ) of the assay (0.4 pg/12.5 uL), as expected. At 3 days post-dose, the BIRC5-SEAP construct dosed animals showed a 7-fold increase of SEAP reporter in the serum over the LLOQ, with no background expression at all in non-tumored animals. The AFP-3 construct promoted expression in tumored animals approximately 97-fold higher than non-tumored animals.
FIGS. 40A, 40B, and 40C show immunohistochemistry (IHC) results for AFP-3-sr39tk, using HA epitope. FIGS. 40A and 40B show representative serial sections from the tumor-bearing left lobe of a mouse in Group 6 (AFP-3-sr39tk) dosed at 2.8mpk of EM-40 stained by H&E and by HA antibody for the reporter expression. The tumor boundary has been outlined in the H&E slide. Reporter expression is confined to the tumor cells only. In FIG. 40C, the same mouse's right liver lobe, devoid of tumor is shown to have no positive cells.
FIGS. 41A, 41B, 41C, 41D, 41E, and 41F show IHC results for positive control CAG-sr39tk. Serial sections of the tumor-containing left lobe from a mouse in Group 10 show positive staining in the tumor (FIGS. 41A and 41B; stained dark purple by H&E). Left and right lobe sections from the same mouse show occasional disperse signal from individual cells (FIGS. 41C and 41D). Serial sections stained by H&E and by IHC for the -HA tag for a second mouse's tumor also show many positive-stained cells throughout the tumor tissue, as outlined in the H&E figure (FIGS. 41E and 41F).
FIG. 42 shows images of animal bioluminescence.
FIGS. 43A, 43B, 43C, and 43D show muti-omics data on benign cell lines.
FIG. 44 shows that there is no reporter expression by synthetic promoter constructs in granulomatous lesions caused by Mycobacterium tuberculosis (M. tb) infection in CBA/J mice despite high disease burden.
FIG. 45 shows the reporter gene expression performance by different synthetic promoters in various cancer and non-cancer cell lines. Combining the FOS element with new core promoters resulted in significant increases in expression across NSCLC cell lines & PDX CL models. Bar graphs from left to right: HIGH-coreBIRC5, FOS-coreBIRC5, FOS-CEACAM5, FOS-FAM111B, FOS-KIF20A, FOS-AGR2, FOS-CST, and FOS-TATA, respectively.
FIG. 46 shows the reporter gene expression performance by different synthetic promoters in various cancer and non-cancer cell lines. Some FOS-newCores combinations had elevated noise in Normal Lung Fibroblasts. Bar graphs from left to right: FOS-BIRC5, FOS-CEACAM5, FOS-FAM111B, FOS-KIF20A, FOS-AGR2, FOS-CST1, and FOS-TATA, respectively.
FIG. 47 shows an exemplary workflow of diagnostic medical sonography (DMS) study.
FIG. 48 shows a schematic of adding activating elements to the new core promoters.
FIG. 49 shows the reporter gene expression performance by different synthetic promoters in H1299 and PDX430 cell lines. HIGH element was observed to be functional in vitro when combined with alternate core promoters. Bar graphs from left to right: BIRC5, CEACAM5, FAM111B, KIF20A, AGR2, and FOS-TATA, respectively.
FIG. 50 shows the reporter gene expression performance by different synthetic promoters in normal small airway epithelial cells and normal lung fibroblasts. In vitro specificity models were predictive of lung noise with HIGH-CEACAM5, HIGH-FAM111B and HIGH-KIF20A. Bar graphs from left to right: HIGH-BIRC5, HIGH-CEACAM5, HIGH-FAM111B, HIGH-KIF20A, HIGH-AGR2, FOS-AGR2, and FOS-TATA, respectively.
FIG. 51 shows the reporter gene expression performance by different synthetic promoters in various PDX cell lines. Synthetic promoters described herein outperform endogenous promoter in PDX cell lines. Bar graphs from left to right: Survivin (endogenous BIRC5 promoter), FOS-coreBIRC5, HIGH-coreBIRC5, FOS-coreAGR2, FOS-coreCST1, HIGH-FAM111B, FOS-TATA-TSS, and EF1A (positive control), respectively.
FIG. 52 shows the reporter gene expression performance by different synthetic promoters in various primary cell lines derived from PDX or primary tissue. Bar graphs from left to right: Survivin (endogenous BIRC5 promoter), FOS-coreBIRC5, HIGH-coreBIRC5, FOS-coreAGR2, FOS-coreCST1, HIGH-FAM111B, FOS-TATA-TSS, and CAG (positive control), respectively.
FIG. 53 shows the reporter gene expression performance by different synthetic promoters in primary lung normal cells (Lonza). Bar graphs from left to right: Survivin (endogenous BIRC5 promoter), FOS-coreBIRC5, HIGH-coreBIRC5, FOS-coreAGR2, FOS-coreCST1, HIGH-FAM111B, FOS-TATA-TSS, and EF1A (positive control), respectively.
FIG. 54 shows the reporter gene expression performance by different synthetic promoters in different primary lung normal cells derived from the same patient.
FIG. 55 shows the comparison of the reporter gene expression performance by synthetic promoters in EMT state cells and wild type A549 cells.
FIG. 56 shows a table of top 10 enhancer candidates.
FIG. 57 shows the reporter gene expression performance by synthetic promoters comprising enhancer elements in various cancer and non-cancer cells. Constructs were tested in vitro across panel of 5 LUAD cell lines, 3 HCC cell lines, and IMR90 lung normal cells for expression profiles of enhancer elements paired with each core promoter (including 7× CRL PDX cell lines and 2× Lonza normal cells).
FIG. 58 shows comparison of the reporter gene expression performance by different synthetic promoters comprising enhancer elements in various cancer cell lines.
FIG. 59 shows the reporter gene expression performance by different synthetic promoters in various cell lines. Bar graphs from left to right: BIRC5, Canscript, FOSL1, GATA1, MYC_MAX, SOX9, AFP, AFP3, Enhancer+AFP3, and NT EF1a, respectively.
FIG. 60 shows a two-step promoter amplification utilizing the yeast GAL4-VP system.
FIG. 61 shows comparison of the reporter gene expression performance by different synthetic promoters and the yeast GAL4-VP system in H1299, LXFA629, and LXFA 737 cell lines. TSTA: two-step transcriptional activation. Bar graphs from left to right: EF1A, CMV, BIRC5, FOSL1, AFP3, TSTA PR-GAL4 only, BIRC5, FOSL1, AFP3, respectively.
FIG. 62 shows comparison of the reporter gene expression performance by different synthetic promoters and the yeast GAL4-VP system in SNU-475, PLC/PRF/5, and C3A cell lines. TSTA: two-step transcriptional activation. Bar graphs from left to right: EF1A, CMV, BIRC5, FOSL1, AFP3, TSTA PR-GAL4 only, BIRC5, FOSL1, AFP3, respectively.
FIG. 63 shows exemplary core promoters with annotations. FIG. 63 discloses SEQ ID NO: 555.
FIG. 64A shows a diagram of an annotated core FAM111B promoter with predicted TF binding sites.
FIG. 64B shows activating and repressing elements within coreFAM111B identified from core promoter element deletion studies.
FIG. 65 shows top 10 ranked response elements from H1299 (Large Cell Carcinoma), LXFA586 (Adenocarcinoma), and LXFL430 (Large Cell Carcinoma). Control response elements containing FOS/CREB (H1299), TP53/TP73 (LXFA586), or TCF (LXFL430) drive strong expression of reporter gene in H1299, LXFA586, and LXFL430 cell lines respectively, and there are several additional hits.
FIGS. 66A, 66B, 66C, and 66D show in vitro low throughput validation of response elements from FIG. 112 using Firefly luciferase (FLuc) assay.
FIGS. 67-68 show a DNA binding consensus sequence of Forkhead Box Protein 01 (FOXO1; FIG. 67, left, e.g., a fragment of SEQ ID NO: 202), ELK3 (FIG. 67, middle, e.g., a fragment of SEQ ID NO: 150), FOXO::ELK (FIG. 67, right, e.g., a fragment of SEQ ID NO: 150), XBP1 (FIG. 68, top left, e.g., a fragment of SEQ ID NO: 155), NFE2L2 (FIG. 68, top right, e.g., a fragment of SEQ ID NO: 152), and MTF1 (FIG. 68, bottom, e.g., a fragment of SEQ ID NO: 151).
FIG. 69 shows validation of response elements with FOS and CREB using Firefly luciferase (FLuc) assay.
FIG. 70 shows Firefly luciferase (FLuc) assay results of combination of TCF and FOS elements.
FIG. 71 shows Firefly luciferase (FLuc) assay results of different elements in patient-derived cancer cells (cancer epithelia and cancer fibroblasts) and normal adjacent tissues. Bar graphs from left to right: Cancer Epithelia, Cancer Fibroblasts, and Normal Adjacent Tissues, respectively.
FIG. 72 shows Synthetic Response Sensors (SRS) that drive cancer specific expression where the SRS comprises a series of Synthetic Response Elements (SREs), or enhancers, and a cancer activated core promoter. TF: Transcription Factor.
FIG. 73 shows a graph of gene expression activated by SRS-G comprising the core promoter specific for lung cancer and a single SRE. A luciferase reporter expression system was used to evaluate the strength of activation in cell lines that represent the three main Non-Small Cell Lung Cancer (NSCLC) subtypes. The expression values are shown as the fold change over a strong constitutive promoter. SRS-G was able to achieve expression that is 10-20% on the expression of the constitutive promoter.
FIGS. 74A, 74C, 74E, 74G, 74I, and 74K show graphs of gene expression activated by different SRSs (SRS-A, SRS-B, SRS-C, SRS-D, SRS-E, and SRS-F) designed to drive gene expression in lung cancers. A luciferase reporter expression system was used to evaluate the strength of activation in cell lines that represent the three main NSCLC subtypes. The expression values are shown as the fold change over a strong constitutive promoter. SRS-A was able to achieve expression that is 5-50% on the expression of the constitutive promoter (FIG. 74A). SRS-B was able to achieve expression that is 20-50% on the expression of the constitutive promoter (FIG. 74C). SRS-C was able to achieve expression similar to or 3-fold above the constitutive promoter (FIG. 74E). SRS-D was able to achieve expression similar to or 2-10-fold above the constitutive promoter (FIG. 74G). SRS-E was able to achieve expression similar to or 2-8-fold above the constitutive promoter (FIG. 74I). SRS-F was able to achieve expression similar to or 3-5-fold above the constitutive promoter. (FIG. 74K).
FIGS. 74B, 74D, 74F, 74H, 74J, and 74L show graphs of gene expression activated by an SRS designed to drive gene expression in lung cancers (SRS-A, SRS-B, SRS-C, SRS-D, SRS-E, and SRS-F). A luciferase reporter expression system was used to evaluate the strength of activation in cell lines that represent the NSCLC subtypes as well as normal primary lung cells. Expression values are shown as the fold change over a strong constitutive promoter on the left. Same data plotted as an ROC curve is presented on the right.
FIG. 75 shows graphs of expression pattern of a reporter gene activated by a constitutive or non-cancer specific promoter, Cytomegalovirus (CMV). A luciferase reporter expression system was used to evaluate the strength of activation in cell lines that represent the NSCLC subtypes as well as normal primary lung cells. Expression values are shown as the fold change over a strong constitutive promoter on the left. Same data plotted as an ROC curve is presented on the right.
FIG. 76 shows graphs of gene expression activated by SRSs, demonstrating that SRSs can be active in both lung and liver cancer models, or selectively active in a target model. H358 lung cancer cells, HepG2 liver cancer cells, and Hep3B liver cancer cells were seeded in 96-well plates at a density of 10,000 cells per well, with each plasmid containing luciferase reporter expression system tested in triplicate. Transfection was performed using Lipofectamine™ 3000, a transfection agent comprising DOSPA (2,3-dioleoyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propaniminium trifluoroacetate) and DOPE (dioleoyl phosphatidylethanolamine), following the manufacturers protocol. After 24 hours of incubation, expression levels were measured using the Promega Luciferase Assay System (E1501). The expression values are shown as the fold change over a strong constitutive promoter, where greater than 10% expression is set as a threshold for positive signal. The results demonstrate that SRS-G and SRS-B are active in both lung and liver cancer cell lines, whereas SRS-H, a liver-specific promoter, is active only in liver cancer cell lines.
FIG. 77 shows a graph of gene expression activated by SRSs in different tissues, illustrating the in vivo performance of several SRSs when administered via intravenous (i.v.) bolus to tumor-bearing mice. Quantification of firefly bioluminescence of tissues ex vivo was taken 24 hours after compound dosing normalized to the average bioluminescence imaging (BLI) of PBS dosed animals (n=3, dotted line set at 1). Plotted by dosing group with each tissue in column. Each point represents a tissue from a unique animal. Circles: CAG constitutive promoter; squares: SRS-F; triangles: SRS-I; diamonds: SRS-E; stars: SRS-J. Error bars represent standard error of the mean (SEM). Tables on the bottom show calculated signal to noise ratios (SNR) for a given promoter over potential background noise tissues (liver, spleen) demonstrating improved SNR and selectivity for synthetic promoters relative to constitutively active CAG promoter.
FIG. 78 shows a graph of reporter gene expression under different SRSs compared to a constitutive promoter. A FLUC reporter readout was used to assess specificity of SRSs comprising combinations of different promoters and SREs in lung cancer (H1299) and two different normal lung cell lines (Lung Normal 1 and Lung Normal 2). Reporter expression under SRS-K (using the non-specific promoter TATA-TSS) was high in both lung cancer and normal cell lines. Reporter expression under SRS-L and SRS-M was lower in all cell lines compared to that under SRS-K, especially in normal cell lines. Specifically, reporter gene expression under SRS-L was reduced 2× in cancer cell line and 10-20× in normal cell lines compared to reporter gene expression under SRS-K, which comprises non-specific promoter TATA-TSS, indicating that core promoters provide selectivity and specificity for cancer cells compared to normal cells.



DETAILED DESCRIPTION
The compositions and methods described herein contemplates a general strategy of identifying important elements of cancer-specific (or cancer-activated) promoters and designing and/or engineering cancer-specific promoters using elements of cancer-specific promoters identified. Cancer-specific promoters or cancer-activated promoters described herein can comprise promoters of genes that are preferentially expressed in cancer cells compared to non-cancer cells or expressed in higher level in cancer cells compared to non-cancer cells. Methods described herein can comprise identifying endogenous cancer-activated promoters by evaluating candidate promoter and/or enhancer sequences using bioinformatic analysis and designing/engineering a minimal cancer-activated promoter sequence (core promoter). For example, a candidate sequence (e.g., low-throughput or high-throughput screening) can be examined using a genome browser. The assessment range (e.g., sequence boundary) can be set based on the predicted transcriptional start site (TSS) of an endogenous promoter. For example, the assessment range can be from about −1000 bp to about +1000 bp relative to the predicted TSS. The assessment range can be adjusted based on chromatin immunoprecipitation (ChIP) data including, but not limited to, ChIP peaks of general transcription factors (TFs), indicators of active promoter regions, and TFs that may indicate cancer specificity by presence in cancer cells and absence in non-cancer cells; and abundance of predicted TF binding sequence (TFBS); and regions of high species conservation. In some embodiments, indicators of active promoter regions can include, but not limited to, RNA Polymerase II, DNAse I, H3K4me1, and H3K4me3. In some embodiments, TFBS abundance can be predicted using methods including, but not limited, to JASPAR or HOMER motif analysis. Methods described herein can also comprise testing highlight regulated TFs using Massively Parallel Reporter Assay (MPRA) to identify optimal sequences, optimal spacing between each sequence, and/or optimal combinations of different enhancer sequences to design synthetic tiled enhancers. Methods described herein can comprise a rationally designed (e.g., low-throughput) screening or a high-throughput screening to identify enhancer elements to increase transcription signal. In some embodiments, a synthetic tiled enhancer can comprise one or more copies of TFBS, or other highly conserved regulatory element repeats with spacing between repeats. One or more synthetic elements described herein can be placed upstream of core promoters. Synthetic elements described herein can also function as a promoter without a promoter or a core promoter.
A cancer-specific promoter described herein can comprise a recombinant polynucleotide comprising a core promoter sequence comprising a transcription start site (TSS). In some embodiments, a core promoter can be derived from a cancer-responsive gene and can be operably linked to an open reading frame (ORF). In some embodiments, a cancer-responsive gene can comprise a human cancer-responsive gene. In some embodiments, a core promoter can comprise a plurality of binding sites for a plurality of transcription factors (TFs) that are expressed in higher levels in cancer cells compared to non-cancer cells. In some embodiments, a core promoter can comprise a plurality of binding sites for a plurality of transcription factors (TFs) that are more active in cancer cells compared to non-cancer cells. In some embodiments, a core promoter can comprise a plurality of enhancers derived from two or more human cancer-response genes. In one embodiment, each of the plurality of enhancers can comprise a transcription regulatory element with at least 80% sequence homology to the enhancer consensus sequence of the two or more human cancer-response genes. In another embodiment, each of the plurality of enhancers can comprise a sequence capable of binding a transcription associated protein as assessed by ChIP.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below.
Definitions
As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. It should also be noted that the term “or” is generally employed in its sense including “and/or” unless the content clearly dictates otherwise. The terms “and/or,” “a combination thereof,” and “any combination thereof” and their grammatical equivalents as used herein, can be used interchangeably. These terms can convey that any combination is specifically contemplated. Solely for illustrative purposes, the following phrases “A, B, and/or C,” “A, B, C, or a combination thereof,” or “A, B, C, or any combination thereof” can mean “A individually; B individually; C individually; A and B; B and C; A and C; and A, B, and C.” The term “or” can be used conjunctively or disjunctively, unless the context specifically refers to a disjunctive use. The term “about” or “approximately” can mean within an acceptable error range for the particular value, which may depend in part on how the value is measured or determined, e.g., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation. Alternatively, “about” can mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, within 5-fold, or within 2-fold, of a value. Where particular values are described in the application and claims, unless otherwise stated the term “about” meaning within an acceptable error range for the particular value should be assumed.
Throughout this disclosure, numerical features are presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of any embodiments. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range to the tenth of the unit of the lower limit unless the context clearly dictates otherwise. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual values within that range, for example, 1.1, 2, 2.3, 5, and 5.9. This applies regardless of the breadth of the range. The upper and lower limits of these intervening ranges may independently be included in the smaller ranges, and are also encompassed within the present disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the present disclosure, unless the context clearly dictates otherwise.
As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method or composition of the present disclosure, and vice versa. Furthermore, compositions of the present disclosure can be used to achieve methods of the present disclosure.
Reference in the specification to “embodiments,” “certain embodiments,” “preferred embodiments,” “specific embodiments,” “some embodiments,” “an embodiment,” “one embodiment” or “other embodiments” means that a particular feature, structure, or characteristic described in connection with the embodiments is included in at least some embodiments, but not necessarily all embodiments, of the present disclosures. To facilitate an understanding of the present disclosure, a number of terms and phrases are defined below.
Certain specific details of this description are set forth in order to provide a thorough understanding of various embodiments. However, one skilled in the art will understand that the present disclosure may be practiced without these details. In other instances, well-known techniques or methods have not been shown or described in detail to avoid unnecessarily obscuring descriptions of the embodiments. Unless the context requires otherwise, throughout the specification and claims which follow, the word “comprise” and variations thereof, such as, “comprises” and “comprising” are to be construed in an open, inclusive sense, that is, as “including, but not limited to.” Further, headings provided herein are for convenience only and do not interpret the scope or meaning of the claimed disclosure.
The terms “nucleic acid sequence,” “polynucleic acid sequence,” and/or “nucleotide sequence” are used herein interchangeably and have the identical meaning herein and refer to DNA or RNA. In some embodiments, a nucleic acid sequence is a polymer comprising or consisting of nucleotide monomers, which are covalently linked to each other by phosphodiester-bonds of a sugar/phosphate-backbone. The terms “nucleic acid sequence,” “polynucleic acid sequence,” and “nucleotide sequence” may encompass unmodified nucleic acid sequences, i.e., comprise unmodified nucleotides, or natural nucleotides. In some embodiments, “natural nucleotide,” “unmodified nucleotide,” and/or “canonical nucleotide” are used herein interchangeably and have the identical meaning herein and refer to the naturally occurring nucleotide bases adenine (A), guanine (G), cytosine (C), uracil (U), and/or thymine (T). The terms “nucleic acid sequence,” “polynucleic acid sequence,” and “nucleotide sequence” may also encompass modified nucleic acid sequences, such as base-modified, sugar-modified or backbone-modified etc., DNA or RNA. The term “nucleic acid sequence” generally is understood to include, as applicable to the embodiment being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides. The term “nucleic acid” generally is understood to include, as applicable to the embodiment being described, polymers containing a non-natural linkage or a non-natural nucleotide.
In some embodiments, a nucleic sequence acid as described herein comprises one or more non-natural linkages or one or more non-natural nucleotides. Non-natural nucleotides can include, but are not limited to, 2′-fluoro, 2′-O-methyl, 2′-O-methyl, 2′-O-methoxy-ethyl, 2′-O-methoxy-ethoxy, 5′-methyl, SNA, hGNA, hhGNA, mGNA, TNA, h′GNA, locked nucleic acids (LNAs), GNA-isoC, GNA-isoG, 5′-mUNA, 4′-mUNA, 3′-mUNA, 2′-mUNA, or an abasic nucleotide (e.g. DNA or RNA). Non-natural linkages can include, but are not limited to, phosphorothioate and methylphosphonate. In some embodiments, an oligonucleotide as described herein comprises a modified uracil. Example nucleobases and nucleosides having a modified uracil include pseudouridine (Ψ), pyridin-4-one ribonucleoside, 5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxy-uridine (ho5U), 5-aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridine or 5-bromo-uridine), 3-methyl-uridine (m3U), 5-methoxy-uridine (mo5U), uridine 5-oxyacetic acid (cmo5U), uridine 5-oxyacetic acid methyl ester (mcmo5U), 5-carboxymethyl-uridine (cm5U), 1-carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm5U), 5-carboxyhydroxymethyl-uridine methyl ester (mchm5U), 5-methoxycarbonylmethyl-uridine (mcm5U), 5-methoxycarbonylmethyl-2-thio-uridine (mcm5s2U), 5-aminomethyl-2-thio-uridine (nm5s2U), 5-methylaminomethyl-uridine (mnm5U), 5-methylaminomethyl-2-thio-uridine (mnm5s2U), 5-methylaminomethyl-2-seleno-uridine (mnm5se2U), 5-carbamoylmethyl-uridine (ncm5U), 5-carboxymethylaminomethyl-uridine (cmnm5U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm5s2U), 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine (τm5U), 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine (Σm5s2U), 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m5U, i.e., having the nucleobase deoxythymine), 1-methylpseudouridine (m1ψ), 5-methyl-2-thio-uridine (m5s2U), 1-methyl-4-thio-pseudouridine (m1s4ψ), 4-thio-1-methyl-pseudouridine, 3-methyl-pseudouridine (m3ψ), 2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine (D), dihydropseudouridine, 5,6-dihydrouridine, 5-methyl-dihydrouridine (m5D), 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, N1-methyl-pseudouridine (aka 1-methylpseudouridine (m1ψ)), 3-(3-amino-3-carboxypropyl)uridine (acp3U), 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine (acp3 ψ), 5-(isopentenylaminomethyl)uridine (inm5U), 5-(isopentenylaminomethyl)-2-thio-uridine (inm5s2U), α-thio-uridine, 2′-O-methyl-uridine (Um), 5,2′-O-dimethyl-uridine (m5Um), 2′-O-methyl-pseudouridine (ψ m), 2-thio-2′-O-methyl-uridine (s2Um), 5-methoxycarbonylmethyl-2′-O-methyl-uridine (mcm5Um), 5-carbamoylmethyl-2′-O-methyl-uridine (ncm5Um), 5-carboxymethylaminomethyl-2′-O-methyl-uridine (cmnm5Um), 3,2′-O-dimethyl-uridine (m3Um), 5-(isopentenylaminomethyl)-2′-O-methyl-uridine (inm5Um), 1-thio-uridine, deoxythymidine, 2′-F-ara-uridine, 2′-F-uridine, 2′-OH-ara-uridine, 5-(2-carbomethoxyvinyl) uridine, and 5-[3-(1-E-propenylamino)uridine. In some embodiments, an oligonucleotide as described herein comprises a modified cytosine. Example nucleobases and nucleosides having a modified cytosine include 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine (m3C), N4-acetyl-cytidine (ac4C), 5-formyl-cytidine (f5C), N4-methyl-cytidine (m4C), 5-methyl-cytidine (m5C), 5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine (hm5C), 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C), 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine (k2C), α-thio-cytidine, 2′-O-methyl-cytidine (Cm), 5,2′-O-dimethyl-cytidine (m5Cm), N4-acetyl-2′-O-methyl-cytidine (ac4Cm), N4,2′-O-dimethyl-cytidine (m4Cm), 5-formyl-2′-O-methyl-cytidine (f5Cm), N4,N4,2′-O-trimethyl-cytidine (m4 2Cm), 1-thio-cytidine, 2′-F-aracytidine, 2′-F-cytidine, and 2′-OH-aracytidine
The term “subject” can generally include human or non-human animals. Thus, the methods and compositions described herein are applicable to both human and veterinary disease and animal models. Preferred subjects are “patients,” i.e., living humans that are receiving medical care for a disease or condition (e.g., cancer). This includes persons with no defined illness who are being investigated for signs of pathology. Also included are persons suspected of possessing or being at-risk for a defined illness. In some embodiments, the subject has at least one risk factor for cancer.
A “vector” as used herein generally refers to a nucleic acid sequence capable of transferring other operably-linked heterologous or recombinant nucleic acid sequences to target cells. In some examples, a vector is a minicircle, plasmid, nanoplasmid, yeast artificial chromosome (YAC), bacterial artificial chromosome (BAC), cosmid, phagemid, bacteriophage genome, or baculovirus genome. Suitable vectors also include vectors derived from bacteriophages or plant, invertebrate, or animal (including human) viruses such as CELiD vectors, doggybone DNA (dbDNA) vectors, closed-end linear duplex DNA vectors (e.g., wherein each end is covalently closed by chemical modification), adeno-associated viral vectors (e.g., AAV1, AAV2, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, or pseudotyped combinations thereof such as AAV2/5, AAV2/2, AAV-DJ, or AAV-DJ8), retroviral vectors (e.g. MLV or self-inactivating or SIN versions thereof, or pseudotyped versions thereof), herpesviral (e.g. HSV- or EBV-based), lentiviral vectors (e.g., HIV-, FIV-, or EIAV-based, or pseudotyped versions thereof), or adenoviral vectors (e.g., AdS-based, including replication-deficient, replication-competent, or helper-dependent versions thereof). In some embodiments, a vector is a replication competent viral-derived vector. In some embodiments, a vector is a replication-incompetent viral-derived vector. In some cases, the vector may comprise an episomal maintenance element to facilitate replication in one or more target cell type, such as a Scaffold/Matrix Attachment Region (S/MAR). S/MAR elements are particularly useful to facilitate replication in the context of “naked” nucleic acid vectors such as minicircles.
Exemplary suitable S/MAR elements include, but are not limited to, EμMAR from the immunoglobulin heavy chain locus, the apoB MAR from the human apolipoprotein B locus, the Ch-LysMAR from the chicken lysozyme locus, and the huIFNβ MAR from the human IFNβ-locus. A vector may comprise a coding sequence capable of being expressed in a target cell. Accordingly, as used herein, the terms “vector construct,” “expression vector,” and “gene transfer vector,” may refer to any nucleic acid construct capable of directing the expression of a gene of interest and which is useful in transferring the gene of interest into target cells. Vectors as described herein may additionally comprise one or more cis-acting elements to stabilize or improve expression of mRNAs therefrom. Such cis-acting elements include, but are not limited to, any of the elements described e.g., in Johansen et al. The Journal of Gene Medicine. (5)12:1080-1089 (doi: 10.1002/jgm.444) or Vlasova-St. Louis and Sagarsky. Mammalian Cis-Acting RNA Sequence Elements (doi: 10.5772/intechopen.72124).
The term “promoter” generally can refer to a DNA sequence that directs the transcription of a polynucleotide. Typically, a promoter can be located in the 5′ region of a polynucleotide to be transcribed, proximal to the transcriptional start site of such polynucleotide. More typically, promoters can be defined as the region upstream of the first exon; more typically, as a region upstream of the first of multiple transcription start sites. Frequently promoters are capable of directing transcription of genes located on each of the complementary DNA strands that are 3′ to the promoter. Stated differently, many promoters can exhibit bidirectionality and can direct transcription of a downstream gene when present in either orientation (i.e., 5′ to 3′ or 3′ to 5′ relative to the coding region of the gene). Additionally, the promoter may also include at least one control element such as an upstream element. Such elements include upstream activator regions (UARs) and optionally, other DNA sequences that affect transcription of a polynucleotide such as a synthetic upstream element. Some promoters may be assembled from fragments of endogenous promoters (e.g., derived from the human genome).
The term “coding sequence,” and “encodes” when used in reference to a polypeptide herein generally refer to a nucleic acid molecule that is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide, for example, when the nucleic acid is present in a living cell (in vivo) and placed under the control of appropriate regulatory sequences (or “control elements”). The boundaries of the coding sequence are typically determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxy) terminus. A coding sequence can include, but is not limited to, cDNA from viral, prokaryotic or eukaryotic mRNA, genomic DNA sequences from viral, eukaryotic, or prokaryotic DNA, and synthetic DNA sequences. A transcription termination sequence may be located 3′ to the coding sequence, and a promoter may be located 5′ to the coding sequence; along with additional control sequences if desired, such as enhancers, introns, poly adenylation site, etc. A DNA sequence encoding a polypeptide may be optimized for expression in a selected cell by using the codons preferred by the selected cell to represent the DNA copy of the desired polypeptide coding sequence.
The term “operably linked” as used herein generally can refer to an arrangement of elements wherein the components so described are configured so as to perform their usual function. Thus, a given promoter that is operably linked to a coding sequence (e.g., a reporter expression cassette) is capable of effecting the expression of the coding sequence when the proper enzymes are present. The promoter or other control elements need not be contiguous with the coding sequence, so long as they function to direct the expression thereof. For example, intervening untranslated yet transcribed sequences can be present between the promoter sequence and the coding sequence and the promoter sequence can still be considered “operably linked” to the coding sequence.
The term “sequence identity” or “percent identity” in the context of two or more nucleic acids or polypeptide sequences, generally refers to two (e.g., in a pairwise alignment) or more (e.g., in a multiple sequence alignment) sequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a local or global comparison window, as measured using a sequence comparison algorithm. Suitable sequence comparison algorithms for polypeptide sequences include, e.g., BLASTP using parameters of a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix setting gap costs at existence of 11, extension of 1, and using a conditional compositional score matrix adjustment for polypeptide sequences longer than 30 residues; BLASTP using parameters of a wordlength (W) of 2, an expectation (E) of 1000000, and the PAM30 scoring matrix setting gap costs at 9 to open gaps and 1 to extend gaps for sequences of less than 30 residues (these are the default parameters for BLASTP in the BLAST suite available at blast.ncbi.nlm.nih.gov); CLUSTALW with parameters of; the Smith-Waterman homology search algorithm with parameters of a match of 2, a mismatch of −1, and a gap of −1; MUSCLE with default parameters; MAFFT with parameters retree of 2 and maxiterations of 1000; Novafold with default parameters; HMMER hmmalign with default parameters.
The term “lipid particle” generally includes a lipid formulation that can be used to deliver an active agent or therapeutic agent, such as a nucleic acid to a target site of interest (e.g., cell, tissue, organ, and the like). In preferred embodiments, the lipid particle of the invention is a nucleic acid-lipid particle (e.g. a particle that has only nucleic acids and lipids), which is typically formed from a cationic lipid, a non-cationic lipid, and optionally a conjugated lipid that prevents aggregation of the particle. In other preferred embodiments, the active agent or therapeutic agent, such as a nucleic acid, may be encapsulated in the lipid portion of the particle, thereby protecting it from enzymatic degradation. In some cases, a “lipid particle” is a lipid nanoparticle (LNP). The lipid particles can be prepared by any suitable method, including but not limited to microfluidic assembly or extrusion. In some embodiments, for a lipid particle (e.g. LNP composition), a particle has a particular composition. In some embodiments, for a lipid particle (e.g. LNP composition), each particle has a particular composition. In some embodiments, for a lipid particle (e.g. LNP composition), at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, 99.9% of the particles have a particular composition.
When nucleic acid sequences are referred to herein, the current disclosure is generally understood to include nucleic acid sequences with at least about 80-100% identity to the sequences described herein, or to reverse complements of the sequences described herein.
In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of the sequences listed in Table 1A, or to reverse complements of any of the sequences listed in Table 1A. In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 1-343, or to reverse complements of any of SEQ ID NOs: 1-343. In some embodiments, the disclosure provides for a promoter comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 1-343, or to reverse complements of any of SEQ ID NOs: 1-343. In some embodiments, the nucleic acid can be a double-stranded nucleic acid.
In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of the sequences listed in Table 1B, or to reverse complements of any of the sequences listed in Table 1B. In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 377-397, or to reverse complements of any of SEQ ID NOs: 377-397. In some embodiments, the disclosure provides for a promoter comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 377-397, or to reverse complements of any of SEQ ID NOs: 377-397. In some embodiments, the disclosure provides for an enhancer comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 377-397, or to reverse complements of any of SEQ ID NOs: 377-397. In some embodiments, the nucleic acid can be a double-stranded nucleic acid.
In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of the sequences listed in Table 1C, or to reverse complements of any of the sequences listed in Table 1C. In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 398-488, or to reverse complements to any of SEQ ID NOs: 398-488. In some embodiments, the disclosure provides for a promoter having a sequence having at least 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of the sequences listed in Table 1C, or to reverse complements of any of the sequences listed in Table 1C. In some embodiments, the disclosure provides for a promoter comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any of SEQ ID NOs: 398-486 and SEQ ID NOs: 556-557, or to reverse complements to any of SEQ ID NOs: 398-486 and SEQ ID NOs: 556-557. In some embodiments, the nucleic acid can be a double-stranded nucleic acid.
In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any one of the of the sequences listed in Table 1J, or to reverse complements of any one of the sequences listed in Table 1J. In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any SEQ ID NOs: 558-587, or to any reverse complements of any SEQ ID NOs: 558-587. In some embodiments, the disclosure provides for a core promoter comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any one of the of the sequences listed in Table 1J, or to reverse complements of any one of the sequences listed in Table 1J. In some embodiments, the disclosure provides for the core promoter comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to any SEQ ID NOs: 558-587, or to any reverse complements of any SEQ ID NOs: 558-587. In some embodiments, the nucleic acid can be a double-stranded nucleic acid.
In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to SEQ ID NO: 556, listed in Table 1C, or to a reverse complement thereof. In some embodiments, the nucleic acid can be a double-stranded nucleic acid.
In some embodiments, the disclosure provides for a nucleic acid comprising a sequence having at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% sequence identity to SEQ ID NO: 557, listed in Table 1C, or to a reverse complement thereof. In some embodiments, the nucleic acid can be a double-stranded nucleic acid.
In some embodiments, any of the nucleic acids disclosed herein can have at least about 20, at least about 40, at least about 60, at least about 80, at least about 100, at least about 120, at least about 140, at least about 160, at least about 180, at least about 200, at least about 220, at least about 240, at least about 260, at least about 280, at least about 300, at least about 320, at least about 340, at least about 360, at least about 380, at least about 400, at least about 420, at least about 440, at least about 460, at least about 480, at least about 500, at least about 520, at least about 540, at least about 560, at least about 580, at least about 600, at least about 620, at least about 640, at least about 680, at least about 700, at least about 720, at least about 740, at least about 760, at least about 780, at least about 800, at least about 820, at least about 840, at least about 860, at least about 880, at least about 900, at least about 920, at least about 940, at least about 960, at least about 980, at least about 1000, at least about 1020, at least about 1040, at least about 1060, at least about 1080, at least about 1100, at least about 1120, at least about 1140, at least about 1160, at least about 1180, at least about 1200, at least about 1220, at least about 1240, at least about 1260, at least about 1280, at least about 1300, at least about 1320, at least about 1340, at least about 1360, at least about 1380, at least about 1400, at least about 1420, at least about 1440, at least about 1460, at least about 1480, at least about 1500, at least about 1520, at least about 1540, at least about 1560, at least about 1580, at least about 1600, at least about 1620, at least about 1640, at least about 1660, at least about 1680, at least about 1700, at least about 1720, at least about 1740, at least about 1760, at least about 1780, at least about 1800, at least about 1820, at least about 1840, at least about 1860, at least about 1880, at least about 2000, at least about 2020, at least about 2040, at least about 2060, at least about 2080, at least about 2100, at least about 2120, at least about 2140, at least about 2160, at least about 2180, at least about 2200, at least about 2220, at least about 2240, at least about 2260, at least about 2280, at least about 2300, at least about 2320, at least about 2340, at least about 2360, at least about 2380, at least about 2400, at least about 2420, at least about 2440, at least about 2460, at least about 2480, at least about 2500, at least about 2520, at least about 2540, at least about 2560, at least about 2580, at least about 2600, at least about 2620, at least about 2640, at least about 2660, at least about 2680, at least about 2700, at least about 2720, at least about 2740, at least about 2760, at least about 2780, at least about 2800, at least about 2820, at least about 2840, at least about 2860, at least about 2880, at least about 2900, at least about 2920, at least about 2940, at least about 2960, at least about 2980, at least about 3000, at least about 3020, at least about 3040, at least about 3060, at least about 3080, at least about 3100, at least about 3120, at least about 3140, at least about 3160, at least about 3180, at least about 3200, at least about 3220, or at least about 3240 consecutive nucleotides of any of the nucleic acid sequences disclosed herein, or of any reverse complements of any of the nucleic acid sequences disclosed herein.
Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods, and materials are described below.
Synthetic Promoter Strategy and Design
Provided herein are synthetic promoters that can be activated in target cells with high sensitivity and specificity. These promoters can be modular and engineerable. In some embodiments, synthetic promoters described herein can be designed to drive specificity and sensitivity. For example, synthetic promoters can be designed to specifically respond to dysregulated pathways in cancer. In one embodiment, synthetic promoters described herein can comprise an endogenous promoter of a gene that is expressed specifically or preferentially in cancer cells compared to non-cancer cells. In another embodiment, synthetic promoters described herein can comprise a core promoter. A core promoter described herein can comprise a minimal promoter sequence of an endogenous promoter of a gene expressed specifically or preferentially in cancer cells compared to non-cancer cells. A minimal promoter can refer to a short DNA sequence that can allow for the formation of a transcription initiation complex or a DNA sequence comprising a minimal number of nucleotides sufficient to allow for the formation of a transcription initiation complex. In some embodiments, synthetic promoters described herein can comprise a structure comprising three major components (1) a cancer-specific promoter or core promoter, (2) cancer-activated response elements (e.g., binding sites of one or more transcription factors specific for cancer cells), and optionally (3) an enhancer to boost signal strength (e.g., see FIG. 1 or FIG. 72). In some embodiments, synthetic promoters described herein can comprise only (1) a cancer-specific promoter or core promoter. In some embodiments, synthetic promoters described herein can comprise only (1) a cancer-specific promoter or core promoter and (3) an enhancer to boost signal strength. In some embodiments, an enhancer or a transcription binding site can be referred to as a Synthetic Response Element (SRE). In some embodiments, a synthetic promoter comprising a promoter or core promoter and one or more SREs can be referred to as a Synthetic Response Sensor (SRS). In some embodiments, cancer-activated response elements can be designed and constructed to respond to specific dysregulated transcription factors. In some embodiments, cancer-activated response elements described herein can demonstrate predictable activity based on transcriptomic and proteomic data when applied in new cancer models.
In some embodiments, bioinformatics can be used to identify endogenous cancer-activated core promoter sequences. In some embodiments, multi-omic approaches can be used to identify transcription factors (TFs) and their binding sites that are master-regulated. In some embodiments, such TF binding sites can be tiled and tested using high-throughput sequencing (HTS) to optimize promoter sequences, spacing, and combinations thereof. In some embodiments, one or more rationally designed enhancer elements that increase transcription and boost reporter signal can be used. An exemplary workflow and synthetic promoter are described in FIGS. 10-13.
In some embodiments, candidate TF binding site sequences can be identified using Multi-Omics Factor Analysis (MOFA). In some embodiments, candidate TF binding site sequences can be highly dysregulated. In some embodiments, Multi-Omics Factor Analysis (MOFA) can be used to identify TFs specific for a cancer. In some embodiments, a cancer can comprise lung cancer, breast cancer, liver cancer, and/or colorectal cancer. In some embodiments, a lung cancer can comprise non-small cell lung cancer (NSCLC).
In some embodiments, a synthetic promoter can comprise a core promoter sequence. In some embodiments, a core promoter can be identified by analyzing one or more endogenous promoters that can drive cancer specific expression in vitro and/or in vivo, that is the one or more endogenous promoters can preferentially activate gene expression of a gene that is functionally or operatively linked to said one or more promotors in cancer cells (e.g., either in a subject or cancer cell lines) compared to corresponding healthy or normal cells. In some embodiments, one or more endogenous promoters can be analyzed and annotated using UCSC genome browser to build and test core promoters. In some embodiments, core promoters identified can be combined with other elements described herein. In some embodiments, a core promoter sequence can comprise a minimal cancer-activated core promoters. For example, a core promoter sequence can comprise a promoter sequence comprising a minimal number of nucleotides sufficient to drive expression (e.g., recruit transcription initiation complex) of a gene that is functionally or operatively linked to the core promoter in cancer cells. Examples of a minimal cancer-activated cores can include, but are not limited to, coreBIRC5, coreCST1, coreAGR2, coreFAM111B, CEACAM5, CEP55, UBE2C, FAM111B, KIF20A, FOXA1, MYC, or TP53 (e.g., FIGS. 2-5 and FIG. 11). In some embodiments, a core promoter sequence can provide specificity. In some embodiments, a synthetic promoter can comprise a response element. In some embodiments, a response element can comprise a binding site for a master regulated transcription factor (TF). Examples of a master regulated TF can include, but are not limited to, tiled TFBS for FOS, CREB, MYC, HOXC10, TCF7, or combinations thereof. In some embodiments, a response element can provide specificity and/or sensitivity. In some embodiments, a synthetic promoter can comprise a signal strength enhancer. In some embodiments, a signal strength enhancer can comprise a synthetic enhancer (also referred herein as a Synthetic Response Element or SRE). Examples of a synthetic enhancer can include, but are not limited to enhancers of SP1, ETS, CEBP, NF-KB, or combinations thereof. In some embodiments, a synthetic enhancer can provide signal strength. Table A shows a table comparing different synthetic promoters. In some embodiments, synthetic promoters (FOS-AGR2, FOS-CST1, and HIGH-FAM111B) can drive high expression of the reporter gene and have improved signal-to-noise ratio (SNR) compared to BIRC5 variant promoters.







TABLE A







Exemplary Synthetic Promoters
















H1299 
H1299 





H1299 
SubQ
SubQ



In 
In 
SubQ
Tumor 
Tumor 



Vitro 
Vitro
Tumor 
SNR
SNR


Promoter
Signal
Noise
Signal
Lung
Liver















CAG
+++
−−−
38/11
10/3 
<<1


FOS-TATA
+++
−−−
9
3.6
<<1


BIRC5
+
−−

n/a at 1.4 mpk



FOSL-
++
−−

n/a at 1.4 mpk



coreBIRC5







HIGH-
+++
−−
3.6
3.2
1.8


coreBIRC5







FOS-
+++
−−
9.3/3  
 10/3.3
3.2


coreAGR2


3.8
5
2.5


FOS-
+++
−−
3.7
4.1
1


coreCST1







HIGH-
+++
−−
7.5
3.4
1.33


coreFAM111B














In some embodiments, synthetic promoters described herein that can drive expression in a broad range of cancer cells or cancer tissues including, but not limited to, lung cancer cells, can be identified using methods described herein. In one example, promoters identified using methods described herein can include promoters or binding sites/motifs of TCF7, one of TCFs that can be activated by Wnt/B-cat pathway, known for functioning in development pathways. In some embodiments, cancer cell lines based on Wnt/B-cat pathway can be used for further analysis. For example, a principal component analysis (PCA) of PDX database and CCLE focused on the B-cat/Wnt pathway can be used to choose cell lines for further analysis (e.g., 163 genes involved in Wnt/B-cat pathway, 50 CCLE lung cell lines, and 91 PDX lung cell lines). In some embodiments, a PCA including all lung-related PDXs from CRL as well as the CCLE transcriptome database can be used. Examples of cell lines include, but are not limited to, PC2, H520, LK2, or PDX430. In some embodiments, these cell lines can have similar level of expressions of Wnt7B, CCND1, FZD3, AXIN2 or NKD1. In another example, promoters identified using methods described herein can include promoters of TP53, a tumor suppressor that can activate or repress expression depending on location of the binding site. In some embodiments, TP53 binding sequence or motifs can be included in a promoter or a core promoter.
In some embodiments, synthetic promoters that can integrate multiple signaling can be engineered using methods described herein. For example, binding sequences or motifs of TCF, TP53, FOS, MNX1, HOXC10, of CREB can be combined with core promoters described herein to engineer synthetic promoters. In some embodiments, synthetic promoters can comprise promoters or binding sequences/motifs/sites TFs of genes in multiple regulatory pathways. In some embodiments, synthetic promoters comprising two or more endogenous or core promoters can result in gene expression with greater signal and coverage. Details of synthetic promoter design and construction are described in Example 1 and Example 2.
Synthetic Response Sensor (SRSs or synthetic promoter) and Synthetic Response Elements (SREs)
In some aspects, provided herein is a recombinant polynucleotide comprising a Synthetic Response Sensor (SRS) that can drive expression of a gene or an ORF operatively linked to the SRS in tissue- or cell-specific manner. In some embodiments, an SRS described herein can drive cancer specific or cancer-activated expression of a gene or an ORF operatively linked to the SRS. For example, an SRS described herein can drive expression of a gene or an ORF operatively linked to the SRS preferentially or specifically in cancer cells or cancer tissues compared to non-cancer cells or non-cancer tissues. In some embodiments, the expression level of a gene or an ORF operatively linked to an SRS is higher in cancer cells or cancer tissues compared to non-cancer cells or non-cancer tissues. In some embodiments, an SRS can comprise a promoter or a core promoter and one or more Synthetic Response Elements (SREs). In some embodiments, the promoter or the core promoter can provide tissue- or cell-specificity for gene expression. In some embodiments, an SRE can provide tissue- or cell-specificity for gene expression and/or enhance the tissue- or cell-specificity of gene expression. In some embodiments, an SRE can comprise a plurality of binding sites for one or more transcription factors or a plurality of enhancers. For example, an SRE can comprise a plurality of binding sites for one or more transcription factors that are activated in cancer cells or cancer pathways or are dysregulated (e.g., expressed in aberrantly higher levels, etc.) in cancer cells or cancer pathways. In some embodiments, an SRS can drive expression of an ORF operatively linked to the SRS in cancer cells or cancer tissues but not in normal cells or tissues (including normal tissues or cells adjacent to cancer cells or cancer tissues) and/or benign lesions.
In some embodiments, an SRS can comprise a promoter and one or more SREs comprising a plurality of binding sites for one or more transcription factors and a plurality of enhancers. In some embodiments, an SRS can comprise a promoter and one or more SREs comprising a plurality of binding sites for one or more transcription factors. In some embodiments, an SRS can comprise a core promoter and one or more SREs comprising a plurality of binding sites for one or more transcription factors. In some embodiments, an SRS can comprise a promoter and one or more SREs comprising a plurality of enhancers. In some embodiments, an SRS can comprise a core promoter and one or more SREs comprising a plurality of enhancers. In some embodiments, an SRS can comprise a core promoter and one or more SREs comprising a plurality of binding sites for one or more transcription factors and a plurality of enhancers. An exemplary SRS is shown in FIG. 72. In one embodiment, an SRE can comprise a plurality of binding sites for one or more transcription factors, wherein each of the plurality of transcription binding sites can comprise the same binding site sequences or motifs (FIG. 72, left). In another embodiment, an SRE can comprise a plurality of binding sites for one or more transcription factors, wherein each of the plurality of transcription binding sites can comprise different binding site sequences or motifs. In yet another embodiment, an SRE can comprise a plurality of binding sites for one or more transcription factors, wherein the plurality of transcription binding sites can comprise a mixture of the same binding site sequences and different binding site sequences (FIG. 72, middle). In some embodiments, an SRS comprising an SRE that comprises a mixture of different transcription factor binding sequences or motifs can drive stronger or higher expression of an ORF operatively linked to the SRS in cancer cells or cancer tissues compared to a corresponding SRS comprising an SRE that that comprises a plurality of the same transcription binding sequences or motifs.
In some embodiments, an SRS can comprise one or more SREs comprising a plurality of binding sites for one or more transcription factors at the 5′ or upstream of a promoter or a core promoter. In some embodiments, an SRS can comprise one or more SREs comprising a plurality of enhancers at the 5′ or upstream of a promoter or a core promoter. In some embodiments, an SRS can comprise a plurality of enhancers at the 5′ or upstream of a plurality of binding sites for one or more transcription factors, wherein the plurality of binding sites for one or more transcription factors are at the 5′ or upstream of a promoter or a core promoter. For example, an SRS can comprise (i) a plurality of enhancers, (ii) a plurality of binding sites for one or more transcription factors, and (iii) a promoter or a core promotor in 5′ to 3′ direction. In some embodiments, an SRS can comprise a plurality of enhancers at the 5′ or upstream of a promoter or a core promoter and at the 3′ or downstream of a plurality of binding sites for one or more transcription factors. For example, an SRS can comprise (i) a plurality of binding sites for one or more transcription factors, (ii) a plurality of enhancers, and (ii) a promoter or a core promoter in 5′ to 3′ direction.
In some embodiments, an SRS described herein can drive the expression of an ORF operably linked to the SRS in one specific type of cancer cells. In some embodiments, an SRS described herein can drive the expression of an ORF operably linked to the SRS in two or more types of cancer cells.
In some embodiments, a recombinant polynucleotide comprising an SRS describe herein can drive the expression of an ORF operably linked to the SRS at a higher level compared to a corresponding recombinant polynucleotide comprising a constitutive promoter and an ORF operatively linked to the constitutive promoter. For example, a recombinant polynucleotide comprising an SRS describe herein can drive the expression of an ORF operably linked to the SRS at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher compared to a corresponding recombinant polynucleotide comprising a constitutive promoter and an ORF operatively linked to the constitutive promoter. In some embodiments, an ORF can comprise an ORF of a natural gene or a synthetic gene. In some embodiments, a natural gene or a synthetic can comprise a gene encoding a reporter protein, a biomarker protein, or a therapeutic protein.
In some embodiments, a recombinant polynucleotide comprising an SRS describe herein can drive the expression of an ORF operably linked to the SRS at a higher level in cancer cells compared to a corresponding recombinant polynucleotide comprising a constitutive promoter and an ORF operatively linked to the constitutive promoter. For example, a recombinant polynucleotide comprising an SRS describe herein can drive the expression of an ORF operably linked to the SRS in cancer cells at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher compared to a corresponding recombinant polynucleotide comprising a constitutive promoter and an ORF operatively linked to the constitutive promoter.
Promoter/Core Promoter
A core promoter described herein can comprise a minimal promoter that can comprise a transcription start site or a transcription start site sequence that is derived from a promoter of one or more genes expressed in cancer cells or cancer tissues (also referred to as a cancer-responsive gene herein). In some embodiments, a core promoter described herein can comprise a minimal promoter that can comprise a transcription start site or a transcription start site sequence that is derived from a promoter of one or more genes expressed at a higher level in cancer cells or cancer tissues compared to non-cancer cells or non-cancer tissues. For example, a core promoter described herein can comprise a minimal promoter that can comprise a transcription start site or a transcription start site sequence that is derived from a promoter of one or more genes expressed at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher in cancer cells or cancer tissues compared to non-cancer cells or non-cancer tissues.
In some embodiments, a core promoter can further comprise one or more promoter elements that are derived from a promoter of one or more genes expressed in cancer cells or cancer tissues. In some embodiments, a core promoter can further comprise one or more promoter elements that are derived from a promoter of one or more genes expressed at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher in cancer cells or cancer tissues compared to non-cancer cells or non-cancer tissues. In some embodiments, promoter elements can include, but are not limited to, elements specific for tissue, elements specific for development or development stage, elements specific for cancer (e.g., transcription factor binding sites specific for cancer or oncogenic transcription factor binding sites), elements important for transcription (e.g., general promoter elements). In some embodiments, a core promoter can comprise two or more promoter elements that are derived from a promoter of two or more genes expressed in cancer cells or cancer tissues. For example, a core promoter can comprise two or more promoter elements that are derived from a promoter of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or at least 20 genes expressed in cancer cells or cancer tissues. Non-limiting examples of cancer-responsive genes can include TCF7, MNX1, HOXC10, TPS3, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4.
In some embodiments, a core promoter can comprise a minimal promoter derived from one or more genes expressed in cancer cells or cancer tissues. In one example, a core promoter can comprise a minimal promoter derived from one or more cancer-responsive genes comprising TCF7, MNX1, HOXC10, TPS3, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4. In another example, a core promoter can comprise a hybrid minimal promoter derived from two or more cancer-responsive genes comprising TCF7, MNX1, HOXC10, TPS3, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4. In some embodiments, a core promoter can comprise a minimal promoter and one or more promoter elements described herein derived from two or more cancer-responsive genes comprising TCF7, MNX1, HOXC10, TPS3, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4. In some embodiments, a core promoter can comprise a minimal promoter and two or more promoter elements described herein derived from TCF7 and HOXC10. In some embodiments, a core promoter can comprise a minimal promoter and two or more promoter elements described herein derived from TP53 and CEP55.
In some embodiments, a core promoter can comprise a minimal promoter and two or more promoter elements described herein derived from FAM111B and KIF20A. In some embodiments, a core promoter can comprise a minimal promoter and two or more promoter elements described herein derived from BIRC5 and E2F2. In some embodiments, a core promoter can comprise a minimal promoter and two or more promoter elements described herein derived from CEACAM5 and TWIST1. In some embodiments, a core promoter can comprise a hybrid promoter comprising two or more promoter elements described herein derived from two or more cancer-responsive genes comprising TCF7, MNX1, HOXC10, TP53, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4. In some embodiments, a core promoter can comprise a hybrid promoter comprising two or more promoter elements described herein derived from TCF7 and HOXC10. In some embodiments, a core promoter can comprise a hybrid promoter comprising two or more promoter elements described herein derived from TP53 and CEP55. In some embodiments, a core promoter can comprise a hybrid promoter comprising two or more promoter elements described herein derived from FAM111B and KIF20A. In some embodiments, a core promoter can comprise a hybrid promoter comprising two or more promoter elements described herein derived from BIRC5 and E2F2. In some embodiments, a core promoter can comprise a hybrid promoter comprising two or more promoter elements described herein derived from CEACAM5 and TWIST1. In some embodiments, a core promoter can comprise a hybrid promoter comprising a minimal promoter and two or more promoter elements described herein derived from two or more cancer-responsive genes comprising TCF7, MNX1, HOXC10, TP53, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4. In some embodiments, a core promoter can comprise a hybrid promoter comprising a minimal promoter and two or more promoter elements described herein derived from TCF7 and HOXC10. In some embodiments, a core promoter can comprise a hybrid promoter comprising a minimal promoter and two or more promoter elements described herein derived from TP53 and CEP55.
In some embodiments, a core promoter can comprise a hybrid promoter comprising a minimal promoter and two or more promoter elements described herein derived from FAM111B and KIF20A. In some embodiments, a core promoter can comprise a hybrid promoter comprising a minimal promoter and two or more promoter elements described herein derived from BIRC5 and E2F2. In some embodiments, a core promoter can comprise a hybrid promoter comprising a minimal promoter and two or more promoter elements described herein derived from CEACAM5 and TWIST1.
In some embodiments, a core promoter can comprise a hybrid promoter comprising a chimeric sequence of two or more promoter elements from two or more cancer-responsive genes comprising TCF7, MNX1, HOXC10, TP53, CEACAM5, CEP55, FAM111B, CST1, BIRC5, AGR2, FOXA1, cMYC, FOS, TWIST1, E2F2, UBE2C, KIF20A, or ETV4. In some embodiments, a core promoter can comprise a hybrid promoter comprising a chimeric sequence of two or more promoter elements derived from TCF7 and HOXC10. In some embodiments, a core promoter can comprise a hybrid promoter comprising a chimeric sequence of two or more promoter elements derived from TPS3 and CEP55. In some embodiments, a core promoter can comprise a hybrid promoter comprising a chimeric sequence of two or more promoter elements derived from FAM111B and KIF20A. In some embodiments, a core promoter can comprise a hybrid promoter comprising a chimeric sequence of two or more promoter elements derived from BIRC5 and E2F2. In some embodiments, a core promoter can comprise a hybrid promoter comprising a chimeric sequence of two or more promoter elements derived from CEACAM5 and TWIST1.
In some embodiments, a core promoter can comprise a TATA box or a TATA box sequence. In some embodiments, a core promoter can comprise a sequence of a region from about −300 bp to about +100 bp, from about −250 bp to about +100 bp, from about −200 bp to about +100 bp, from about −150 bp to about +100 bp, from about −100 bp to about +100 bp, from about −90 bp to about +100 bp, from about −80 bp to about +100 bp, from about −70 bp to about +100 bp, from about −60 bp to about +100 bp, from about −50 bp to about +100 bp, from about −40 bp to about +100 bp, or from about −30 bp to about +100 bp relative to a transcription start site (TSS) of a cancer-responsive gene. In some embodiments, a core promoter can comprise a sequence of a region from about 300 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 250 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 200 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 150 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 100 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 90 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 80 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 70 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 60 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 50 bp upstream of a TSS to about 100 bp downstream of a TSS, from about 40 bp upstream of a TSS to about 100 bp downstream of a TSS, or from about 30 bp upstream of a TSS to about 100 bp downstream of a TSS of a cancer-responsive gene. In some embodiments, a cancer-responsive gene can comprise a human cancer-responsive gene.
In some embodiments, the sequence of a region from about −300 bp to about +100 bp relative to a TSS (or from about 300 bp upstream of a TSS to about 100 bp downstream of a TSS) can comprise elements that are important for transcription, elements that are tissue specific, elements that are specific for certain development stage, and/or one or more binding sites for transcription factors specific for cancer (e.g., oncogenic transcription factors). In some embodiments, a promoter or a core promoter can comprise one or more elements or sequences binding to NKX2-1, NANOG, GATA3, TRPS1, SOX9, KSLF14, Sp5, ZEB1, ZEB2, TGIF, PITX, NKX6-1, THRb, ERRa, COUP-TFII, PR, Asc12, Slug, E2A, PITX1, or NKX3.2.
In some embodiments, a promoter or a core promoter can be operably linked to an open reading frame (ORF) of a gene of interest. A gene of interest can be any gene for which expression is desired specifically in cancer cells. Non-limiting examples of a gene of interest can include a gene encoding a therapeutic protein, a gene encoding a synthetic protein, a gene encoding a marker protein (e.g., biomarker for diagnostics, etc.), or a gene encoding a reporter protein.
In some embodiments, the core promoter can be derived from a promoter of one or more genes that are expressed at a higher level in cancer cells compared to non-cancer cells. For example, the core promoter can be derived from a promoter of one or more genes that are expressed at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher in cancer cells compared to non-cancer cells. In some embodiments, the core promoter can be derived from a promoter of one or more genes that are more active in cancer cells compared to non-cancer cells. For example, the core promoter can be derived from a promoter of one or more genes that are at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% more active in cancer cells compared to non-cancer cells.
In some embodiments, a phosphorylation assay can be used to measure activation or activity levels of cancer-responsive genes described herein.
In some embodiments, the core promoter can be derived from one or more cancer-responsive genes that are expressed at a higher level in cancer cells compared to non-cancer cells. For example, the core promoter can be derived from one or more cancer-responsive genes that are either expressed at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher in cancer cells compared to non-cancer cells. In some embodiments, the core promoter can be derived from one or more cancer-responsive genes that are more active in cancer cells compared to non-cancer cells. For example, the core promoter can be derived from one or more cancer-responsive genes that are at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% more active in cancer cells compared to non-cancer cells. In some embodiments, a phosphorylation assay can be used to measure activation or activity levels of cancer-responsive genes described herein.
Synthetic Response Elements—Transcription Factors (TFs)
In some embodiments, an SRS can comprise one or more SREs, wherein the one or more SREs can comprise a plurality of binding sites for one or more transcription factors. In some embodiments, a plurality of binding sites (e.g., binding site DNA sequence) for one or more transcription factors can be identified from a multi-omics approach, including but not limited to, transcriptomics, proteomics, and/or phospho-proteomics to be upregulated in cancer cells or tissues compared to normal (e.g., non-cancer) cells or tissues. In some embodiments, the one or more SREs can comprise a plurality of binding sites for one or more transcription factors that are expressed in higher levels in cancer cells compared to non-cancer cells. In some embodiments, ChIP assay can be used to measure expression levels of transcription factors described herein. In some embodiments, the one or more SREs can comprise a plurality of binding sites for one or more transcription factors that are more active in cancer cells compared to non-cancer cells. For example, the one or more SREs can comprise a plurality of binding sites for one or more transcription factors that have higher level of phosphorylation in cancer cells compared to non-cancer cells. In some embodiments, a phosphorylation assay can be used to measure activation or activity levels of transcription factors described herein.
In some embodiments, an SRS comprising a promoter (or a core promoter) and a plurality of binding sites for one or more transcription factors can drive the expression of an ORF operably linked to the promoter (or the core promoter) at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 1.6-fold, at least 1.7-fold, at least 1.8-fold, at least 1.9-fold, at least 2-fold, at least 2.1-fold, at least 2.2-fold, at least 2.3-fold, at least 2.4-fold, at least 2.5-fold, at least 2.6-fold, at least 2.7-fold, at least 2.8-fold, at least 2.9-fold, at least 3-fold, at least 3.1-fold, at least 3.2-fold, at least 3.3-fold, at least 3.4-fold, at least 3.5-fold, at least 3.6-fold, at least 3.7-fold, at least 3.8-fold, at least 3.9-fold, at least 4-fold, at least 4.1-fold, at least 4.2-fold, at least 4.3-fold, at least 4.4-fold, at least 4.5-fold, at least 4.6-fold, at least 4.7-fold, at least 4.8-fold, at least 4.9-fold, at least 5-fold, at least 10-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, at least 60-fold, at least 70-fold, at least 80-fold, at least 90-fold, or at least 100-fold higher than the expression of a corresponding ORF driven by a promoter (or a core promoter) without the plurality of binding sites for one or more transcription factors.
In some embodiments, an SRS comprising a promoter described herein (or a core promoter described herein, e.g., a cancer-specific core promoter comprising a TATA-TSS and other elements in−300 bp to about +100 bp relative to a TSS) and a plurality of binding sites for one or more transcription factors can drive the expression of an ORF operably linked to the promoter (or the core promoter) at least 1.1-fold, at least 1.2-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 1.6-fold, at least 1.7-fold, at least 1.8-fold, at least 1.9-fold, at least 2-fold, at least 2.1-fold, at least 2.2-fold, at least 2.3-fold, at least 2.4-fold, at least 2.5-fold, at least 2.6-fold, at least 2.7-fold, at least 2.8-fold, at least 2.9-fold, at least 3-fold, at least 3.1-fold, at least 3.2-fold, at least 3.3-fold, at least 3.4-fold, at least 3.5-fold, at least 3.6-fold, at least 3.7-fold, at least 3.8-fold, at least 3.9-fold, at least 4-fold, at least 4.1-fold, at least 4.2-fold, at least 4.3-fold, at least 4.4-fold, at least 4.5-fold, at least 4.6-fold, at least 4.7-fold, at least 4.8-fold, at least 4.9-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 11-fold, at least 12-fold, at least 13-fold, at least 14-fold, at least 15-fold, at least 16-fold, at least 17-fold, at least 18-fold, at least 19-fold, at least 20-fold, at least 21-fold, at least 22-fold, at least 23-fold, at least 24-fold, at least 25-fold, at least 26-fold, at least 27-fold, at least 28-fold, at least 29-fold, at least 30-fold, at least 31-fold, at least 32-fold, at least 33-fold, at least 34-fold, at least 35-fold, at least 36-fold, at least 37-fold, at least 38-fold, at least 39-fold, at least 40-fold, at least 41-fold, at least 42-fold, at least 43-fold, at least 44-fold, at least 45-fold, at least 46-fold, at least 47-fold, at least 48-fold, at least 49-fold, at least 50-fold, at least 55-fold, at least 60-fold, at least 65-fold, at least 70-fold, at least 75-fold, at least 80-fold, at least 85-fold, at least 90-fold, at least 95-fold, or at least 100-fold higher than the expression of a corresponding ORF driven by a non-cancer specific promoter (e.g., TATA-TSS promoter only) and the plurality of binding sites for one or more transcription factors.
Non-limiting examples of transcription factors can include TRPS1, MNX1, TWIST1, ETV4, FOSL2, NFIC, EN2, TFDP1, PITX2, TCF7L1, VENTX, HOXB9, DLX1, MYCN, SIX4, TP63, SOX11, E2F8, TFDP1, SURV, TOXE, EN1, ZBTB7B, SP3, SIX2, XBP1, HIF-1A, CREB3L1, HSF-1, MTF1, NFE2L2, USF2, TP73, POU2F2, HOXA1, FOXO1, TFAP4, BACH1, E2F4, HOXC10, KLF11, FOXM1, E2F2, E2F3, E2F1, GLIS3, GATA1, DLX3, LHX2, BARX1, HOXC9, FOXK1, RUNX2, RUNX1, SOX4, RREB1, HES6, ASCL1, FOXA3, HOXB2, DLX4, GRHL1, FOXA, HIF, E2F6, FOSL1, JUN, JUNB, FOSB, AP-1, NF-1, RFX6, EL4, TCF3, TCF12, SNAI2, REST, DMRTA2, RFX7, NRF1, ZNF148, ZNF652, PRDM1, HIF1A, TGIF1, STAT2, ESRRA, RELB, HSF1, MAFB, TFAP2C, YBX1, YY1, PITX1, SATB1, ARID3A, POU3F1, SP4, MGA, SALL4, AHR, MLXIP, PRDM4, NFIL3, TFAP2A, ZBTB17, ZFP91, ARID5A, IRF6, ZFX, POU2F1, NKX2-1, NKX2-8, FOXA1, NFKB1, HNF4G, ARID1A, NFATC2, SMAD2, ARID3B, TPS3, FOS, FOS-CREB, ELK3, FOXO1::ELK3, TCF7, E2F2, CREB3L1, SHOX2, TCF7L1, HOXA1, MYBL2, NR2C2, MYCN, FOXN1, PITX2, EN2, NFIC, MYC, DLX4, SP3, FOXE1, VENTX, TPS3, GLIS3, CUX1, MGA, DLX1, DLX6, GATA1, RUNX2, E2F7, GRHL1, ZBTB7B, HNF1A, FOXA3, NPAS2, TP63, RREB1, SOX4, ZIC2, TCF7, EN1, DMBX1, E2F8, FOSL2, PBX3, NKX3-2, DLX3, HOXB7, TRPS1, SOX11, PAX8, HES6, HOXC10, MNX1, SIX2, ZNF281, ETV4, ZNF384, ASCL1, BARX1, PAX7, LHX2, OTX1, RUNX1, ETV6, FOXK1, HOXB9, E2F4, NR2F6, TWIST1 HOXC9, IRF6, NR2E1, RORB, E2F1, E2F3, TFDP1, FOXJ3, SIX4, MAX::MYC, ONECUT1, or NFκB.
In some embodiments, transcription factors enriched in lung adenocarcinoma (LUAD) can comprise E2F2, CREB3L1, SHOX2, TCF7L1, HOXA1, MYBL2, NR2C2, MYCN, FOXN1, PITX2, EN2, NFIC, MYC, DLX4, SP3, FOXE1, VENTX, TP53, GLIS3, CUX1, MGA, DLX1, DLX6, GATA1, RUNX2, E2F7, GRHL1, ZBTB7B, HNF1A, FOXA3, NPAS2, TP63, RREB1, SOX4, ZIC2, TCF7, EN1, DMBX1, E2F8, FOSL2, PBX3, NKX3-2, DLX3, HOXB7, TRPS1, SOX11, PAX8, HES6, HOXC10, MNX1, SIX2, ZNF281, ETV4, ZNF384, ASCL1, BARX1, PAX7, LHX2, OTX1, RUNX1, ETV6, FOXK1, HOXB9, E2F4, NR2F6, TWIST1, HOXC9, IRF6, NR2E1, RORB, E2F1, E2F3, TFDP1, FOXJ3, SIX4, MAX::MYC, or ONECUT1.
In some embodiments, transcription factors can comprise E2F4, E2F3, E2F1, GLIS3, GATA1, DLX1, DLX3, LHX2, BARX1, PBX3, HOXC9, FOXK1, FOXA3, TRPS1, RUNX2, HOXA1, NFE2L2, TCF3, TCF12, SNAI2, REST, DMRTA2, RFX7, NRF1, ZNF148, ZNF652, PRDM1, HIF1A, TGIF1, STAT2, ESRRA, RELB, HSF1, MAFB, TFAP2C, YBX1, YY1, PITX1, SATB1, ARID3A, USF2, POU3F1, SP4, MGA, SALL4, AHR, MLXIP, MTF1, PRDM4, ZBTB7B, NFIL3, TFAP2A, ZBTB17, ZFP91, BACH1, MLXIP, ARID5A, IRF6, ZFX, POU2F1, NKX2-1, NKX2-8, FOXA1, NFKB1, MGA, HNF4G, ARID1A, NFATC2, POU2F2, SMAD2, PRDM4, MLXIP, or ARID3B. In some embodiments, control TF tiles can comprise TCF7_v2, TCF7L1_v19, TP53_v5, TP53_v22, Control-1-FOSL1_v1, HOXC10_v24, HOXC10_v14, CREB3L1_v6, CREB3L1_v14, Control-Filler_v1, Control-Filler_v2, Control-Filler_v3, Control-Filler_v4, or Control-Filler_v5. In some embodiments, TF tiles can comprise homotypic TF-tiles or heterotypic TF tiles. For examples, TF-tiles comprising mixed binding sequences/sites/motifs from the same TF can be referred to as homotypic TF-tiles. For example, TF-tiles comprising mixed binding sequences/sites/motifs from different TF can be referred to as heterotypic TF-tiles. In some embodiments, SREs can comprise binding sequences, sites, or motifs of TFs of dysregulated genes that are involved in the EGFR, KRAS or p53 pathways in NSCLC.
In some embodiments, a binding site for a transcription factor can comprise a known transcription factor binding site (TFBS) sequence element or DNA binding site sequence element. In some embodiments, a transcription factor can bind to TFBS sequence element or DNA binding site sequence element and can recruit additional transcriptional machinery and co-factors (e.g., RNA polymerase, etc.) to the promoter or the core promoter. In some embodiments, a transcription factor can comprise a transcription co-factor.
In one embodiment, transcription factors that bind to the plurality of transcription binding sites can drive the expression of an ORF operably linked to the promoter in one specific type of cancer cells. In another embodiment, transcription factors that bind to the plurality of transcription binding sites can drive the expression of an ORF operably linked to the promoter in two or more types of cancer cells.
In some embodiments, an SRE can comprise at least about one, at least about two, at least about three, at least about four, at least about five, at least about six, at least about seven, at least about eight, at least about nine, or at least about ten binding sites for one or more transcription factors. In some embodiments, an SRE can comprise at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, or at least about 50 binding sites for one or more transcription factors. In some embodiments, an SRE can comprise at most about 50, at most about 45, at most about 40, at most about 35, at most about 30, at most about 25, at most about 24, at most about 23, at most about 22, at most about 21, at most about 20, at most about 19, at most about 18, at most about 17, at most about 16, at most about 15, at most about 14, at most about 13, at most about 12, at most about 11, at most about 10, at most about 9, at most about 8, at most about 7, at most about 6, or at most about 5 binding sites for one or more transcription factors.
In some embodiments, an SRE can comprise a plurality of binding sites for at least about one, at least about two, at least about three, at least about four, at least about five, at least about six, at least about seven, at least about eight, at least about nine, or at least about ten transcription factors. In some embodiments, an SRE can comprise a plurality of binding sites for at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, or at least about 50 transcription factors. In some embodiments, an SRE can comprise a plurality of binding sites for at most about 50, at most about 45, at most about 40, at most about 35, at most about 30, at most about 25, at most about 24, at most about 23, at most about 22, at most about 21, at most about 20, at most about 19, at most about 18, at most about 17, at most about 16, at most about 15, at most about 14, at most about 13, at most about 12, at most about 11, at most about 10, at most about 9, at most about 8, at most about 7, at most about 6, or at most about 5 transcription factors.
In some embodiments, an SRE can comprise two or more transcription factor binding sites for one transcription factor, wherein each of the two or more transcription factor binding sites can be sequentially arranged or tiled in a sequential manner. For example, an SRE can comprise two or more transcription factor binding site sequences for one transcription factor and each of the two or more transcription factor binding sites can be sequentially arranged or tiled in a sequential manner (e.g., arranged side by side). In some embodiments, an SRE can comprise two or more transcription factor binding sites for one transcription factor, wherein each of two or more transcription factor binding sites can be sequentially arranged or tiled in a sequential manner at 5′ to a core promoter in the recombinant polynucleotide comprising the SRE and the core promoter.
In some embodiments, an SRE can comprise two or more transcription factor binding sites for two or more transcription factors, wherein each of two or more transcription factor binding sites can be non-sequentially arranged or tiled in a non-sequential manner. For example, an SRE can comprise two or more transcription factor binding site sequences for two or more transcription factors and the two or more transcription factor binding site sequences may be (i) the same, (ii) different, or (iii) a combination of (i) and (ii). In this example, the two or more transcription binding sites can comprise (ii) different transcription factor binding site sequences that are non-sequentially arranged or tiled in a non-sequential manner (e.g., shuffled) in the recombinant polynucleotide. In another example, the two or more transcription factor binding sites can comprise (iii) a combination of the same and different transcription factor binding site sequences, wherein all of the two or more transcription factor binding sites are non-sequentially arranged or tiled in a non-sequential manner in the recombinant polynucleotide. In yet another example, the two or more transcription factor binding sites can comprise (iii) a combination of the same and different transcription factor binding site sequences, wherein some of the two or more transcription factor binding sites are sequentially arranged or tiled in a sequential manner and the some of the two or more transcription factor binding sites are non-sequentially arranged or tiled in a non-sequential manner in the recombinant polynucleotide. In some embodiments, an SRE can comprise two or more transcription factor binding sites for two or more transcription factors, wherein each of two or more transcription factor binding sites can be non-sequentially arranged or tiled in a non-sequential manner at 5′ to a core promoter in the recombinant polynucleotide comprising the SRE and the core promoter.
In some embodiments, an SRE comprising a plurality of binding sites for one or more transcription factors can further comprise a spacer element between each of the plurality of binding sites for one or more transcription factors. In some embodiments, a spacer element can comprise a nucleotide sequence of from about 1 to about 10 nucleotides or base pairs. For example, a spacer element can comprise a nucleotide sequence of from about 1 to about 10 nucleotides, from about 2 to about 15 nucleotides, from about 3 to about 20 nucleotides, from about 4 to about 25 nucleotides, from about 4 to about 30 nucleotides, from about 5 to about 35 nucleotides, from about 6 to about 40 nucleotides, from about 7 to about 50 nucleotides, from about 8 to about 55 nucleotides, from about 9 to about 60 nucleotides, from about 10 to about 65 nucleotides, from about 15 to about 70 nucleotides, from about 20 to about 75 nucleotides, from about 25 to about 80 nucleotides, from about 30 to about 85 nucleotides, from about 35 to about 90 nucleotides, from about 40 to about 95 nucleotides, or from about 45 to about 100 nucleotides. In some embodiments, a spacer element can comprise a nucleotide sequence of at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, or at least about 100 nucleotides. In some embodiments, a spacer element can comprise a nucleotide sequence of at most about 100, at most about 95, at most about 90, at most about 85, at most about 80, at most about 75, at most about 70, at most about 65, at most about 60, at most about 55, at most about 50, at most about 45, at most about 40, at most about 35, at most about 30, at most about 25, at most about 24, at most about 23, at most about 22, at most about 21, at most about 20, at most about 19, at most about 18, at most about 17, at most about 16, at most about 15, at most about 14, at most about 13, at most about 12, at most about 11, or at most about 10 nucleotides. In some embodiments, a spacer element can comprise a nucleotide sequence of 0, 3, 7, or 10 nucleotides or base pairs.
In some embodiments, an SRS can comprise a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels in cancer cells compared to non-cancer cells. For example, the one or more TFs core promoter may be expressed at a level that is at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% higher in cancer cells compared to non-cancer cells.
In some embodiments, an SRS can comprise a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are more active in cancer cells compared to non-cancer cells. For example, the one or more TFs may be at least 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%, 320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 410%, 420%, 430%, 440%, 450%, 460%, 470%, 480%, 490%, 500%, 510%, 520%, 530%, 540%, 550%, 560%, 570%, 580%, 590%, 600%, 610%, 620%, 630%, 640%, 650%, 660%, 670%, 680%, 690%, 700%, 710%, 720%, 730%, 740%, 750%, 760%, 770%, 780%, 790%, 800%, 810%, 820%, 830%, 840%, 850%, 860%, 870%, 880%, 890%, 900%, 110%, 920%, 930%, 940%, 950%, 960%, 970%, 980%, 990%, or at least 1000% more active in cancer cells compared to non-cancer cells. In some embodiments, a phosphorylation assay can be used to measure activation or activity levels of TFs described herein.
Synthetic Response Elements—Enhancers
In some embodiments, an SRE can comprise a plurality of enhancers. For example, an SRE can comprise a plurality of any known enhancers that can increase the level of transcription of a gene. In some embodiments, an SRE can comprise a plurality of endogenous enhancer sequences. In some embodiments, an SRE can comprise a plurality of enhancers derived from a cancer-responsive gene described herein. In some embodiments, a cancer-responsive gene can comprise a human cancer-responsive gene. In some embodiments, an SRE can comprise at least about one, at least about two, at least about three, at least about four, at least about five, at least about six, at least about seven, at least about eight, at least about nine, or at least about ten enhancers derived from a cancer-responsive gene. In some embodiments, an SRE can comprise at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, or at least about 50 enhancers derived from a cancer-responsive gene. In some embodiments, an SRE can comprise at most about 50, at most about 45, at most about 40, at most about 35, at most about 30, at most about 25, at most about 24, at most about 23, at most about 22, at most about 21, at most about 20, at most about 19, at most about 18, at most about 17, at most about 16, at most about 15, at most about 14, at most about 13, at most about 12, at most about 11, at most about 10, at most about 9, at most about 8, at most about 7, at most about 6, or at most about 5 enhancers derived from a cancer-responsive gene.
In some embodiments, an SRE can comprise a plurality of enhancers derived from two or more cancer-responsive genes described herein. In some embodiments, a cancer-responsive gene can refer to a gene specifically or preferentially expressed in cancer cells or cancer tissues compared to non-cancer cells or non-cancer tissues. In some embodiments, a cancer-responsive gene can comprise a human cancer-responsive gene. In some embodiments, an SRE can comprise a plurality of enhancers derived from at least about two, at least about three, at least about four, at least about five, at least about six, at least about seven, at least about eight, at least about nine, or at least about ten cancer-responsive genes. In some embodiments, an SRE can comprise a plurality of enhancers derived from at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, or at least about 100 cancer-responsive genes. In some embodiments, an SRE can comprise a plurality of enhancers derived from at most about 100, at most about 95, at most about 90, at most about 85, at most about 80, at most about 75, at most about 70, at most about 65, at most about 60, at most about 55, at most about 50, at most about 45, at most about 40, at most about 35, at most about 30, at most about 25, at most about 24, at most about 23, at most about 22, at most about 21, at most about 20, at most about 19, at most about 18, at most about 17, at most about 16, at most about 15, at most about 14, at most about 13, at most about 12, at most about 11, at most about 10, at most about 9, at most about 8, at most about 7, at most about 6, or at most about 5 cancer-responsive genes.
In some embodiments, a plurality of enhancers described herein can comprise a transcription regulatory element (TRE). A TRE can refer to a region of DNA that can regulate transcription of a gene.
In some embodiments, a TRE can increase the transcription of a gene. In some embodiments, a TRE can decrease the transcription of a gene. In some embodiments, a TRE can comprise a transcription binding site. In some embodiments, a plurality of enhancers can comprise a transcription regulatory element that has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes. In some embodiments, a plurality of enhancers can comprise a transcription regulatory element that has 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes.
In some embodiments, a plurality of enhancers can comprise an enhancer consensus sequence of two or more homologous cancer-responsive genes. In some embodiments, an enhancer consensus sequence of two or more homologous cancer-responsive genes can comprise a consensus sequence of an enhancer sequence derived from two or more cancer-responsive genes that has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity between the two or more cancer-responsive genes. In some embodiments, an enhancer consensus sequence of two or more homologous cancer-responsive genes can comprise a consensus sequence of an enhancer sequence derived from two or more cancer-responsive genes that has at least 90% sequence identity between the two or more cancer-responsive genes.
In some embodiments, an SRE can comprise a plurality of enhancers comprising at least two enhancer sequences, wherein each of the at least two enhancer sequences can comprise (i) the same enhancer sequences, (ii) different enhancer sequences, or (iii) a combination of (i) and (ii). In some embodiments, each of the at least two enhancer sequences can be sequentially arranged or tiled in a sequential manner in a recombinant polynucleotide. In some embodiments, each of the at least two enhancer sequences can be sequentially arranged or tiled in a sequential manner at 5′ to a core promoter in the recombinant polynucleotide comprising the core promoter and an SRE comprising the plurality of enhancers. In some embodiments, each of said at least two enhancer sequences can be sequentially arranged or tiled in a sequential manner at 5′ to a core promoter and/or at 3′ to a plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide comprising the core promoter, an SRE comprising the plurality of enhancers, and/or the plurality of transcription factor binding sites.
In some embodiments, an SRE can comprise a plurality of enhancers comprising at least two enhancer sequences, wherein each of the at least two enhancer sequences can comprise (ii) different enhancer sequences. In this embodiment, each of said plurality of enhancers comprising different enhancer sequences can be non-sequentially arranged or tiled in a non-sequential manner. In some embodiments, each of said plurality of enhancers comprising different enhancer sequences can be non-sequentially arranged or tiled in a non-sequential manner at 5′ to a core promoter in the recombinant polynucleotide comprising the core promoter and an SRE comprising the plurality of enhancers. In some embodiments, each of said plurality of enhancers comprising different enhancer sequences can be non-sequentially arranged or tiled in a non-sequential manner at 5′ to a core promoter and/or at 3′ to a plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide comprising the core promoter, an SRE comprising the plurality of enhancers, and/or the plurality of transcription factor binding sites.
In some embodiments, an SRE can comprise a plurality of enhancers comprising at least two enhancer sequences, wherein each of the at least two enhancer sequences can comprise (iii) a combination of the same and different enhancer sequences. In this embodiment, each of said plurality of enhancers comprising a combination of the same and different enhancer sequences can be non-sequentially arranged or tiled in a non-sequential manner. In some embodiments, each of said plurality of enhancers comprising a combination of the same and different enhancer sequences can be non-sequentially arranged or tiled in a non-sequential manner at 5′ to a core promoter in the recombinant polynucleotide comprising the core promoter and an SRE comprising the plurality of enhancers. In some embodiments, each of said plurality of enhancers comprising a combination of the same and different enhancer sequences can be non-sequentially arranged or tiled in a non-sequential manner at 5′ to a core promoter and/or at 3′ to a plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide comprising the core promoter, an SRE comprising the plurality of enhancers, and/or the plurality of transcription factor binding sites.
In some embodiments, a plurality of enhancers described herein can comprise a sequence capable of binding to a transcription associated protein. A transcription associated protein as described herein can comprise any protein that is involved in transcription of a DNA sequence to an RNA sequence. In some embodiments, a transcription associated protein can bind to an enhancer sequence. In some embodiments, an assay can be used to determine if a transcription associated protein can bind to a sequence comprised in a plurality of enhancers. For example, chromatin immunoprecipitation (ChIP) assay, an in vitro transfection reporter assay, or any other suitable assays or methods can be used to determine if a transcription associated protein can bind to a sequence comprised in a plurality of enhancers. In some embodiments, a plurality of enhancers described herein can comprise a sequence capable of binding to a transcription associated protein determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some embodiments, a plurality of enhancers can comprise a CpG island. For example, at least one enhancer of the plurality of enhancers can comprise a CpG island. In some embodiments, a plurality of enhancers may not comprise a CpG island. For example, at least one enhancer of the plurality of enhancers may not comprise a CpG island.
In some embodiments, an SRS can comprise a core promoter and a plurality of binding sites for one or more transcription factors derived from two or more cancer-responsive genes, wherein the core promoter and the plurality of binding sites for one or more transcription factors are not derived from the same cancer-responsive gene. In some embodiments, an SRS can comprise a core promoter and a plurality of enhancers derived from two or more cancer-responsive genes, wherein the core promoter and the plurality of enhancers are not derived from the same cancer-responsive gene. In some embodiments, an SRS can comprise a core promoter, a plurality of binding sites for one or more transcription factors, and a plurality of enhancer derived from two or more cancer-responsive genes, wherein the core promoter, the plurality of binding sites for one or more transcription factors, and the plurality of enhancer are not derived from the same cancer-responsive gene. In some embodiments, a cancer-responsive gene can comprise a human cancer-responsive gene.
In some embodiments, a plurality of enhancers can comprise an enhancer sequence that can bind to SP1, ETS, CEBP, NF-KB, EBS, C/EBP, ARE, DRE, NFκB, GC-box, UN5CL, BOP1, RTN4RL2, ARNTL2, AGR2, LHX2, TRNP1, MU5AC, or DOK4. In some embodiments, a plurality of enhancers can comprise at least two, at least about three, at least about four, at least about five, at least about six, at least about seven, at least about eight, at least about nine, or at least about ten enhancer sequences. In some embodiments, a plurality of enhancers can comprise at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, or at least about 100 enhancer sequences. In some embodiments, a plurality of enhancers can comprise at least two SP1, ETS, CEBP, NF-KB, EBS, C/EBP, ARE, DRE, NFκB, GC-box, UN5CL, BOP1, RTN4RL2, ARNTL2, AGR2, LHX2, TRNP1, MU5AC, or DOK4 enhancer sequences.
In some embodiments, core promoter, plurality of binding sites for one or more transcription factors, or plurality of enhancers derived from two or more cancer-responsive genes can comprise a sequence listed in Table 1A, Table 1B, or Table 1C. In some embodiments, an SRS described herein can comprise a sequence listed in Table 1A, Table 1B, or Table 1C.
In some embodiments, an SRS can comprise a sequence comprising a human alpha-fetoprotein (AFP) promoter sequence comprising a plurality of HNF-1A transcription binding sites. AFP level is elevated in liver cancer including, but not limited to, hepatic carcinomas. In some embodiments, an HNF-1A transcription binding site can comprise a sequence of 5′-GTTAATTATTAAC-3′ (SEQ ID NO: 128).
Cancer Cells or Cell Lines
Described herein is a method of selectively expressing a protein in cancer or tumor cells. In some embodiments, the method can comprise contacting cancer or tumor cells with a recombinant polynucleotide comprising any SRS described herein that comprises a promoter or a core promoter, one or more SREs, and an open reading frame (ORF) encoding a protein. In some embodiments, the ORF can be operatively linked to the SRS or the promoter (or the core promoter) in the SRS. In some embodiments, cancer or tumor cells described herein can comprise malignant cancer cells. Examples of cancer or tumor cells include, but are not limited to, colorectal cancer (CRC) cells, hepatocellular carcinoma cells, breast cancer cells, or lung cancer cells. In some embodiments, cancer or tumor cells can comprise cancer or tumor cells associated with colorectal cancer (CRC), hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer. In some embodiments, adenocarcinoma (LUAD) cells can comprise LXFA586, LXFA629, LXFA2184, or A549.
In some embodiments, large cell carcinoma cells can comprise H1299, LXFL430, LXFL1121, or LXFL529. In some embodiments, squamous cell carcinoma (LUSC) cells can comprise LK2, H520, H1703, SK-MES-1, or Calu-1. In some embodiments, hepatocellular carcinoma (HCC) cells can comprise HUH7.
In some embodiments, promoters active in LXFA586 cell lines can comprise promoters of TP53, HES6, FOS, FOS-CREB, FOXO1::ELK3, or MTF1. In some embodiments, promoters active in LXFA629 cell lines can comprise promoters of FOS, CREB3L1, or HES6. In some embodiments, promoters active in LXFA2184 cell lines can comprise promoters of FOS or MNX. In some embodiments, promoters active in H1299 cell lines can comprise promoters of FOS, CREB3L1, HES6, FOS-CREB, NFE2L2, FOXO1::ELK3, or XBP1. In some embodiments, promoters active in LXFL430 cell lines can comprise promoters of TCF7, ETV4, HOXC10, FOS-CREB, FOXO1::ELK3, or XBP1. In some embodiments, promoters active in LXFL1121 cell lines can comprise promoters of FOS, CREB3L1, or ETV4. In some embodiments, promoters active in LXFL529 cell lines can comprise promoters of FOS.
In some embodiments, expression of the protein encoded by the ORF may be increased in cancer cells compared to non-cancer cells. In some embodiments, expression of the protein encoded by the ORF may be increased when the recombinant polynucleotide comprising the SRS and the ORF is introduced to cancer cells compared to non-cancer cells. For example, expression of the protein encoded by the ORF may be increased at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 100%, at least about 110%, at least about 120%, at least about 130%, at least about 140%, at least about 150%, at least about 160%, at least about 170%, at least about 180%, at least about 190%, at least about 200%, or at least about 250% in cancer cells compared to non-cancer cells. In some embodiments, the ORF can comprise a sequence encoding a therapeutic protein, marker protein (e.g., for diagnostic imaging, etc.), or a reporter protein (e.g., luciferase). In some embodiments, the ORF can comprise a sequence encoding a recombinant, synthetic, or engineered protein.
In some embodiments, expression of the protein encoded by the ORF may be increased in a first plurality of cancer cells when said recombinant polynucleotide is introduced to the first plurality of cancer cells compared to a second plurality of cancer cells, wherein the first plurality of cancer cells and the second plurality of cancer cells are different types of cancer cells. In some embodiments, expression of the protein encoded by the ORF may be increased in a first plurality of cancer cells when the recombinant polynucleotide comprising the SRS and the ORF is introduced to the first plurality of cancer cells compared to a second plurality of cancer cells, wherein the first plurality of cancer cells and the second plurality of cancer cells are different types of cancer cells. For example, expression of the protein encoded by the ORF operatively linked to a first type of SRS in the recombinant polynucleotide may be increased in cells of one type of cancer in which the first type of SRS can drive expression of the ORF compared to in cells of another type of cancer in which the first type of SRS cannot drive expression of the ORF. For example, expression of the protein encoded by the ORF operatively linked to an SRS that is specific for lung cancer may be increased in lung cancer cells compared to in liver cancer cells.
In some embodiments, expression of the protein encoded by the ORF may be increased in a first plurality of cancer cells comprising two or more types of cancer cells when the recombinant polynucleotide comprising the SRS and the ORF is introduced to the first plurality of cancer cells compared to a second plurality of cancer cells. For example, expression of the protein encoded by the ORF operatively linked to a first type of SRS in the recombinant polynucleotide may be increased in cells of two or more types of cancer in which the first type of SRS can drive expression of the ORF compared to in cells of another type of cancer in which the first type of SRS cannot drive expression of the ORF. For example, expression of the protein encoded by the ORF operatively linked to an SRS that is specific for lung and liver cancer may be increased in lung cancer cells and liver cancer cells compared to in non-lung cancer cells and non-liver cancer cells (e.g., breast cancer cells, etc.). In some embodiments, the first plurality of cancer cells comprising two or more types of cancer cells can comprise cells associated with two or more cancers comprising colorectal cancer, hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
Therapeutic or Diagnostic Applications
Provided herein are recombinant polynucleotides (or any vector, pharmaceutical composition, or lipid nanoparticle comprising any recombinant polynucleotides described herein) useful for the diagnosis or the treatment of a disease or condition. In some aspects, recombinant polynucleotides described herein (or any vector, pharmaceutical composition, or lipid nanoparticle comprising any recombinant polynucleotides described herein) are present or administered in an amount for sufficient expression of a protein (e.g., a reporter protein or a biomarker) useful for a diagnosis of a disease or condition. In some embodiments, the disease or condition comprise a cancer. In some aspects, provided herein is a method of selectively expressing a reporter protein or a biomarker in a cancer or tumor cell. In some aspects, the method comprises contacting a tumor cell with any of recombinant polynucleotides described herein, any of vectors comprising recombinant polynucleotide described herein, any of pharmaceutical composition comprising recombinant polynucleotide described herein, or any of lipid nanoparticle (LNP) comprising the recombinant polynucleotide, the vector, or the pharmaceutical composition described herein, wherein recombinant polynucleotides can comprise an open reading frame (ORF) encoding the reporter protein or the biomarker operatively linked to a synthetic promoter described herein (e.g., a synthetic promoter that can drive expression of the ORF preferentially or specifically in cancer cells).
In some aspects, provided herein is a method for diagnosing a disease or a condition. In some embodiments, the method can comprise administering to any of recombinant polynucleotide described herein, a vector comprising the recombinant polynucleotide described herein, the pharmaceutical composition comprising the recombinant polynucleotide described herein, or a lipid nanoparticle (LNP) comprising the recombinant polynucleotide, the vector, or the pharmaceutical composition described herein to a subject. In some embodiments, the recombinant polynucleotide can further comprise an open reading frame (ORF) encoding a reporter protein or a biomarker, wherein the ORF is operatively linked to a synthetic promoter in the recombinant polynucleotide that can drive expression of the ORF selectively, preferentially, or specifically in diseased cells compared to non-disease cells. In some embodiments, the method can further comprise detecting the reporter protein or a biomarker of which expression can be induced by a synthetic promoter in the recombinant polynucleotide described herein selectively, preferentially, or specifically in diseased cells compared to non-disease cells. In some embodiments, a relative ratio of the reporter protein or the biomarker expressed in the diseased cells over the non-diseased cells can be greater than 1.0. For example, a relative ratio of the reporter protein or the biomarker expressed in the diseased cells over the non-diseased cells can be greater than about 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0, 85.0, 90.0, 95.0, or about 100.0. In some embodiments, the disease or condition can comprise a cancer.
In some aspects, recombinant polynucleotides (or any vector, pharmaceutical composition, or lipid nanoparticle comprising any recombinant polynucleotides described herein) are present or administered in an amount sufficient to treat or prevent a disease or condition. In some aspects, provided herein, is a method of treating a disease or condition comprising administering to a subject in need thereof the recombinant polynucleotide described herein, a vector comprising the recombinant polynucleotide described herein, a pharmaceutical composition comprising the recombinant polynucleotide described herein, or a lipid nanoparticle (LNP) comprising the vector, the pharmaceutical composition or the recombinant polynucleotide described herein. In some aspects, provided herein, is recombinant polynucleotide described herein, a vector comprising the recombinant polynucleotide described herein, the pharmaceutical composition comprising the recombinant polynucleotide described herein, or a lipid nanoparticle (LNP) comprising the recombinant polynucleotide, the vector, or the pharmaceutical composition described herein for use in a method of treating a disease or a condition in a subject in need thereof. In some aspects, provided herein, is the use of recombinant polynucleotide described herein, a vector comprising the recombinant polynucleotide described herein, the pharmaceutical composition comprising the recombinant polynucleotide described herein, or a lipid nanoparticle (LNP) comprising the recombinant polynucleotide, the vector, or the pharmaceutical composition described herein for the manufacture of a medicament for treating a disease or a condition in a subject in need thereof.
In some aspects, provided herein is a method for treating a subject having or suspected of having a disease or a condition. In some embodiments, the method can comprise administering any of recombinant polynucleotide described herein, a vector comprising the recombinant polynucleotide described herein, the pharmaceutical composition comprising the recombinant polynucleotide described herein, or a lipid nanoparticle (LNP) comprising the recombinant polynucleotide, the vector, or the pharmaceutical composition described herein to a subject. In some embodiments, the recombinant polynucleotide can further comprise an open reading frame (ORF) encoding a therapeutic protein, wherein the ORF is operatively linked to a synthetic promoter in the recombinant polynucleotide that can drive expression of the ORF selectively, preferentially, or specifically in diseased cells compared to non-disease cells. In some embodiments, a relative ratio of the therapeutic protein expressed in the diseased cells over the non-diseased cells can be greater than 1.0. For example, a relative ratio of the therapeutic protein expressed in the diseased cells over the non-diseased cells can be greater than about 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5, or about 15.0.
In some embodiments, the disease or disorder can comprise a cancer. Examples of cancer can include, but are not limited to, colorectal cancer (CRC), hepatocellular carcinoma, breast cancer, lung cancer, liver cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
Also provided herein are pharmaceutical compositions comprising any recombinant polynucleotide described herein or any vector comprising the recombinant polynucleotide described herein and a pharmaceutically acceptable excipient, carrier, or diluent. A pharmaceutical composition can denote a mixture or solution comprising a therapeutically effective amount of an active pharmaceutical ingredient together with one or more pharmaceutically acceptable excipients to be administered to a subject in need thereof. The term “pharmaceutically acceptable” can denote an attribute of a material which is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and neither biologically nor otherwise undesirable and is acceptable for veterinary as well as human pharmaceutical use. The term “Pharmaceutically acceptable” can refer to a material, such as a excipient, carrier, or diluent, which does not abrogate the biological activity or properties of the recombinant polynucleotide or the compound, and is relatively nontoxic, i.e., the material may be administered to an individual without causing undesirable biological effects or interacting in a deleterious manner with any of the components of the composition in which it is contained. A pharmaceutically acceptable excipient can denote any pharmaceutically acceptable ingredient in a pharmaceutical composition having no therapeutic activity and being non-toxic to the subject administered, such as disintegrators, binders, fillers, solvents, buffers, tonicity agents, stabilizers, antioxidants, surfactants, carriers, diluents, excipients, preservatives, or lubricants used in formulating pharmaceutical products. Pharmaceutical compositions can facilitate administration of a recombinant polynucleotide, a vector comprising recombinant polynucleotide, or a compound to an organism and can be formulated in a conventional manner using one or more pharmaceutically acceptable inactive ingredients that facilitate processing of the active compounds into preparations that can be used pharmaceutically. A proper formulation is dependent upon the route of administration chosen and a summary of pharmaceutical compositions can be found, for example, in Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pennsylvania 1975; Liberman, H. A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins 1999), herein incorporated by reference. In some embodiments, pharmaceutical compositions can be formulated by dissolving active substances (e.g., recombinant polynucleotides or vectors comprising the recombinant polynucleotides described herein) in aqueous solution for administration into a cell, a tissue or a subject (e.g., a disease cell, disease tissue, or a subject in need thereof). In some embodiments, pharmaceutical compositions can be formulated by dissolving active substances (e.g., recombinant polynucleotides or vectors comprising the recombinant polynucleotides described herein) in aqueous solution for administration into a cell, a tissue or a subject (e.g., a disease cell, disease tissue, or a subject in need thereof).
Also provided herein are methods of treating a disease or condition in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of any recombinant polynucleotide described herein, any vector comprising recombinant polynucleotide described herein, or pharmaceutical compositions described herein. The terms “effective amount” or “therapeutically effective amount,” as used herein, can refer to a sufficient amount of an agent, a compound, any recombinant polynucleotide described herein, any vector comprising recombinant polynucleotide described herein, or pharmaceutical compositions described herein being administered which will relieve to some extent one or more of the symptoms of the disease or the condition being treated; for example a reduction and/or alleviation of one or more signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. For example, an “effective amount” for therapeutic uses can be an amount of an agent that provides a clinically significant decrease in one or more disease symptoms. An appropriate “effective” amount may be determined using techniques, such as a dose escalation study, in individual cases. In some embodiments, an “effective amount” can comprise an amount for sufficient expression of a protein (e.g., a reporter protein or a biomarker) useful for diagnosing a disease or condition in a subject.
The terms “treat,” “treating” or “treatment,” as used herein, can include alleviating, abating or ameliorating at least one symptom of a disease or a condition, preventing additional symptoms, inhibiting the disease or the condition, e.g., arresting the development of the disease or the condition, relieving the disease or the condition, causing regression of the disease or the condition, relieving a condition caused by the disease or the condition, or stopping the symptoms of the disease or the condition either prophylactically and/or therapeutically. In some embodiments, treating a disease or condition comprises reducing the size of disease tissues or diseased cells. In some embodiments, treating a disease or a condition in a subject comprises increasing the survival of a subject. In some embodiments, treating a disease or condition comprises reducing or ameliorating the severity of a disease, delaying onset of a disease, inhibiting the progression of a disease, reducing hospitalization of or hospitalization length for a subject, improving the quality of life of a subject, reducing the number of symptoms associated with a disease, reducing or ameliorating the severity of a symptom associated with a disease, reducing the duration of a symptom associated with a disease, preventing the recurrence of a symptom associated with a disease, inhibiting the development or onset of a symptom of a disease, or inhibiting of the progression of a symptom associated with a disease. In some embodiments, treating a cancer comprises reducing the size of tumor or increasing survival of a patient with a cancer.
In some cases, a subject can encompass mammals. Examples of mammals include, but are not limited to, any member of the mammalian class: humans, non-human primates such as chimpanzees, and other apes and monkey species; farm animals such as cattle, horses, sheep, goats, swine; domestic animals such as rabbits, dogs, and cats; laboratory animals including rodents, such as rats, mice and guinea pigs, and the like. In some cases, the mammal is a human. In some cases, the subject may be an animal. In some cases, an animal may comprise human beings and non-human animals. In one embodiment, a non-human animal may be a mammal, for example a rodent such as rat or a mouse. In another embodiment, a non-human animal may be a mouse. In some instances, the subject is a mammal. In some instances, the subject is a human. In some instances, the subject is an adult, a child, or an infant. In some instances, the subject is a companion animal. In some instances, the subject is a feline, a canine, or a rodent. In some instances, the subject is a dog or a cat.
Recombinant polynucleotides, vectors, or pharmaceutical compositions described herein can be administered to a subject using any suitable methods known in the art. Suitable formulations for use in the present invention and methods of delivery are generally well known in the art. For example, compositions described herein can be administered to the subject in a variety of ways, including parenterally, intravenously, intradermally, intramuscularly, colonically, rectally, or intraperitoneally. In some embodiments, compositions described herein is administered by intraperitoneal injection, intramuscular injection, subcutaneous injection, or intravenous injection of the subject. In some embodiments, compositions described herein can be administered parenterally, intravenously, intramuscularly or orally. In some embodiments, compositions described herein can be administered via injection into disease tissues or cells.
In some embodiments, compositions or pharmaceutical compositions comprising any recombinant polynucleotide described herein can be delivered to a cell via direct DNA transfer (Wolff et al. (1990) Science 247, 1465-1468). In some embodiments, recombinant polynucleotides can be delivered to cells following mild mechanical disruption of the cell membrane, temporarily permeabilizing the cells. Such a mild mechanical disruption of the membrane can be accomplished by gently forcing cells through a small aperture (Sharei et al. PLOS ONE (2015) 10(4), e0118803). In another embodiment, compositions or pharmaceutical compositions comprising any recombinant polynucleotide described herein can be delivered to via liposome or lipid nanoparticle (LNP) (e.g., Gao & Huang (1991) Biochem. Ciophys. Res. Comm. 179, 280-285, Crystal (1995) Nature Med. 1, 15-17, Caplen et al. (1995) Nature Med. 3, 39-46). A liposome or LNP can encompass a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Recombinant polynucleotides can be encapsulated in the aqueous interior of a liposome or LNP, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, or complexed with a liposome.
In some aspects, provided herein is a method comprising: (a) administering to a subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) localizing a tumor or an absence thereof in a body of said subject via expression of said reporter protein using an imaging technique performed on said body of said subject. In some embodiments, the imaging technique comprises photoacoustic imaging, Magnetic resonance imaging (MRI) imaging, positron emission tomography (PET) imaging, or single-photon emission computed tomography (SPECT) imaging.
Embodiments
In some aspects, provided herein is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells. In some embodiments, the recombinant polynucleotide further comprises a plurality of enhancers.
In some aspects, provided herein is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS) and two or more promoter elements derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells. In some embodiments, the recombinant polynucleotide further comprises a plurality of enhancers.
In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some aspects, provided herein is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and (b) a plurality of enhancers. In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some aspects, provided herein, is a recombinant polynucleotide comprising: (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF), (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells, and (c) a plurality of enhancers. In some embodiments, said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells. In some embodiments, said plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some embodiments, said core promoter further comprises two or more promoter elements derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF). In some embodiments, said one or more cancer-responsive genes are derived from a human subject. In some embodiments, (a) said core promoter, and (b) said plurality of binding sites for one or more TFs or said plurality of enhancers derived from one or more cancer-responsive genes are not derived from a same cancer-responsive gene. In some embodiments, said enhancer consensus sequence of two or more homologous cancer-responsive genes is a consensus sequence of an enhancer sequence derived from two or more cancer-responsive genes that has at least 90% sequence identity between two or more human cancer-responsive genes.
In some embodiments, the recombinant polynucleotide comprises (a) a plurality of binding sites for one or more transcription factors (TFs), wherein one or more TFs are expressed in higher levels or more active in cancer cells compared to non-cancer cells and (b) a plurality of enhancers derived from two or more cancer-responsive genes, wherein each of said plurality of enhancers comprising: (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
In some embodiments, at least one of the plurality of enhancers comprises a CpG island. In some embodiments, at least one of the plurality of enhancers does not comprise a CpG island. In some embodiments, said higher levels of TF expression in cancer cells compared to non-cancer cells is determined by chromatin immunoprecipitation (ChIP).
In some embodiments, the recombinant polynucleotide further comprises an open reading frame (ORF), wherein said core promoter is operably linked to said ORF. In some embodiments, said plurality of binding sites for one or more TFs are 5′ to said core promoter. In some embodiments, said plurality of enhancers are 5′ to said core promoter and 3′ to said plurality of binding sites for one or more TFs, if present. In some embodiments, said plurality of binding sites for one or more TFs comprises two or more binding sites for one TF, wherein each of the plurality of binding sites for one or more TFs is sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide. In some embodiments, said plurality of binding sites for one or more TFs comprises two or more binding sites for two or more TFs, wherein each of the plurality of binding sites for one or more TFs is non-sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide.
In some embodiments, said plurality of binding sites for one or more TFs comprise a plurality of TRPS1, MNX1, TWIST1, ETV4, FOSL2, NFIC, EN2, TFDP1, PITX2, TCF7L1, VENTX, HOXB9, DLX1, MYCN, SIX4, TP63, SOX11, E2F8, TFDP1, SURV, TOXE1, EN1, ZBTB7B, SP3, SIX2, XBP1, HIF-1A, CREB3L1, HSF-1, MTF1, NFE2L2, USF2, TP73, USF2, POU2F2, HOXA1, FOXO1, TFAP4, BACH1, E2F4, HOXC10, KLF11, FOXM1, E2F2, RUNX1, SOX4, RREB1, ETV4, HES6, ASCL1, TWIST1, FOXA3, PITX2, HOXB2, EN2, DLX4, GRHL1, FOXA, HIF, E2F6, FOSL1, NF-1, RFX6, EL4, or NFκB TF binding sites.
In some embodiments, the recombinant polynucleotide further comprises a spacer element comprising 1-10 nucleotides between each of plurality of binding sites for one or more TFs. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprises TCF7, MNX1, HOXC10, TP53, CEACAM5, CEP55, FAM111B, CST1, BIRC5, FOS, TWIST1, E2F2, KIF20A, or ETV4. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprise two or more of TCF7, MNX1, HOXC10, TP53, CEACAM5, CEP55, FAM111B, CST1, BIRC5, FOS, TWIST1, E2F2, KIF20A, or ETV4. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprise TCF7 and HOXC10. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprise TP53 and CEP55. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprise FAM111B and KIF20A. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprise BIRC5 and E2F2. In some embodiments, said one or more cancer-responsive genes from which said core promoter is derived comprise CEACAM5 and TWIST1. In some embodiments, said core promoter comprises a region from about −300 bp to +100 bp relative to said TSS.
In some embodiments, said plurality of enhancers comprises at least two enhancer sequences, wherein each of said at least two enhancer sequences comprises (i) the same enhancer sequences, (ii) different enhancer sequences, or (iii) a combination thereof. In some embodiments, each of said at least two enhancer sequences is sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide. In some embodiments, each of said at least two enhancer sequences is sequentially arranged at 5′ to said core promoter and at 3′ to said plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide. In some embodiments, each of said at least two enhancer sequences comprises (ii), wherein each of said plurality of enhancers comprising different enhancer sequences is non-sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide. In some embodiments, each of said at least two enhancer sequences comprises (ii), wherein each of said plurality of enhancers is non-sequentially arranged at 5′ to said core promoter and at 3′ to said plurality of binding sites of one or more TF binding sites, if present, in the recombinant polynucleotide. In some embodiments, each of said at least two enhancer sequences comprises (iii), wherein each of said plurality of enhancers comprising a combination of the same and different enhancer sequences is non-sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide. In some embodiments, each of said at least two enhancer sequences comprises (iii), wherein each of said plurality of enhancers comprising a combination of the same and different enhancer sequences is non-sequentially arranged at 5′ to said core promoter and at 3′ to said plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide. In some embodiments, said plurality of enhancers comprises at least two EBS, C/EBP, ARE, DRE, NFκB, GC-box, UN5CL, BOP1, RTN4RL2, ARNTL2, AGR2, LHX2, TRNP1, MU5AC, or DOK4 enhancer sequences.
In some embodiments, expression of said ORF is increased when said recombinant polynucleotide is introduced to cancer cells compared to non-cancer cells. In some embodiments, expression of said ORF is increased in a first plurality of cancer cells when said recombinant polynucleotide is introduced to said first plurality of cancer cells compared to a second plurality of cancer cells, wherein said first plurality of cancer cells and said second plurality of cancer cells are different types of cancer cells. In some embodiments, said cancer cells comprise malignant cancer cells. In some embodiments, said cancer cells comprise lung cancer cells, colorectal cancer cells, breast cancer cells, or hepatocellular carcinoma cells. In some embodiments, said cancer cells comprise cells associated with colorectal cancer, hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer. In some embodiments, said cancer cells comprise cells associated with two or more cancers comprising colorectal cancer, hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
In some embodiments, said core promoter, said plurality of binding sites for one or more transcription factors (TFs), said plurality of enhancers, or said recombinant polynucleotide comprises a sequence from Table 1A, Table 1B, or Table 1C.
In some aspects, provided herein is a recombinant polynucleotide comprising any of the sequences from Table 1A, Table 1B, or Table 1C.
In some aspects, provided herein is a recombinant polynucleotide comprising a human alpha-fetoprotein (AFP) promoter sequence comprising a plurality of HNF-1A TF binding sites, wherein each HNF-1A binding site comprises the sequence 5′-GTTAATTATTAAC-3′ (SEQ ID NO: 128).
In some aspects, provided herein is a vector comprising any of the recombinant polynucleotide described herein. In some aspects, provided herein is a pharmaceutical composition comprising any of the recombinant polynucleotide described herein or any the vector described herein and a pharmaceutically acceptable excipient, carrier, or diluents. In some aspects, provided herein is a lipid nanoparticle (LNP) comprising any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the pharmaceutical composition described herein. In some aspects, provided herein is a cell comprising any the recombinant polynucleotide described herein, any of the vector described herein, any of the pharmaceutical composition described herein, or any of the LNP described herein.
In some aspects, provided herein is a method of selectively expressing a reporter protein in a cancer or tumor cell, comprising contacting said tumor cell with any of the recombinant polynucleotide described herein, any of the vector described herein, any of the pharmaceutical composition described herein, or any of the LNP described herein, wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding said reporter protein, wherein said ORF is operatively linked to said synthetic promoter.
In some aspects, provided herein is a method comprising: (a) administering to a subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) detecting said reporter protein, wherein said pharmaceutical composition or said composition induces expression of said reporter protein preferentially in diseased cells in said subject compared to in non-disease cells, and wherein a relative ratio of said reporter protein expressed in said diseased cells over said non-diseased cells is greater than 1.0. In some embodiments, said relative ratio of said reporter protein expressed in said diseased cells over said non-diseased cells is greater than 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5, or about 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0, 85.0, 90.0, 95.0, or about 100.0.
In some aspects, provided herein is a method for treating a subject having or suspected of having a disease, comprising administering to said subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a therapeutic protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, wherein said pharmaceutical composition or said composition induces expression of said therapeutic protein preferentially in diseased cells in said subject compared to in non-disease cells, and wherein a relative ratio of said therapeutic protein expressed in said diseased cells over said non-diseased cells is greater than 1.0.
In some embodiments, said diseased cells comprise a cancer or tumor cell. In some embodiments, said cancer or tumor cell is associated with colorectal cancer (CRC), hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
In some aspects, provided herein is a method comprising: (a) administering to a subject any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) localizing a tumor or an absence thereof in a body of said subject via expression of said reporter protein using an imaging technique performed on said body of said subject.
In some aspects, provided herein is a method comprising: (a) introducing to a subject suspected of having a cancer via intravenous administration any of the pharmaceutical composition described herein; or a composition any of the recombinant polynucleotide described herein, any of the vector described herein, or any of the LNP described herein; wherein said recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and (b) detecting said reporter protein from said subject.
In some aspects, provided herein is a method comprising: (a) introducing to a subject suspected of having a cancer via intravenous administration a plurality of recombinant polynucleotides, wherein: said plurality of recombinant polynucleotides comprises a plurality of different promoters of genes overexpressed in a tumor cell versus a normal tissue or functional fragments thereof operably linked to genes encoding reporter proteins, wherein said plurality of different promoters of genes overexpressed in said tumor cell versus said normal tissue drive expression of said corresponding reporter proteins in a cell affected by said cancer, wherein said DNA molecules are selected from the group consisting of nanoplasmids and linear double-stranded DNA molecules; and (b) detecting said reporter proteins from said subject.







TABLE 1A







Sequences of engineered promoters according to the disclosure










SEQ
EA




ID
RLI.




NO:
ID
Name
Regulatory element sequence (nucleotide)













1
PL1
1-
ggcctaactggccggtaccacatcggctatgctgctgctatgcgagcgtcagtattt



009
TRPS1_
tatctttgatcagctattttatctttagtatcgtattttatctttctcatcgtattt




v22-
tatctttatccgattattttatctttcagcagttattttatctttggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


2
PL1
2-
ggcctaactggccggtaccagctcatgcctatccgattagcttatcttttgaccaga



010
TRPS1_
gctagcttatctttctaactcgcatagcttatcttttgcaagctactagcttatctt




v9-
tcgatgctcattagcttatctttagacgtactctagcttatctttggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


3
PL1
3-
ggcctaactggccggtaccatcactgctgaggtacagatgcacgatgtagctgagcg



011
MNX1_v
acagtatagtgcacagtgagtcattatgatacgtgtcattatcaccattgtcattat




18-
tagacgtgtcattatctgctatgtcattatgctacaggtcattatggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


4
PL1
4-
ggcctaactggccggtacccagcagtcattatacgtcgcctaaatcgagatgctgta



012
TWIST1_
ctgatctatattccagatgttttcaattccagatgttttacattccagatgttttac




v3-
attccagatgtttctcattccagatgttttgaattccagatgtttggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


5
PL1
5-
ggcctaactggccggtaccctgagcgacagtatagtgcacagtgacattacagatgt



013
TWIST1_
ttacgacgaattacagatgtttctcatcgattacagatgtttcagctcaattacaga




v18-
tgtttgctgctgattacagatgtttaccagagattacagatgtttggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


6
PL1
6-
ggcctaactggccggtacccgatgtagctgagcgacagtatagtgcacagtgactgc



014
HOXA1_
agcagtcattatacgtcgcctaaatcgagatgctgtactgatctataaggatcggta




v8-
atgacgtaatgacgtaatgacgtaatgacgtaatgacgtaatgacggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


7
PL1
7-
ggcctaactggccggtaccagctgagcgacagtatagtgcacagtgactgcagcagt



015
HOXC10_
cattatacgtcgcctaaatcgagatgctgtactgatctataagtcgtaaactgtcgt




v24-
aaactgtcgtaaactgtcgtaaactgtcgtaaactgtcgtaaactggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


8
PL1
8-
ggcctaactggccggtacctgtagctgagcgacagtatagtgcacagtgactgcagc



016
HOXC10_
agtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcgtaaattagcgac




v14-
agtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaattggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


9
PL1
9-
ggcctaactggccggtaccatccgatgtgcctgacgaactcatttctaatctatcga



017
GATA1_
tgtagctttctaatctatgcagtcattattctaatctattcgcaatctattctaatc




v1-
tatcttctaactcttctaatctattgctacagctttctaatctatggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


10
PL1
10-
ggcctaactggccggtaccgcacagtgactgcagcagtcattatacgtcgcctaaat



018
NFIC_v1
cgagatgctgtactgatctatttcttggcagatgattcttggcagatcgttcttggc




5-
agagcattcttggcagaggtttcttggcagactcttcttggcagaggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


11
PL1
11-
ggcctaactggccggtaccgtgcaccattagtacctgatcagcgatgctcatctcga



019
EN2_v7-
cctgatcggtacaacttctcacggaggcttctaactcgccgcaattataacgcaatt




coreBIR
attccgcaattactacgcaattacctcgcaattaactcgcaattaggtacctgcgct





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


12
PL1
12-
ggcctaactggccggtaccacatcggctatgctgctgctaatgccacgtcaccacat



020
CREB3L
cgacatgccacgtcaccatcatgccatgccacgtcaccactgcaagatgccacgtca




1_v6-
ccacagtataatgccacgtcaccaagttactatgccacgtcaccaggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


13
PL1
13-
ggcctaactggccggtaccccccaaatcaccccccccccaccgtaaagtccccaaat



021
RREB1_
caccccccccccaaggtaagacccccaaatcacccccccccccgtcgcctaacccca




v17-
aatcacccccccccctactctgctcccccaaatcaccccccccccggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


14
PL1
14-
ggcctaactggccggtaccgaccgtaaagtggtgtgcaccattgaaacttgagctta



022
SIX4_v9
caccatcgaaacttgagcgtatcgcatcgaaacttgagcggtacagatggaaacttg




coreBIR
agcaccattagtagaaacttgagcagcgacagtagaaacttgagcggtacctgcgct




C5-
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




FLUC
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


15
PL1
15-
ggcctaactggccggtacctgcacagtgactgcagcagtcgggcgtgcgctcccgac



023
SURV_v
tagcccagggcgtgcgctcccgactagccccgggcgtgcgctcccgactagccctgg




11-
gcgtgcgctcccgactagccccgggcgtgcgctcccgactagcccggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


16
PL1
16-
ggcctaactggccggtaccaggatcgactagaagtcgcagattagacgacgatacgt



024
TCF7_v3
actactctgctcctagacgtatcctttgatgtaaatcctttgatgtcaatcctttga




coreBIR
tgttaatcctttgatgttagtcctttgatgtctgtcctttgatgtggtacctgcgct




C5-
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




FLUC
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


17
PL1
17-
ggcctaactggccggtacctgagcgacagtatagtgcacagtgactgcagcagtcat



025
TCF7L1_
tatacgtcgcctaaaagacatcaaaggtccagacatcaaaggtacagacatcaaagg




v19-
ggaagacatcaaagggacagacatcaaaggtgcagacatcaaaggggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


18
PL1
18-
ggcctaactggccggtaccatgcacgatgtagctgagaaacatcaaaggacgcaacg



026
TCF7L1_
ccaaacatcaaaggagcctacacgaaacatcaaagggacgctgctaaaacatcaaag




v5-
gctacacgaccaaacatcaaagggccttacaccaaacatcaaaggggtacctgcgct




coreBIR
cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




C5-
gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc




FLUC
aatccggtactgttggtaaagccacc


 


19
PL1
CREB3L
GAATTCTAGTGCACAGTGACTGCAGCAATGCCACGTCAACATCATGCCATGCCACGT



030
1_v14
CAACACCTACACATGCCACGTCAACAACCAGAGATGCCACGTCAACACTAGCATATG





CCACGTCAACATAAGGATATGCCACGTCAACAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


20
PL1
EN2_v7
GAATTCGTGCACCATTAGTACCTGATCAGCGATGCTCATCTCGACCTGATCGGTACA



031

ACTTCTCACGGAGGCTTCTAACTCGCCGCAATTATAACGCAATTATTCCGCAATTAC





TACGCAATTACCTCGCAATTAACTCGCAATTAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


21
PL1
ETV4_v
ggcctaacgaattcgacgctgctacagctcagcctacacgaccgtaaagtggtgtgc



032
14
acaccggaaatgagtatagaccggaaatggccttacaccggaaatgcagctcaaccg





gaaatgactgcagaccggaaatgcgctgctaccggaaatgggtacctgcgctcccga





catgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcaga





ggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatcc





ggtactgttggtaaagccaccatggtggcc


22
PL1
ETV4_v
ggcctaactggccgaattctgagcgacagtatagtgcacagtgactgcagcagtcat


 



033
2
tatacgtaccggaagtgtgtgcctaccggaagtgctatgcgaccggaagtgtagacg





aaccggaagtgcagattaaccggaagtggctgctaaccggaagtgggtacctgcgct





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg





gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


23
PL1
MYCN
GAATTCGTGCACCATTAGTACCTGATCAGCGATGCTCATCTCGACCTGATCGGTACA



034
v22
ACTTCTCACGGAGGCTTCTAACTCGCCGCAATTATAACGCAATTATTCCGCAATTAC





TACGCAATTACCTCGCAATTAACTCGCAATTAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


24
PL1
PAX8_v
GAATTCGTCATTATACGTCGCGTCATGCATGACTGCCTGAGCGGTCATGCATGACTG



035
18
CTACTCAAGTCATGCATGACTGCGACCAGAGTCATGCATGACTGCCGCCTAAGTCAT





GCATGACTGCCTCTGCTGTCATGCATGACTGCGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


25
PL1
PITX2_v
GAATTCAAGTCGCAGATTAGACGACGATACGTACTACTCTGCTCCTAGACGTACTCA



036
22
AGTATATTAATCCAGTGACCATTAATCCACTCATGCTTAATCCAATAACTGTTAATC





CAGTATCGCTTAATCCACTACAGCTTAATCCAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


26
PL1
SIX2_v7
ggcctaactggccgaattccagatgcacgatgtagctgagcgacagtaaactgtaac



037

ctgatacagcaactgtaacctgataccctaactgtaacctgatacgataactgtaac





ctgatacaaaaactgtaacctgatacggcaactgtaacctgatacggtacctgcgct





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg





gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


27
PL1
SOX11_
ggcctaactggccgaattcgactgcagcagtcattatacgtcgcctaaatcggagaa



038
v2
caaaggatggtgtggagaacaaaggataactgagagaacaaaggaaggatcggagaa





caaaggaactgctggagaacaaaggatatagtggagaacaaaggaggtacctgcgct





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg





gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


28
PL1
TCF7_v2
ggcctaactggccgaattcctgagcgacagtatagtgcacagtgactgcagcagtca



039

ttcctttgatgtacgcaactcctttgatgtctatgcgtcctttgatgttaaggattc





ctttgatgtaggtacatcctttgatgtccgtaaatcctttgatgtggtacctgcgct





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg





gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


29
PL1
TCF7_v3
GAATTCAGGATCGACTAGAAGTCGCAGATTAGACGACGATACGTACTACTCTGCTCC



040

TAGACGTATCCTTTGATGTAAATCCTTTGATGTCAATCCTTTGATGTTAATCCTTTG





ATGTTAGTCCTTTGATGTCTGTCCTTTGATGTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


30
PL1
TFDP1_
ggcctaactggccgaattccaagactgcaagctacgtgtgaccagagccgataactg



041
v6
agggcgggaacgcgcaacggggcgggaacgatgctgtggggggaacgacagctcgg





gcgggaacgctctgctggggggaacggctcctagggcgggaacgggtacctgcgct





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg





gcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


31
PL1
E2F7_v1
GAATTCAGGATCGACTAGAAGTCGCAGATTAGACGACGATACGTACTACTCTGCTCC



042
1
TAGACGTATCCTTTGATGTAAATCCTTTGATGTCAATCCTTTGATGTTAATCCTTTG





ATGTTAGTCCTTTGATGTCTGTCCTTTGATGTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


32
PL1
E2F7_v1
GAATTCAGGTAAGTTTCCCGCCAAAATGTGACCAGAGTTTCCCGCCAAAATGACGAA



043
3
CTCGTTTCCCGCCAAAAATGTAGCTGAGTTTCCCGCCAAAACATAGTTACTGTTTCC





CGCCAAAACCTAAATCGAGTTTCCCGCCAAAAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


33
PL1
FOXA3_
GAATTCTGCTATGCGAGCGTCAGCTCATGCCTATCCGATGTGCCTATGTAAACATAA



044
v2
GAGCCGATGTAAACATATAAGGATATGTAAACATATAGACGAATGTAAACATAGAGG





TACATGTAAACATAACACGACATGTAAACATAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


34
PL1
GLIS3_v
GAATTCTACAGCTCAGCCTACACGACCGTAAAGTGGTGTGCACCATTGACCCCCCAC



045
7
AAAGCAGGACCCCCCACAAAGCGAGACCCCCCACAAAGGACGACCCCCCACAAAGCC





TGACCCCCCACAAAGAGTGACCCCCCACAAAGGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


35
PL1
GLIS3_v
GAATTCAAGGTAGACCCCCCACTAAGCTCAAGTATAGACCCCCCACTAAGATAGTGC



046
9
ACAGACCCCCCACTAAGTATCCGATGTGACCCCCCACTAAGCGCAACGCCTGACCCC





CCACTAAGTCCTAGACGTGACCCCCCACTAAGGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


36
PL1
HOXC9_
GAATTCAACTGAGTATCGCATCGCTCAAGATCAGTGGTCATAAATTAGCAGTCATTG



047
v21
TCATAAATTCCTGATCGGTGTCATAAATTGCCTAAATCGGTCATAAATTCAGCTCAT





GCGTCATAAATTACGCTGCTACGTCATAAATTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


37
PL1
NR2F6_
GAATTCAGTATAGTGCACAGTGACTGCAGCAGTCATTATACGTCGCCGGGGTCAAAG



048
v11
GTCACCAGGGGTCAAAGGTCATCTGGGGTCAAAGGTCATTAGGGGTCAAAGGTCATA





GGGGGTCAAAGGTCACGAGGGGTCAAAGGTCAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


38
PL1
NR2F6_
AATTCACATCGGCTATGCTGCTGCTACAGGTCAAAGGTCATTAGACGCAGGTCAAAG



049
v18
GTCACACAGTGCAGGTCAAAGGTCAAGGTACACAGGTCAAAGGTCACTGACGACAGG





TCAAAGGTCACTCATCTCAGGTCAAAGGTCAGGTACCTGCGCTCCCGACATGCCCCG





CGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCTA





GCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTT





GGTAAAGCCACC


 


39
PL1
E2F3_v1
GAATTCTGCACCATTAGTACCTGATCAGCGATGCTATTTTGGCGCCCAAATCATATT



050
1
TTGGCGCCCAAATGACATTTTGGCGCCCAAATACAATTTTGGCGCCCAAATACGATT





TTGGCGCCCAAATAGCATTTTGGCGCCCAAATGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


40
PL1
E2F4_v2
GAATTCGGTACAACTTCTCACGGAGGCTTTTGGCGCCATTTCGACGATTTTTGGCGC



051

CATTTACTCAAGTTTTGGCGCCATTTTAGTGCATTTTGGCGCCATTTCGCAATCTTT





TGGCGCCATTTGGAGGCTTTTTGGCGCCATTTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


41
PL1
EN2_v6
GAATTCACGATACGTACTACTCTGCTCCTAGACGTACTCAAGTATAAGGTAAGACAT



052

AGTTACCGCAATTATAAGACACGCAATTACTAGAAGCGCAATTAACGTCGCCGCAAT





TAGACTGCACGCAATTAGAATCTCCGCAATTAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


42
PL1
FOXK1_
GAATTCAAGTATAATGTAAACACGGCAGCATCGTCCAATGTAAACACGGCAAGACAT



053
v9
AGTAATGTAAACACGGCTCTCACGGAGAATGTAAACACGGCCTAGCATCGTAATGTA





AACACGGCGATGCTCATCAATGTAAACACGGCGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


43
PL1
GRHL1_
GAATTCAAGTCGCAGATTAGACGAAAAACCGGTTATGACGTACTCAAAAACCGGTTA



054
v5
TGAGATGCTGTAAAACCGGTTATTCCGACGCAAAAAACCGGTTATACGAACTCATAA





AACCGGTTATAGCTCAGCCTAAAACCGGTTATGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


44
PL1
HOXB9_
GAATTCTGACTGCAGCAGTCATTATACGTCGCCTAAATCGAGATGCTGTACGTCGTA



055
v6
AATTCACGACCGTCGTAAATTCGATAACGTCGTAAATTCTAGCATGTCGTAAATTTG





CAGCAGTCGTAAATTAGATTAGGTCGTAAATTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


45
PL1
MNX1_v
GAATTCATTAGACGACGATACGTACTACTCTGCTCCTAGACGTACTCAAGTATAAGG



056
10
TAAGACGCAATTATTGCACAGGCAATTATTCAGCCTGCAATTATCTACAGCGCAATT





ATCTGATCAGCAATTATGATACGTGCAATTATGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


46
PL1
MYC_v2
GAATTCACTCTGCTCCTAGACGTACTCAAGTATAAGGTAGGACACGTGCCCGATGCA



057
2
CGGACACGTGCCCCCGTAAAGGACACGTGCCCTAAATCGGGACACGTGCCCTAGACG





TGGACACGTGCCCGACTAGAGGACACGTGCCCGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


47
PL1
OTX1_v
GAATTCCACAGTGACTGCAGCAGTCATTATACGTCGCCTAAATCGAGATGCTGTACT



058
14
GATCTATTAAGCCGCGTACTCTTAAGCCGGTCATTATTAAGCCGCTATAAGTTAAGC





CGCAACGCCTTAAGCCGACGACCGTTAAGCCGGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


48
PL1
PITX2_v
GAATTCTCGGCTATGCTGCTGCTATGCGAGCGTCAGCTCATGCCTATCCGATGTGCC



059
19
TGACGAACTCATCGACGCTGCTACAGCTAATCCTATGCTAATCCTAACCTAATCCTA





CCCTAATCCTAGCCTAATCCTTGCCTAATCCTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


49
PL1
RUNX1_
GAATTCTGTACTGATCTATAAGGATCGACTAGAAGTCGCAGATTAGTATGTGGTTTA



060
v22
GTACCTGTATGTGGTTTTCGCAATGTATGTGGTTTATGCTGCGTATGTGGTTTAGCA





GTCGTATGTGGTTTGAGCGTCGTATGTGGTTTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


50
PL1
RUNX1_
GAATTCCTGCAGCAGTCATTATACGTCGCCTAAATCGAGATGCTGTACTGATCTATA



061
v23
AGGATCGAGTATGTGGTTTATCGTATGTGGTTTGTAGTATGTGGTTTCTGGTATGTG





GTTTTGTGTATGTGGTTTCCAGTATGTGGTTTGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


51
PL1
SHOX2_
GAATTCCACGATGTAGCTGAGCGACAGTATAGTGCACAGTGACTGCAGCCAATTAAC



062
v5
TGACGAACTCCAATTAAATCAGTGATCCCAATTAATGCAAGCTACCCAATTAATATG





CTGCTGCCAATTAACATCGGCTATCCAATTAAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


52
PL1
SHOX2_
GAATTCTTAGTACCTGATCAGCGATGCTCATCTCGACCTGATCGGTACTCAATTAAT



063
v21
GTACTGATCTCAATTAAGTCGCCTAAATCAATTAACGTACTACTCTCAATTAAGATC





GGTACATCAATTAAAAGTCGCAGATCAATTAAGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


53
PL1
SIX4_v2
GAATTCCTACGTGTGACCAGAGCCGATAACTGAGTATCGCATCGCTCAAGATCAGTG



064
3
ATCACTGCGAAATTTGAGCCCTGAAATTTGAGCCGAGAAATTTGAGCGCTGAAATTT





GAGCCACGAAATTTGAGCTTAGAAATTTGAGCGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


54
PL1
TCF7_v1
GAATTCGACCTGATCGGTACAACTTCTCACGGAGGCTTCTAACTCTCCTTTGATATA



065
0
ACTCGCTCCTTTGATATAGCAGTCTCCTTTGATATCTCATCTTCCTTTGATATCTGT





ACTTCCTTTGATATTGCTATGTCCTTTGATATGGTACCTGCGCTCCCGACATGCCCC





GCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGGCAGAGGTGGGCT





AGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCAATCCGGTACTGT





TGGTAAAGCCACC


 


55
PL1
PL-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



068
3XFOSL
ggtgatcatgctagcctcgaggatatcaagatcggtaccacctcttaacaatacgtt




1-
tcacaaatagttaaaaacatgcatactgaaaagcatacttttgcaatgttattttta




coreAGR
aaaacaaggaactctttaacccagggaagataatcacttggggaaaggaaggttcgt




2_2
ttctgagttagcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctg





gtgcataaatagagactcagctgtgctggcacactcagaagcttggaccgcatccta





gccgccgactcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagc





agctttagaagggtacttgctggagtgaattcgggcctctgattaccggtgctagcc





tcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggt





aaagccacc


 


56
PL1
PL-
ggcctaactggccggtaccgatcttgatatcctcgaggctagcatgatcaccatgag



069
revFOSL
tcacccatgagtcacccatgagtcacccatgagtcacccatgagtcacccatgagtc




1-
acccatgagtcacccatgagtcacccatgagtcaccactagtggtaccacctcttaa




coreAGR
caatacgtttcacaaatagttaaaaacatgcatactgaaaagcatacttttgcaatg




2_2
ttatttttaaaaacaaggaactctttaacccagggaagataatcacttggggaaagg





aaggttcgtttctgagttagcaacaagtaaatgcagcactagtgggtgggattgagg





tgtgccctggtgcataaatagagactcagctgtgctggcacactcagaagcttggac





cgcatcctagccgccgactcacacaaggcaggtgggtgaggaaatccaggtaaggct





cctgacagcagctttagaagggtacttgctggagtgaattcgggcctctgattaccg





gtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggt





actgttggtaaagccacc


 


57
PL1
PL-
ggcctaactggccggtaccgattcttgatatcctcgaggctagcatgatcaccatga



070
revFOSL
gtcacccatgagtcacccatgagtcacccatgagtcacccatgagtcacccatgagt




1-
cacccatgagtcacccatgagtcacccatgagtcaccactagtggtaccgatcttga




coreCST
tatcctcgaggctagcatgatcaccatgagtcacccatgagtcacccatgagtcacc




1
catgagtcacccatgagtcacccatgagtcacccatgagtcacccatgagtcaccca





tgagtcaccactagtggtaccagtggtgggggagtgaaaagagagatggagaaagag





gggatgggcagaaagaggaggaggagtcaggggcagggcatggaggtgggtggggct





gggctgccaaagcaggataaatgcacacctgcctgctggtctgggctccctgcctcg





ggctctcaccctcctctcctgcagctccagctttgtgcttctaccggtgctagcctc





gaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaa





agccacc


 


58
PL1
PL-
ggcctaactggccggtaccactagtgacgtcaccggaagtaagaaccggaagtatcg



071
ETV4-
accggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgg




coreCST
aagtagacgtctacgtaagtggtgggggagtgaaaagagagatggagaaagagggga





tgggcagaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctgggc





tgccaaagcaggataaatgcacacctgcctgctggtctgggctccctgcctcgggct





ctcaccctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgagga





tatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagcca





CC


 


59
PL1
PL-
ggcctaactggccggtaccactagtgacgtcaccggaagtaagaaccggaagtatcg



072
ETV4-
accggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgg




coreKIF
aagtagacgtctacgtaggcccgccccctttccttacgcggattggtagctgcaggc





ttccctatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctgta





acaaagctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagcttcg





gcgactaggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcgggt





gagtgtgcggctgtgctggagcccgggttaccagctctttaccggtgctagcctcga





ggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaag





ccacc


 


60
PL1
PL-
ggcctaactggccggtacactagtgacgtcaccggaagtaagaaccggaagtatcga



073
ETV4-
ccggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgga




coreAGR
agtagacgtctacgtacatactgaaaagcatacttttgcaatgttatttttaaaaac




2
aaggaactctttaacccagggaagataatcacttggggaaaggaaggttcgtttctg





agttagcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgca





taaatagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccgc





cgactcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctt





tagaagggtacttgctggagtgaattcgggcctctgattactagcctcgaggatatc





aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


61
PL1
PL-
ggcctaactggccggtaccactagtgacgtcaccggaagtaagaaccggaagtatcg



074
ETV4-
accggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgg




coreCEA
aagtagacgtctacgtaacccacgtgatgctgagaagtactcctgccctaggaagag




CAM
actcagggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaa





acgttcctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcggc





caagcttggcaatccggtactgttggtaaagccacc


 


62
PL1
PL-
GGCCTAACTGGCCGGTACCACTAGTGACGTCACCGGAAGTAAGAACCGGAAGTATCG



075
ETV4-
ACCGGAAGTAGACACCGGAAGTACTAACCGGAAGTAACTACCGGAAGTATGCACCGG




coreFA
AAGTAGACGTCTACGTACGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTT




M111B
CCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGACA





GACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAG





GGGGATGGCTGAACCGGTGCTAGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCA





AGCTTGGCAATCCGGTACTGTTGGTAAAGCCACC


 


63
PL1
PL-
ggcctaactggccggtaccactagtgacgtcaccggaagtaagaaccggaagtatcg



076
ETV4-
accggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgg




Twist_v1
aagtagacgtctacgtactgagcgacagtatagtgcacagtgacattacagatgttt




8-
acgacgaattacagatgtttctcatcgattacagatgtttcagctcaattacagatg




coreCST
tttgctgctgattacagatgtttaccagagattacagatgttttacgtaagtggtgg





gggagtgaaaagagagatggagaaagaggggatgggcagaaagaggaggaggagtca





ggggcagggcatggaggtgggtggggctgggctgccaaagcaggataaatgcacacc





tgcctgctggtctgggctccctgcctcgggctctcaccctcctctcctgcagctcca





gctttgtgctctaccggtgctagcctcgaggatatcaagatctggcctcggcggcca





agcttggcaatccggtactgttggtaaagccacc


 


64
PL1
PL-
ACTAGTGACGTCACCGGAAGTAAGAACCGGAAGTATCGACCGGAAGTAGACACCGGA



077
ETV4-
AGTACTAACCGGAAGTAACTACCGGAAGTATGCACCGGAAGTAGACGTCTACGTACT




Twist_v1
GAGCGACAGTATAGTGCACAGTGACATTACAGATGTTTACGACGAATTACAGATGTT




8-
TCTCATCGATTACAGATGTTTCAGCTCAATTACAGATGTTTGCTGCTGATTACAGAT




coreKIF
GTTTACCAGAGATTACAGATGTTTTACGTAGGCCCGCCCCCTTTCCTTACGCGGATT





GGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAA





TATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGA





AAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGG





CACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTTtaccg





gtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggt





actgttggtaaagccacc


 


65
PL1
PL-
ggcctaactggccggtacactagtgacgtcaccggaagtaagaaccggaagtatcga



078
ETV4-
ccggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgga




Twist_v1
agtagacgtctacgtactgagcgacagtatagtgcacagtgacattacagatgttta




8-
cgacgaattacagatgtttctcatcgattacagatgtttcagctcaattacagatgt




coreAGR
ttgctgctgattacagatgtttaccagagattacagatgttttacgtacatactgaa




2
aagcatacttttgcaatgttatttttaaaaacaaggaactctttaacccagggaaga





taatcacttggggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagcac





tagtgggtgggattgaggtgtgccctggtgcataaatagagactcagctgtgctggc





acactcagaagcttggaccgcatcctagccgccgactcacacaaggcaggtgggtga





ggaaatccaggtaaggctcctgacagcagctttagaagggtacttgctggagtgaat





tcgggcctctgattactagcctcgaggatatcaagatctggcctcggcggccaagct





tggcaatccggtactgttggtaaagccacc


 


66
PL1
PL-
ggcctaactggccggtaccactagtgacgtcaccggaagtaagaaccggaagtatcg



079
ETV4-
accggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgg




Twist_v1
aagtagacgtctacgtactgagcgacagtatagtgcacagtgacattacagatgttt




8-
acgacgaattacagatgtttctcatcgattacagatgtttcagctcaattacagatg




coreFA
tttgctgctgattacagatgtttaccagagattacagatgttttacgtacgggaaaa




M111B
gttcagctgagagatataaaagagcagtctttccagcacctgcaaatccagagcggc





gggcactgacgggcacttgcaccgtgtggacagactctccggttctgtgagtggttt





ttcttttcccgggtcggacctggagttcttagggggatggctgaaccggtgctagcc





tcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggt





aaagccacc


 


67
PL1
PL-
ggcctaactggccggtaccactagtgacgtcaccggaagtaagaaccggaagtatcg



080
ETV4-
accggaagtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccgg




Twist_v1
aagtagacgtctacgtactgagcgacagtatagtgcacagtgacattacagatgttt




8-
acgacgaattacagatgtttctcatcgattacagatgtttcagctcaattacagatg




coreCEA
tttgctgctgattacagatgtttaccagagattacagatgttttacgtaacccacgt




CAM
gatgctgagaagtactcctgccctaggaagagactcagggcagagggaggaaggaca





gcagaccagacagtcacagcagccttgacaaaacgttcctggaactaccggtgctag





cctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttg





gtaaagccacc


 


68
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgagcgacagtatagtgca



081
Twist_v1
cagtgacattacagatgtttacgacgaattacagatgtttctcatcgattacagatg




8-
tttcagctcaattacagatgtttgctgctgattacagatgtttaccagagattacag




coreCST
atgttttacgtaagtggtgggggagtgaaaagagagatggagaaagaggggatgggc





agaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctgggctgcca





aagcaggataaatgcacacctgcctgctggtctgggctccctgcctcgggctctcac





cctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgaggatatca





agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


69
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgagcgacagtatagtgca



082
Twist_v1
cagtgacattacagatgtttacgacgaattacagatgtttctcatcgattacagatg




8-
tttcagctcaattacagatgtttgctgctgattacagatgtttaccagagattacag




coreKIF
atgttttacgtaggcccgccccctttccttacgcggattggtagctgcaggcttccc





tatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctgtaacaaa





gctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagcttcggcgac





taggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcgggtgagtg





tgcggctgtgctggagcccgggttaccagctctttaccggtgctagcctcgaggata





tcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


70
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgagcgacagtatagtgca



083
Twist_v1
cagtgacattacagatgtttacgacgaattacagatgtttctcatcgattacagatg




8-
tttcagctcaattacagatgtttgctgctgattacagatgtttaccagagattacag




coreAGR
atgttttacgtacatactgaaaagcatacttttgcaatgttatttttaaaaacaagg




2
aactctttaacccagggaagataatcacttggggaaaggaaggttcgtttctgagtt





agcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgcataaa





tagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccgccgac





tcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctttaga





agggtacttgctggagtgaattcgggcctctgattagctagcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


71
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



084
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8.2-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




coreKIF
gacgtctacgtaggcccgccccctttccttacgcggattggtagctgcaggcttccc





tatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctgtaacaaa





gctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagcttcggcgac





taggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcgggtgagtg





tgcggctgtgctggagcccgggttaccagctctttaccggtgctagcctcgaggata





tcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


72
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



085
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8.2-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




coreCST
gacgtctacgtactgatcagcgatgctcatctcgacctgatcggtacaacttctcac





ggaggcttctaagtcattacatacgtagtcattactatacgtgtcattacagatgct





gtcattacacgaactgtcattacgtactcagtcattactacgtaagtggtgggggag





tgaaaagagagatggagaaagaggggatgggcagaaagaggaggaggagtcaggggc





agggcatggaggtgggtggggctgggctgccaaagcaggataaatgcacacctgcct





gctggtctgggctccctgcctcgggctctcaccctcctctcctgcagctccagcttt





gtgctctaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagctt





ggcaatccggtactgttggtaaagccacc


 


73
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgagcgacagtatagtgca



086
Twist_v1
cagtgacattacagatgtttacgacgaattacagatgtttctcatcgattacagatg




8-
tttcagctcaattacagatgtttgctgctgattacagatgtttaccagagattacag




coreFA
atgttttacgtacgggaaaagttcagctgagagatataaaagagcagtctttccagc




M111B
acctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggacagactc





tccggttctgtgagtggtttttcttttcccgggtcggacctggagttcttaggggga





tggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagctt





ggcaatccggtactgttggtaaagccacc


 


74
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgagcgacagtatagtgca



087
Twist_v1
cagtgacattacagatgtttacgacgaattacagatgtttctcatcgattacagatg




8-
tttcagctcaattacagatgtttgctgctgattacagatgtttaccagagattacag




coreCEA
atgttttacgtaacccacgtgatgctgagaagtactcctgccctaggaagagactca




CAM
gggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaaacgtt





cctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


75
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



088
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8.2-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




coreAGR
gacgtctacgtacatactgaaaagcatacttttgcaatgttatttttaaaaacaagg




2
aactctttaacccagggaagataatcacttggggaaaggaaggttcgtttctgagtt





agcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgcataaa





tagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccgccgac





tcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctttaga





agggtacttgctggagtgaattcgggcctctgattagctagcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


76
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



089
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8.2-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




coreCEA
gacgtctacgtaacccacgtgatgctgagaagtactcctgccctaggaagagactca




CAM
gggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaaacgtt





cctggaactaccggtgctagcctcgaggatatcaagatctggcctcggggccaagc





ttggcaatccggtactgttggtaaagccacc


 


77
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



090
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8.2-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




coreFA
gacgtctacgtacgggaaaagttcagctgagagatataaaagagcagtctttccagc




M111B
acctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggacagactc





tccggttctgtgagtggtttttcttttcccgggtcggacctggagttcttaggggga





tggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagctt





ggcaatccggtactgttggtaaagccacc


 


78
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



091
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




HOXA1_
gacgtctacgtactgatcagcgatgctcatctcgacctgatcggtacaacttctcac




v10-
ggaggcttctaagtcattacatacgtagtcattactatacgtgtcattacagatgct




coreKIF
gtcattacacgaactgtcattacgtactcagtcattactacgtaggcccgccccctt





tccttacgcggattggtagctgcaggcttccctatctgattggccgaacgaacgcag





cgcgtaatttaaaatattgtatctgtaacaaagctgcacctcgtgggcggagttgtg





ctctgcggctgcgaaagtccagcttcggcgactaggtgtgagtaagccagtatccca





ggaggagcaagtggcacgtcttcgggtgagtgtgcggctgtgctggagcccgggtta





ccagctctttaccggtgctagcctcgaggatatcaagatctggcctcggcggccaag





cttggcaatccggtactgttggtaaagccacc


 


79
PL1
PL-
ggcctaactggccggtaccacactagtgacgtcctgagcgacagtatagtgcacagt



092
Twist_v1
gacattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttc




8-
agctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgt




HOXA1_
ttgacgtctacgtactgatcagcgatgctcatctcgacctgatcggtacaacttctc




v10-
acggaggcttctaagtcattacatacgtagtcattactatacgtgtcattacagatg




coreCST
ctgtcattacacgaactgtcattacgtactcagtcattactacgtacatactgaaaa





gcatacttttgcaatgttatttttaaaaacaaggaactctttaacccagggaagata





atcacttggggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagcacta





gtgggtgggattgaggtgtgccctggttaagtggtgggggagtgaaaagagagatgg





agaaagaggggatgggcagaaagaggaggaggagtcaggggcagggcatggaggtgg





gtggggctgggctgccaaagcaggataaatgcacacctgcctgctggtctgggctcc





ctgcctcgggctctcaccctcctctcctgcagctccagctttgtgctctaccggtgc





tagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactg





ttggtaaagccacc


 


80
PL1
PL-
ggcctaactggccggtacaactagtgactcctttgatgtacgcaactcctttgatgt



093
Twist_v1
ctatgcgtcctttgatgttaaggattcctttgatgtaggtacatcctttgatgtccg




8-
taaatcctttgatgtggtaccgtctactacctgatcaaacatgcccggacatgtcgt




HOXA1_
aagacataaacatgcccggacatgtcctcgcaatctaacatgcccggacatgtcctc




v10-
gcaatctaacatgcccggacatgtctgcaagctacaacatgcccggacatgtcgtac




coreAGR
tcagtcattactacgtacatactgaaaagcatacttttgcaatgttatttttaaaaa




2
caaggaactctttaacccagggaagataatcacttggggaaaggaaggttcgtttct





gagttagcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgc





ataaatagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccg





ccgactcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagct





ttagaagggtacttgctggagtgaattcgggcctctgattactagcctcgaggatat





caagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


81
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



094
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




HOXA1_
gacgtctacgtactgatcagcgatgctcatctcgacctgatcggtacaacttctcac




v10-
ggaggcttctaagtcattacatacgtagtcattactatacgtgtcattacagatgct




coreCEA
gtcattacacgaactgtcattacgtactcagtcattactacgtaacccacgtgatgc




CAM
tgagaagtactcctgccctaggaagagactcagggcagagggaggaaggacagcaga





ccagacagtcacagcagccttgacaaaacgttcctggaactaccggtgctagcctcg





aggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaa





gccacc


 


82
PL1
PL-
ggcctaactggccggtaccactagtgacgtcctgagcgacagtatagtgcacagtga



095
Twist_v1
cattacagatgtttacgacgaattacagatgtttctcatcgattacagatgtttcag




8-
ctcaattacagatgtttgctgctgattacagatgtttaccagagattacagatgttt




HOXA1_
gacgtctacgtactgatcagcgatgctcatctcgacctgatcggtacaacttctcac




v10-
ggaggcttctaagtcattacatacgtagtcattactatacgtgtcattacagatgct




coreFA
gtcattacacgaactgtcattacgtactcagtcattactacgtacgggaaaagttca




M111B
gctgagagatataaaagagcagtctttccagcacctgcaaatccagagcggcgggca





ctgacgggcacttgcaccgtgtggacagactctccggttctgtgagtggtttttctt





ttcccgggtcggacctggagttcttagggggatggctgaaccggtgctagcctcgag





gatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagc





cacc


 


83
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



096
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




coreKIF
gacgtctacgtaggcccgccccctttccttacgcggattggtagctgcaggcttccc





tatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctgtaacaaa





gctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagcttcggcgac





taggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcgggtgagtg





tgcggctgtgctggagcccgggttaccagctctttaccggtctagcctcgaggatat





caagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


84
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgatcagcgatgctcatct



097
HOXA1_
cgacctgatcggtacaacttctcacggaggcttctaagtcattacatacgtagtcat




v10-
tactatacgtgtcattacagatgctgtcattacacgaactgtcattacgtactcagt




coreCST
cattactacgtaagtggtgggggagtgaaaagagagatggagaaagaggggatgggc





agaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctgggctgcca





aagcaggataaatgcacacctgcctgctggtctgggctccctgcctcgggctctcac





cctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgaggatatca





agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


85
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgatcagcgatgctcatct



098
HOXA1_
cgacctgatcggtacaacttctcacggaggcttctaagtcattacatacgtagtcat




v10-
tactatacgtgtcattacagatgctgtcattacacgaactgtcattacgtactcagt




coreKIF
cattactacgtaggcccgccccctttccttacgcggattggtagctgcaggcttccc





tatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctgtaacaaa





gctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagcttcggcgac





taggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcgggtgagtg





tgcggctgtgctggagcccgggttaccagctctttaccggtgctagcctcgaggata





tcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


86
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgatcagcgatgctcatct



099
HOXA1_
cgacctgatcggtacaacttctcacggaggcttctaagtcattacatacgtagtcat




v10-
tactatacgtgtcattacagatgctgtcattacacgaactgtcattacgtactcagt




coreCEA
cattactacgtaacccacgtgatgctgagaagtactcctgccctaggaagagactca




CAM
gggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaaacgtt





cctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


87
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgatcagcgatgctcatct



100
HOXA1_
cgacctgatcggtacaacttctcacggaggcttctaagtcattacatacgtagtcat




v10-
tactatacgtgtcattacagatgctgtcattacacgaactgtcattacgtactcagt




coreAGR
cattactacgtacatactgaaaagcatacttttgcaatgttatttttaaaaacaagg




2
aactctttaacccagggaagataatcacttggggaaaggaaggttcgtttctgagtt





agcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgcataaa





tagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccgccgac





tcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctttaga





agggtacttgctggagtgaattcgggcctctgattagctagcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


88
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



101
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




coreCST
gacgtctacgtaagtggtgggggagtgaaaagagagatggagaaagaggggatgggc





agaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctgggctgcca





aagcaggataaatgcacacctgcctgctggtctgggctccctgcctcgggctctcac





cctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgaggatatca





agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


89
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



102
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




coreFA
gacgtctacgtacgggaaaagttcagctgagagatataaaagagcagtctttccagc




M111B
acctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggacagactc





tccggttctgtgagtggtttttcttttcccgggtcggacctggagttcttaggggga





tggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagctt





ggcaatccggtactgttggtaaagccacc


 


90
PL1
PL-
ggcctaactggccggtacaactagtgacgtctgtagctgagcgacagtatagtgcac



103
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




coreAGR
gacgtctacgtacatactgaaaagcatacttttgcaatgttatttttaaaaacaagg




2
aactctttaacccagggaagataatcacttggggaaaggaaggttcgtttctgagtt





agcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgcataaa





tagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccgccgac





tcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctttaga





agggtacttgctggagtgaattcgggcctctgattactagcctcgaggatatcaaga





tctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


91
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



104
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




coreCEA
gacgtctacgtaacccacgtgatgctgagaagtactcctgccctaggaagagactca




CAM
gggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaaacgtt





cctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


92
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtactgatcagcgatgctcatct



105
HOXA1_
cgacctgatcggtacaacttctcacggaggcttctaagtcattacatacgtagtcat




v10-
tactatacgtgtcattacagatgctgtcattacacgaactgtcattacgtactcagt




coreFA
cattactacgtacgggaaaagttcagctgagagatataaaagagcagtctttccagc




M111B
acctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggacagactc





tccggttctgtgagtggtttttcttttcccgggtcggacctggagttcttaggggga





tggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagctt





ggcaatccggtactgttggtaaagccacc


 


93
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



106
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




CREB V
gacgtctacgtaacatcggctatgctgctgctaatgccacgtcaccacatcgacatg




6-
ccacgtcaccatcatgccatgccacgtcaccactgcaagatgccacgtcaccacagt




coreCST
ataatgccacgtcaccaagttactatgccacgtcaccaggtacctacgtaagtggtg





ggggagtgaaaagagagatggagaaagaggggatgggcagaaagaggaggaggagtc





aggggcagggcatggaggtgggtggggctgggctgccaaagcaggataaatgcacac





ctgcctgctggtctgggctccctgcctcgggctctcaccctcctctcctgcagctcc





agctttgtgctctaccggtgctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


94
PL1
PL-
ggcctaactggccggtacactagtgacgtctgtagctgagcgacagtatagtgcaca



107
HOXC10_
gtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcgt




v14-
aaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaattg




CREB_v
acgtctacgtaacatcggctatgctgctgctaatgccacgtcaccacatcgacatgc




6-
cacgtcaccatcatgccatgccacgtcaccactgcaagatgccacgtcaccacagta




coreKIF
taatgccacgtcaccaagttactatgccacgtcaccaggtacctacgtaggcccgcc





ccctttccttacgcggattggtagctgcaggcttccctatctgattggccgaacgaa





cgcagcgcgtaatttaaaatattgtatctgtaacaaagctgcacctcgtgggcggag





ttgtgctctgcggctgcgaaagtccagcttcggcgactaggtgtgagtaagccagta





tcccaggaggagcaagtggcacgtcttcgggtgagtgtgcggctgtgctggagcccg





ggttaccagctctttaccggtctagcctcgaggatatcaagatctggcctcggcggc





caagcttggcaatccggtactgttggtaaagccacc


 


95
PL1
PL-
ggcctaactggccggtacaactagtgacgtctgtagctgagcgacagtatagtgcac



108
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




CREB_
gacgtctacgtaacatcggctatgctgctgctaatgccacgtcaccacatcgacatg




6-
ccacgtcaccatcatgccatgccacgtcaccactgcaagatgccacgtcaccacagt




coreAGR
ataatgccacgtcaccaagttactatgccacgtcaccaggtacctacgtacatactg




2
aaaagcatacttttgcaatgttatttttaaaaacaaggaactctttaacccagggaa





gataatcacttggggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagc





actagtggggggattgaggtgtgccctggtgcataaatagagactcagctgtgctg





gcacactcagaagcttggaccgcatcctagccgccgactcacacaaggcaggtgggt





gaggaaatccaggtaaggctcctgacagcagctttagaagggtacttgctggagtga





attcgggcctctgattactagcctcgaggatatcaagatctggcctcggcggccaag





cttggcaatccggtactgttggtaaagccacc


 


96
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



109
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




CREB_v
gacgtctacgtaacatcggctatgctgctgctaatgccacgtcaccacatcgacatg




6-
ccacgtcaccatcatgccatgccacgtcaccactgcaagatgccacgtcaccacagt




coreCEA
ataatgccacgtcaccaagttactatgccacgtcaccaggtacctacgtaacccacg




CAM
tgatgctgagaagtactcctgccctaggaagagactcagggcagagggaggaaggac





agcagaccagacagtcacagcagccttgacaaaacgttcctggaactaccggtgcta





gcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgtt





ggtaaagccacc


 


97
PL1
PL-
ggcctaactggccggtaccactagtgacgtctgtagctgagcgacagtatagtgcac



110
HOXC10_
agtgactgcagcagtcattgtcgtaaattgagtatcgtcgtaaattgacgaacgtcg




v14-
taaattagcgacagtcgtaaattagtacctgtcgtaaattactctgcgtcgtaaatt




CREB_v
gacgtctacgtaacatcggctatgctgctgctaatgccacgtcaccacatcgacatg




6-
ccacgtcaccatcatgccatgccacgtcaccactgcaagatgccacgtcaccacagt




coreFA
ataatgccacgtcaccaagttactatgccacgtcaccaggtacctacgtacgggaaa




M111B
agttcagctgagagatataaaagagcagtctttccagcacctgcaaatccagagcgg





cgggcactgacgggcacttgcaccgtgtggacagactctccggttctgtgagtggtt





tttcttttcccgggtcggacctggagttcttagggggatggctgaaccggtgctagc





ctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttgg





taaagccacc


 


98
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtaacatcggctatgctgctgct



111
CREB_v
aatgccacgtcaccacatcgacatgccacgtcaccatcatgccatgccacgtcacca




6-
ctgcaagatgccacgtcaccacagtataatgccacgtcaccaagttactatgccacg




coreCST
tcaccaggtacctacgtaagtggtgggggagtgaaaagagagatggagaaagagggg





atgggcagaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctggg





ctgccaaagcaggataaatgcacacctgcctgctggtctgggctccctgcctcgggc





tctcaccctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgagg





atatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagcc





acc


 


99
PL1
PL-
ggcctaactggccggtacaactagtgacgtctacgtaacatcggctatgctgctgct



112
CREB_v
aatgccacgtcaccacatcgacatgccacgtcaccatcatgccatgccacgtcacca




6-
ctgcaagatgccacgtcaccacagtataatgccacgtcaccaagttactatgccacg




coreAGR
tcaccaggtacctacgtacatactgaaaagcatacttttgcaatgttatttttaaaa




2
acaaggaactctttaacccagggaagataatcacttggggaaaggaaggttcgtttc





tgagttagcaacaagtaaatgcagcactagtggggggattgaggtgtgccctggtg





cataaatagagactcagctgtgctggcacactcagaagcttggaccgcatcctagcc





gccgactcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagc





tttagaagggtacttgctggagtgaattcgggcctctgattactagcctcgaggata





tcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


100
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtaacatcggctatgctgctgct



113
CREB_v
aatgccacgtcaccacatcgacatgccacgtcaccatcatgccatgccacgtcacca




6-
ctgcaagatgccacgtcaccacagtataatgccacgtcaccaagttactatgccacg




coreKIF
tcaccaggtacctacgtaggcccgccccctttccttacgcggattggtagctgcagg





cttccctatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctgt





aacaaagctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagcttc





ggcgactaggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcggg





tgagtgtgcggctgtgctggagcccgggttaccagctctttaccggtctagcctcga





ggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaag





ccacc


 


101
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtaacatcggctatgctgctgct



114
CREB_v
aatgccacgtcaccacatcgacatgccacgtcaccatcatgccatgccacgtcacca




6-
ctgcaagatgccacgtcaccacagtataatgccacgtcaccaagttactatgccacg




coreCEA
tcaccaggtacctacgtaacccacgtgatgctgagaagtactcctgccctaggaaga




CAM
gactcagggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaa





aacgttcctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcgg





ccaagcttggcaatccggtactgttggtaaagccacc


 


102
PL1
PL-
ggcctaactggccggtaccactagtgacgtctacgtaacatcggctatgctgctgct



115
CREB_v
aatgccacgtcaccacatcgacatgccacgtcaccatcatgccatgccacgtcacca




6-
ctgcaagatgccacgtcaccacagtataatgccacgtcaccaagttactatgccacg




coreFA
tcaccaggtacctacgtacgggaaaagttcagctgagagatataaaagagcagtctt




M111B
tccagcacctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggac





agactctccggttctgtgagtggtttttcttttcccgggtcggacctggagttctta





gggggatggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


103
PL1
HES6_v
GAATTCaagaCtgcaagCGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTA



144
11-
TACGTCGCCTAAATCGAGATGCTGTAGGCACGTGTATCTGGCACGTGTACTCGGCAC




coreBIR
GTGTACTAGGCACGTGTAAGAGGCACGTGTACGCGGCACGTGTAGGTACCTGCGCTC




C5
CCGACATGCCCCGCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGG





CAGAGGTGGGCTAGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCA





ATCCGGTACTGTTGGTAAAGCCACCATGGAAG


 


104
PL1
HES6_v
GAATTCaagaCtgcaagCGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTA



145
11-
TACGTCGCCTAAATCGAGATGCTGTAGGCACGTGTATCTGGCACGTGTACTCGGCAC




TATA-
GTGTACTAGGCACGTGTAAGAGGCACGTGTACGCGGCACGTGTAGGTACCTATAAAA




TSS
GGCCAGCAGCAGCCTGACCACATCTCATCCGCTAGCCTCGAGGATATCAAGATCTGG





CCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACC


 


105
PL1
NPAS2_
GAATTCaagaCtgcaagCCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCAT



146
v11-
TATACGTCGCCTAAATCGAGATGCTGGACACGTGTCCGAGACACGTGTCTGTGACAC




coreBIR
GTGTCCGGGACACGTGTCGCAGACACGTGTCGTGGACACGTGTCGGTACCTGCGCTC




C5
CCGACATGCCCCGCGGCGCGCCATTAACCGCCAGATTTGAGTCGCGGGACCCGTTGG





CAGAGGTGGGCTAGCCTCGAGGATATCAAGATCTGGCCTCGGCGGCCAAGCTTGGCA





ATCCGGTACTGTTGGTAAAGCCACC


 


106
PL1
NPAS2_
GAATTCaagaCtgcaagCCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCAT



147
v11-
TATACGTCGCCTAAATCGAGATGCTGGACACGTGTCCGAGACACGTGTCTGTGACAC




TATA-
GTGTCCGGGACACGTGTCGCAGACACGTGTCGTGGACACGTGTCGGTACCTATAAAA




TSS
GGCCAGCAGCAGCCTGACCACATCTCATCCGCTAGCCTCGAGGATATCAAGATCTGG





CCTCGGCGGCCAAGCTTGGCAATCCGGTACTGTTGGTAAAGCCACC


 


107
PL1
pGL4.10-
ggcctaactggccggtaccactagtatcgatccttcatagggcagggaggggtgggc



15
FAM83
acttgggtgtgaccaaggagaggaggcgcgcctggtcaacagctctccctggcccgt




A-43
gtccagctccctcctcacacagagaggggggcgcatctcagggatggcatctttccc





ccccacagggaaattcttatctttgaaacagcatgggaatcgaggcacccaggaggg





gagcagaggcaggcaggcctccttcaggcccatcctccagctgggctggtggtgcca





gggaggctccctgcttggtaacaaaggcctgagggagagttgcgaaacccagcagga





aagccggctcaccttcgcctccccctgcggctgggaggagaggaaatatcccatggc





tgactgtgccaaggaggtgtctgagccagccctcccggcccgagggcagggcaggtg





gccctgagagataagccaatcccgcagctgcagatgaggagttctgagaagcattgc





tcaggacagcggtaaatcacttcttggaggtgccctgcacgccggtcctgggagcag





gcggcctcccgggggtgcgggagccccactcctccgtggtgtgttccatttgcttcc





cacatctggaggagctgacgtgccagcctcccccagcaccacccagggacgggaggc





aaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaat





ccggtactgttggtaaagccacc


 


108
PL1
PL-
ggcctaactggccggtaccgacgtctacctgatcaaacatgcccggacatgtcgtaa



156
TP53_v5-
gacataaacatgcccggacatgtcctcgcaatctaacatgcccggacatgtcctcgc




TATA-
aatctaacatgcccggacatgtctgcaagctacaacatgcccggacatgtctacgta




TSS
gctagctataaaaggccagcagcagcctgaccacatctcatcctcctcgaggatatc




FLUC
aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


109
PL1
PL-
ggcctaactggccggtaccgacgtccctgatcggtacaacttctcacaacatgcctg



157
TP53_v2
ggcatgtcgctatgcaacatgcctgggcatgtcagatgcaaacatgcctgggcatgt




2-TATA-
cctgctataacatgcctgggcatgtcctgctataacatgcctgggcatgtctacgta




TSS
gctagctataaaaggccagcagcagcctgaccacatctcatcctcctcgaggatatc




FLUC
aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


110
PL1
PL-TP53
ggcctaactggccggtaccgacgtctcgggcaagcgctcccgacatgcccgggcaag



158
SURV_v
cgctcccgacatgcccgggcaagcgctcccgacatgcccgggcaagcgctcccgaca




3-TATA-
tgcccgggcaagcgctcccgacatgcccgggcaagcgctcccgacatgccctacgta




TSS
gctagctataaaaggccagcagcagcctgaccacatctcatcctcctcgaggatatc




FLUC
aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


111
PL1
PL-
ggcctaactggccggtaccttttgataaaaatcattaggtacggccgcggtgccagg



159
TCF7_v2-
gcgtgcccttgggctccccgggcgcgaaactagtgacgtcctgagcgacagtatagt




FOS-
gcacagtgactgcagcagtcattcctttgatgtacgcaactcctttgatgtctatgc




coreBIR
gtcctttgatgttaaggattcctttgatgtaggtacatcctttgatgtccgtaaatc




C5
ctttgatgtgacgtctacgtaggtgactcatgggtgactcatgtacgtaacgcgtcc





cgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggc





agaggtgggaattcaccggtgctagcctcgaggatatcaagatctggcctcggcggc





caagcttggcaatccggtactgttggtaaagccacc


 


112
PL1
PL-FOS-
ggcctaactggccggtaccttttgataaaaatcattaggtacggccgcggtgccagg



160
TCF_v2-
gcgtgcccttgggctccccgggcgcgaaactagtgacgtcggtgactcatgggtgac




coreBIR
tcatgacgtctacgtactgagcgacagtatagtgcacagtgactgcagcagtcattc




C5
ctttgatgtacgcaactcctttgatgtctatgcgtcctttgatgttaaggattcctt





tgatgtaggtacatcctttgatgtccgtaaatcctttgatgttacgtaacgcgtccc





gacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca





gaggtgggaattcaccggtgctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


113
PL1
PL-
ggcctaactggccggtaccaactagtgacgtcctgagcgacagtatagtgcacagtg



161
TCF7_v2-
actgcagcagtcattcctttgatgtacgcaactcctttgatgtctatgcgtcctttg




FOS-
atgttaaggattcctttgatgtaggtacatcctttgatgtccgtaaatcctttgatg




coreAGR
tgacgtctacgtaggtgactcatgggtgactcatgtacgtacatactgaaaagcata




2
cttttgcaatgttatttttaaaaacaaggaactctttaacccagggaagataatcac





ttggggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagcactagtggg





tgggattgaggtgtgccctggtgcataaatagagactcagctgtgctggcacactca





gaagcttggaccgcatcctagccgccgactcacacaaggcaggtgggtgaggaaatc





caggtaaggctcctgacagcagctttagaagggtacttgctggagtgaattcgggcc





tctgattagctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaa





tccggtactgttggtaaagccacc


 


114
PL1
PL-FOS-
ggcctaactggccggtaccaactagtgacgtcggtgactcatgggtgactcatggac



162
TCF7_v2-
gtctacgtactgagcgacagtatagtgcacagtgactgcagcagtcattcctttgat




coreAGR
gtacgcaactcctttgatgtctatgcgtcctttgatgttaaggattcctttgatgta




2
ggtacatcctttgatgtccgtaaatcctttgatgttacgtacatactgaaaagcata





cttttgcaatgttatttttaaaaacaaggaactctttaacccagggaagataatcac





ttggggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagcactagtggg





tgggattgaggtgtgccctggtgcataaatagagactcagctgtgctggcacactca





gaagcttggaccgcatcctagccgccgactcacacaaggcaggtgggtgaggaaatc





caggtaaggctcctgacagcagctttagaagggtacttgctggagtgaattcgggcc





tctgattagctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaa





tccggtactgttggtaaagccacc


 


115
PL1
PL-
ggcctaactggccggtaccaactagtgacgtcctgagcgacagtatagtgcacagtg



163
TCF7_v2
actgcagcagtcattcctttgatgtacgcaactcctttgatgtctatgcgtcctttg




coreAGR
atgttaaggattcctttgatgtaggtacatcctttgatgtccgtaaatcctttgatg




2
tgacgtctacgtacatactgaaaagcatacttttgcaatgttatttttaaaaacaag





gaactctttaacccagggaagataatcacttggggaaaggaaggttcgtttctgagt





tagcaacaagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgcataa





atagagactcagctgtgctggcacactcagaagcttggaccgcatcctagccgccga





ctcacacaaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctttag





aagggtacttgctggagtgaattcgggcctctgattagctagcctcgaggatatcaa





gatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


116
PL1
PL-
CAACTAGTGACGTCCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCT



164
TCF7_v2-
TTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




FOS-
ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACGTCTACGTAGGTGA




coreCEA
CTCATGGGTGACTCATGTACGTAACCCACGTGATGCTGAGAAGTACTCCTGCCCTAG




CAM5
GAAGAGACTCAGGGCAGAGGGAGGAAGGACAGCAGACCAGACAGTCACAGCAGCCTT





GACAAAACGTTCCTGGAACTACCGGT


 


117
PL1
PL-
ggcctaactggccggtaccaactagtgacgtcctgagcgacagtatagtgcacagtg



165
TCF7_v2
actgcagcagtcattcctttgatgtacgcaactcctttgatgtctatgcgtcctttg




coreCEA
atgttaaggattcctttgatgtaggtacatcctttgatgtccgtaaatcctttgatg




CAM5
tgacgtctacgtaacccacgtgatgctgagaagtactcctgccctaggaagagactc





agggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaaacgt





tcctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcggccaag





cttggcaatccggtactgttggtaaagccacc


 


118
PL1
PL-
AACTAGTGACGTCCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTT



166
TCF7_v2-
TGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGA




coreFA
TGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACGTCTACGTATACGTA




M111B
CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCC





AGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTG





AGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTGaaccgg





t


 


119
PL1
PL-
CTAGTGACGTCCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTTTG



167
TCF7_v2
ATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATG




coreCST
TAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACGTCTACGTATACGTAAG





TGGTGGGGGAGTGAAAAGAGAGATGGAGAAAGAGGGGATGGGCAGAAAGAGGAGGAG





GAGTCAGGGGCAGGGCATGGAGGTGGGTGGGGCTGGGCTGCCAAAGCAGGATAAATG





CACACCTGCCTGCTGGTCTGGGCTCCCTGCCTCGGGCTCTCACCCTCCTCTCCTGCA





GCTCCAGCTTTGTGCTCTa


 


120
PL1
PL-
CTAGTGACGTCCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTTTG



168
TCF7_v2
ATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATG




coreKIF2
TAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACGTCTACGTATACGTAGG




0A
CCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCG





AACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGG





GCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAG





CCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGG





AGCCCGGGTTACCAGCTCTTTA


 


121
PL1
pGL4.10-
ggcctaactggccggtaccaccatggggaaggtggggtgatcacaggacagtcagcc



17
CEACA
tcgcagaggacagagaccacccaggactgtcagggagaacatggacaggccctgagc




M5
cgcagctcagccaacagacacggagagggagggtccccctggagccttccccaagga





cagcagagcccagagtcacccacctccctccaccacagtcctctctttccaggacac





acaagacacctccccctccacatgcaggatctggggactcctgagacctctgggcct





gggtctccatccctgggtcagtggggggttggtggtactggagacagagggctggt





ccctccccagccaccacccagtgagcctttttctagcccccagagccacctctgtca





ccttcctgttgggcatcatcccaccttcccagagccctggagagcatggggagaccc





gggaccctgctgggtttctctgtcacaaaggaaaataatccccctggtgtgacagac





ccaaggacagaacacagcagaggtcagcactggggaagacaggttgtcctcccaggg





gatgggggtccatccaccttgccgaaaagatttgtctgaggaactgaaaatagaagg





gaaaaaagaggagggacaaaagaggcagaaatgagaggggaggggacagaggacacc





tgaataaagaccacacccatgacccacgtgatgctgagaagtactcctgccctagga





agagactcagggcagagggaggaaggacagcagaccagacagtcacagcagccttga





caaaacgttcctggaactaccggtgctagcctcgaggatatcaagatctggcctcgg





cggccaagcttggcaatccggtactgttggtaaagccacc


 


122
PL1
PL-
ggcctaactggccggtaccttttgataaaaatcattaggtacggccgcggtgccagg



183
TP53_v5-
gcgtgcccttgggctccccgggcgcgaaactagtgacgtctacctgatcaaacatgc




coreBIR
ccggacatgtcgtaagacataaacatgcccggacatgtcctcgcaatctaacatgcc




C5
cggacatgtcctcgcaatctaacatgcccggacatgtctgcaagctacaacatgccc





ggacatgtctacgtaacgcgtcccgacatgccccgcggcgcgccattaaccgccaga





tttgagtcgcgggacccgttggcagaggtgggaattcaccggtgctagcctcgagga





tatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagcca





CC


 


123
PL1
PL-
ggcctaactggccggtaccaactagtgacgtctacctgatcaaacatgcccggacat



184
TP53_v5-
gtcgtaagacataaacatgcccggacatgtcctcgcaatctaacatgcccggacatg




coreAGR
tcctcgcaatctaacatgcccggacatgtctgcaagctacaacatgcccggacatgt




2
ctacgtacatactgaaaagcatacttttgcaatgttatttttaaaaacaaggaactc





tttaacccagggaagataatcacttggggaaaggaaggttcgtttctgagttagcaa





caagtaaatgcagcactagtgggtgggattgaggtgtgccctggtgcataaatagag





actcagctgtgctggcacactcagaagcttggaccgcatcctagccgccgactcaca





caaggcaggtgggtgaggaaatccaggtaaggctcctgacagcagctttagaagggt





acttgctggagtgaattcgggcctctgattagctagcctcgaggatatcaagatctg





gcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


124
PL1
PL-
ggcctaactggccggtaccaactagtgacgtctacctgatcaaacatgcccggacat



185
TP53_v5-
gtcgtaagacataaacatgcccggacatgtcctcgcaatctaacatgcccggacatg




coreFA
tcctcgcaatctaacatgcccggacatgtctgcaagctacaacatgcccggacatgt




M111B
ctacgtacgggaaaagttcagctgagagatataaaagagcagtctttccagcacctg





caaatccagagcggcgggcactgacgggcacttgcaccgtgtggacagactctccgg





ttctgtgagtggtttttcttttcccgggtcggacctggagttcttagggggatggct





gaaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaa





tccggtactgttggtaaagccacc


 


125
PL1
PL-
ggcctaactggccggtaccaactagtgacgtctacctgatcaaacatgcccggacat



186
TP53_v5-
gtcgtaagacataaacatgcccggacatgtcctcgcaatctaacatgcccggacatg




coreCST
tcctcgcaatctaacatgcccggacatgtctgcaagctacaacatgcccggacatgt





ctacccgttcgacaagcccggacatgctaagacataaacatgcccggacatgtcctc





gcaatctaaccatgcccggacatgtcctcgcaatctaacatgcccggacatgtctgc





aagctacaacatgcccggacatgtctacgtaagtggtgggggagtgaaaagagagat





ggagaaagaggggatgggcagaaagaggaggaggagtcaggggcagggcatggaggt





gggtggggctgggctgccaaagcaggataaatgcacacctgcctgctggtctgggct





ccctgcctcgggctctcaccctcctctcctgcagctccagctttgtgctctaccggt





gctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtac





tgttggtaaagccacc


 


126
PL1
PL-
ggcctaactggccggtaccttttgataaaaatcattaggtacggccgcggtgccagg



187
TCF7_v2
gcgtgcccttgggctccccgggcgcgaaactagtgacgtcctgagcgacagtatagt




TP53_v5
gcacagtgactgcagcagtcattcctttgatgtacgcaactcctttgatgtctatgc




coreBIR
gtcctttgatgttaaggattcctttgatgtaggtacatcctttgatgtccgtaaatc




C5
ctttgatgtgacgtctacgtatctacctgatcaaacatgcccggacatgtcgtaaga





cataaacatgcccggacatgtcctcgcaatctaacatgcccggacatgtcctcgcaa





tctaacatgcccggacatgtctgcaagctacaacatgcccggacatgtctacgtaac





gcgtcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggaccc





gttggcagaggtgggaattcaccggtgctagcctcgaggatatcaagatctggcctc





ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


127
PL1
PL-
ggcctaactggccggtaccaactagtgacgtcctgagcgacagtatagtgcacagtg



188
TCF7_v2-
actgcagcagtcattcctttgatgtacgcaactcctttgatgtctatgcgtcctttg




TP53_v5-
atgttaaggattcctttgatgtaggtacatcctttgatgtccgtaaatcctttgatg




coreAGR
tgacgtctacgtatctacctgatcaaacatgcccggacatgtcgtaagacataaaca




2
tgcccggacatgtcctcgcaatctaacatgcccggacatgtcctcgcaatctaacat





gcccggacatgtctgcaagctacaacatgcccggacatgtctacaatatacgtatct





acctgatcaaacatgcccggacatgtcgtaagacataaacatgcccggacatgtcct





cgcaatctaacatgcccggacatgtcctcgcaatctaacatgcccggacatgtctgc





aagctacaacatgcccggacatgtctacgtacatactgaaaagcatacttttgcaat





gttatttttaaaaacaaggaactctttaacccagggaagataatcacttggggaaag





gaaggttcgtttctgagttagcaacaagtaaatgcagcactagtgggtgggattgag





gtgtgccctggtgcataaatagagactcagctgtgctggcacactcagaagcttgga





ccgcatcctagccgccgactcacacaaggcaggtgggtgaggaaatccaggtaaggc





tcctgacagcagctttagaagggtacttgctggagtgaattcgggcctctgattagc





tagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactg





ttggtaaagccacc


 


130
PL1
pGL4.10-
ggcctaactggccggtaccactagtaagcctcaagatttcctttaggctcttaggta



21
KIF20A
agaaatgtctaaggttcaaggaaaaaggttaagttggaagaatcccaggcaaaataa





gtgcgaatccacgacagttggtaacccggacccacattagaactcagaggtcaagca





gaagcgaacgactggaattccagtcaggcccgccccctttccttacgcggattggta





gctgcaggcttccctatctgattggccgaacgaacgcagcgcgtaatttaaaatatt





gtatctgtaacaaagctgcacctcgtgggcggagttgtgctctgcggctgcgaaagt





ccagcttcggcgactaggtgtgagtaagccagtatcccaggaggagcaagtggcacg





tcttcgggtgagtgtgcggctgtgctggagcccgggttaccagctcttaccggtgct





agcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgt





tggtaaagccacc


 


145
PL1
PL-
ggcctaactggccggtaccactagtggggcggggtgatgacacagcaattcgggact



236
HIGH-
ttccacgcttgcgtgagaagagaccggaagtgaatgacacagcaattcgcttgcgtg




coreFA
agaagctgggactttcctaggggcggggttgggactttccacatgacacagcaatac




M111B-
actagtaacatttctctggcctaactggccggtaccgggaaaagttcagctgagaga




FLUC-
tataaaagagcagtctttccagcacctgcaaatccagagcgggggcactgacgggc




HA
acttgcaccgtgtggacagactctccggttctgtgagtggtttttcttttcccgggt





cggacctggagttcttagggggatggctgaagaattcaccggtcgacgctagc


 


147
PL1
PL-
ggcctaactggccggtaccactagtgtcatctctttgaatattctgtagtttgagga



238
AFP3-
gaatatttgttatattgcacaataaaataagtttgcaagttttttttttctgcccca




FLUC-
aagagctctgtgtccttgaacataaaatacaaataaccgctatgctgttaattatta




HA
acaaatgtcccattttcaacctaaggaaataccataaagtaacagatataccaacaa





aaggttaataattaacaggcattgcctgaaaagagtataaaaggctttcagcatgat





tttccatattgtgcttccaccactgccaataacaaaccggtgaattcaccggtcgac





gctagc


 


148
PL1
FOSL1-
GAATTCACTAGTGACAGTATAGTGCACAGTGACTGCAGCAGGGTGACTCATGATGCC



239
v1-
ACGTCACCAGGTGACTCATGATGCCACGTCACCAGGTGACTCATGATGCCACGTCAC




CREB3L
CAGGTGACTCATGATGCCACGTCACCAGGTGACTCATGGGTACCTATAAAAGGCCAG




1-v6-
CAGCAGCCTGACCACATCTCATCCA




1x1_v1



 


149
PL1
FOSL1-
GAATTCACTAGTAGTATAGTGCACAGTGACTGCAGCAGGGTGACTCATGATGATGCC



240
v1-
ACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGATGCCACGTCAC




CREB3L
CAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCTATAAAAGGCCAG




1-v6-
CAGCAGCCTGACCACATCTCATCCA




2×2_v1



 


150
PL1
FOXO1 ::
GAATTCACTAGTCTCAAGTATAAGGTAAGACATAGTTACTGCGACATCGGCTAGTAA



241
ELK3_v
ACCGGAAGTGTCTGTAAACCGGAAGTGATCGTAAACCGGAAGTGAGCGTAAACCGGA




6
AGTGCTAGTAAACCGGAAGTGGAAGTAAACCGGAAGTGGGTACCTATAAAAGGCCAG





CAGCAGCCTGACCACATCTCATCCA


 


151
PL1
MTF1_v
GAATTCACTAGTGTACTCAAGTATAAGGTAAGATTTGCACACGGTACGTACTCATTT



242
9
GCACACGGTACATGCGAGTTTGCACACGGTACAGCTCAGTTTGCACACGGTACGTCA





GCTTTTGCACACGGTACATCAGAATTTGCACACGGTACGGTACCTATAAAAGGCCAG





CAGCAGCCTGACCACATCTCATCCACCGGTG


 


152
PL1
NFE2L2_
GAATTCACTAGTTAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCC



243
v14
TATCCTAATTGCTGAGTCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATA





ATTGCTGAGTCATTCTAACTCGCTAATTGCTGAGTCATGGTACCTATAAAAGGCCAG





CAGCAGCCTGACCACATCTCATCCA


 


153
PL1
NFKB1_
GAATTCACTAGTGCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTATAC



244
v3
GTAGGGGAATCCCCTCGAAGGGGAATCCCCTTTAAGGGGAATCCCCTCGCAGGGGAA





TCCCCTCTCAGGGGAATCCCCTAACAGGGGAATCCCCTGGTACCTATAAAAGGCCAG





CAGCAGCCTGACCACATCTCATCCA


 


154
PL1
TP53-v5-
GAATTCACTAGTGCATCCTTTGATGTTACCTGATCAAACATGCCCGGACATGTCGTA



245
TCF7-
AGACATATCCTTTGATGTCTCGCAATCTAACATGCCCGGACATGTCCTCGCAATCTT




v2-
CCTTTGATGTTGCAAGCTACAACATGCCCGGACATGTCGGTACCTATAAAAGGCCAG




1x1_v1
CAGCAGCCTGACCACATCTCATCCA


 


155
PL1
XBP1_v
GAATTCACTAGTGCACCATTAGTACTTGATCAGTATGCCACGTCATCACTACTCTAT



246
19
GCCACGTCATCTCCTAGATATGCCACGTCATCGTAAGACTATGCCACGTCATCTACA





GCTTATGCCACGTCATCACGTACTTATGCCACGTCATCGGTACCTATAAAAGGCCAG





CAGCAGCCTGACCACATCTCATCCA


 


156
PL5
Cancript-
ggcctaactggccggtaccactagtgtccccacccacacattcctgtccccacccac



50
coreBIR
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc




C5-
cacacattcctgtccccacccacacattcctgtgcgctcccgacatgccccgcggcg




FLUC
cgccattaaccgccagatttgagtcgcgggacccgttggcagaggtgggctagcctc





gaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaa





agccacc


 


157
PL5
UAS-
ggcctaactggccggtaccagcttgcatgcctgcaggtcggagtactgtcctccgag



51
minB-
cggagtactgtcctccgagcggagtactgtcctccgagcggagtactgtcctccgag




FLUC_n
cggagtactgtcctccgagcggtgcgctcccgacatgccccgcggcgcgccattaac




o KPNI
cgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatca





agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


158
PL5
TTF-
ggcctaactggccggtaccactagtggttttgtggggttttgtggggttttgtgggg



73
1_1_no
ttttgtggggttttgtggggttttgtggggttttgtggggttttgtggggttttgtg




space_mi
gggttttgtggtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttg




nBIRC5
agtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcct





cggcggccaagcttggcaatccggtactgttggtaaagccacc


 


159
PL5
TTF-
ggcctaactggccggtaccactagtagccacttgaaattagccacttgaaattagcc



74
1_2_no
acttgaaattagccacttgaaattagccacttgaaattagccacttgaaattagcca




space_mi
cttgaaatttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgag




nBIRC5
tcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcg





gcggccaagcttggcaatccggtactgttggtaaagccacc


 


160
PL5
TTF-
ggcctaactggccggtaccactagtctgggaacaagtgctgggaacaagtgctggga



75
1_3_no
acaagtgctgggaacaagtgctgggaacaagtgctgggaacaagtgctgggaacaag




space_mi
tgctgggaacaagtgtgcgctcccgacatgccccgcggcgcgccattaaccgccaga




nBIRC5
tttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctg





gcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


161
PL5
TTF-
ggcctaactggccggtaccactagtgactcctcaaggggactcctcaaggggactcc



76
1_4_no
tcaaggggactcctcaaggggactcctcaaggggactcctcaaggggactcctcaag




space_mi
gggactcctcaagggtgcgctcccgacatgccccgcggcgcgccattaaccgccaga




nBIRC5
tttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctg





gcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


162
PL5
TCF7_no
ggcctaactggccggtaccactagtcgggctttgatctttcgggctttgatctttcg



77
space_mi
ggctttgatctttcgggctttgatctttcgggctttgatctttcgggctttgatctt




nBIRC5
tcgggctttgatcttttgcgctcccgacatgccccgcggcgcgccattaaccgccag





atttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatct





ggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


163
PL5
TCF7:L2_
ggcctaactggccggtaccactagtgcgctttgatgtgcggggcggccctttgaagt



78
no
tggcgctttgatgtgcggggcggccctttgaagttggcgctttgatgtgcggggcgg




space_mi
ccctttgaagttgtgcgctcccgacatgccccgcggcgcgccattaaccgccagatt




nBIRC5
tgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggc





ctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


164
PL5
MSC_no
ggcctaactggccggtaccactagtaacagctgttaacagctgttaacagctgttaa



79
space_mi
cagctgttaacagctgttaacagctgttaacagctgttaacagctgttaacagctgt




nBIRC5
ttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggga





cccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


165
PL5
ZEB1_no
ggcctaactggccggtaccactagtcacctgcacctgcacctgcacctgcacctgca



80
space_mi
cctgcacctgcacctgcacctgcacctgcacctgcacctgtgcgctcccgacatgcc




nBIRC5
ccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtggg





ctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtact





gttggtaaagccacc


 


166
PL5
MAX_M
ggcctaactggccggtaccactagtagttcaacacgtggtctgggagttcaacacgt



81
YC_no
ggtctgggagttcaacacgtggtctgggagttcaacacgtggtctgggagttcaaca




space_mi
cgtggtctgggtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttg




nBIRC5
agtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcct





cggcggccaagcttggcaatccggtactgttggtaaagccacc


 


167
PL5
GATA6
ggcctaactggccggtaccactagtgacagataagaaagacagataagaaagacaga



82
no
taagaaagacagataagaaagacagataagaaagacagataagaaagacagataaga




space_mi
aagacagataagaaatgcgctcccgacatgccccgcggcgcgccattaaccgccaga




nBIRC5
tttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctg





gcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


168
PL5
GATA1-
ggcctaactggccggtaccactagtttctaatctatttctaatctatttctaatcta



83
BIRC5co
tttctaatctatttctaatctatttctaatctatttctaatctatttctaatctatt




re
tctaatctattgcgctcccgacatgccccgcggcgcgccattaaccgccagatttga





gtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctc





ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


169
PL5
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



84
no
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




space_mi
gtgactcatgtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttga




nBIRC5
gtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctc





ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


170
PL5
STAT3_
ggcctaactggccggtaccactagtcttctgggaaacttctgggaaacttctgggaa



85
no
acttctgggaaacttctgggaaacttctgggaaacttctgggaaacttctgggaaac




space_mi
ttctgggaaatgcgctcccgacatgccccgcggcgcgccattaaccgccagatttga




nBIRC5
gtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctc





ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


171
PL5
STAT:S
ggcctaactggccggtaccactagtaattcttagaaataaattcttagaaataaatt



86
TAT_no
cttagaaataaattcttagaaataaattcttagaaataaattcttagaaataaattc




space_mi
ttagaaatatgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgag




nBIRC5
tcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcg





gcggccaagcttggcaatccggtactgttggtaaagccacc


 


172
PL5
SOX9_no
ggcctaactggccggtaccactagtaaaacaaaggatcctttgttttaaaacaaagg



87
space_mi
atcctttgttttaaaacaaaggatcctttgttttaaaacaaaggatcctttgtttta




nBIRC5
aaacaaaggatcctttgttttctgcgctcccgacatgccccgcggcgcgccattaac





cgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatca





agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


173
PL5
HNF4_no
ggcctaactggccggtaccactagtaaagtccaagtccaaaagtccaagtccaaaag



88
space_mi
tccaagtccaaaagtccaagtccaaaagtccaagtccaaaagtccaagtccaaaagt




nBIRC5
ccaagtccatgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgag





tcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcg





gcggccaagcttggcaatccggtactgttggtaaagccacc


 


174
PL5
TTF-
ggcctaactggccggtaccactagtggttttgtggagaggttttgtggtcgggtttt



89
1_1_3bp
gtgggacggttttgtggctaggttttgtggactggttttgtggtgcggttttgtggg




space_mi
taggttttgtggtgcgctcccgacatgccccgcggcgcgccattaaccgccagattt




nBIRC5
gagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcc





tcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


175
PL5
TTF-
ggcctaactggccggtaccactagtagccacttgaaattagaagccacttgaaattt



90
1_2_3bp
cgagccacttgaaattgacagccacttgaaattctaagccacttgaaattactagcc




space_mi
acttgaaatttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttga




nBIRC5
gtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctc





ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


176
PL5
TTF-
ggcctaactggccggtaccactagtctgggaacaagtgagactgggaacaagtgtcg



91
1_3_3bp
ctgggaacaagtggacctgggaacaagtgctactgggaacaagtgactctgggaaca




space_mi
agtgtgcctgggaacaagtgtgcgctcccgacatgccccgcggcgcgccattaaccg




nBIRC5
ccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


177
PL5
TTF-
ggcctaactggccggtaccactagtgactcctcaagggagagactcctcaagggtcg



92
1_4_3bp
gactcctcaaggggacgactcctcaagggctagactcctcaagggactgactcctca




space_mi
agggtgcgactcctcaagggtgcgctcccgacatgccccgcggcgcgccattaaccg




nBIRC5
ccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


178
PL5
TCF7_3bp
ggcctaactggccggtaccactagtccggctttgatctttagacgggctttgatctt



93
space_mi
ttcgcgggctttgatctttgaccgggctttgatctttctacgggctttgatctttac




nBIRC5
tcgggctttgatcttttgcgctcccgacatgccccgcggcgcgccattaaccgccag





atttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatct





ggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


179
PL5
TCF7:L2_
ggcctaactggccggtaccactagtgcgctttgatgtgcggggcggccctttgaagt



94
3bp
tgagagcgctttgatgtgcggggcggccctttgaagttgtcggcgctttgatgtgcg




space_mi
gggcggccctttgaagttgtgcgctcccgacatgccccgcggcgcgccattaaccgc




nBIRC5
cagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaaga





tctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


180
PL5
MSC_3bp
ggcctaactggccggtaccactagtaacagctgttagaaacagctgtttcgaacagc



95
space_mi
tgttgacaacagctgttctaaacagctgttactaacagctgtttgcaacagctgttg




nBIRC5
taaacagctgtttgcgctcccgacatgccccgcggcgcgccattaaccgccagattt





gagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcc





tcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


181
PL5
ZEB1_3
ggcctaactggccggtaccactagtcacctgagacacctgtcgcacctggaccacct



96
bp
gctacacctgactcacctgtgccacctgagacacctgtcgcacctggaccacctgtg




space_mi
cgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggaccc




nBIRC5
gttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagct





tggcaatccggtactgttggtaaagccacc


182
PL5
MAX_M
ggcctaactggccggtaccactagtagttcaacacgtggtctgggagaagttcaaca


 



97
YC_3bp
cgtggtctgggtcgagttcaacacgtggtctggggacagttcaacacgtggtctggg




space_mi
ctaagttcaacacgtggtctgggtgcgctcccgacatgccccgcggcgcgccattaa




nBIRC5
ccgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatc





aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


183
PL5
GATA6_
ggcctaactggccggtaccactagtgacagataagaaaagagacagataagaaatcg


 



98
3bp
gacagataagaaagacgacagataagaaactagacagataagaaaactgacagataa




space_mi
gaaatgcgacagataagaaatgcgctcccgacatgccccgcggcgcgccattaaccg




nBIRC5
ccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


184
PL5
GATA1_
ggcctaactggccggtaccactagtttctaatctatagattctaatctattcgttct



99
3bp
aatctatgacttctaatctatctattctaatctatactttctaatctattgcttcta




space_mi
atctattgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcg




nBIRC5
cgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcg





gccaagcttggcaatccggtactgttggtaaagccacc


 


185
PL6
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgagaggtgactcatgtcgggtg



00
3bp
actcatggacggtgactcatgctaggtgactcatgactggtgactcatgtgcggtga




space_mi
ctcatgctgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtc




nBIRC5
gcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggc





ggccaagcttggcaatccggtactgttggtaaagccacc


 


186
PL6
STAT3_
ggcctaactggccggtaccactagtcttctgggaaaagacttctgggaaatcgcttc



01
3bp
tgggaaagaccttctgggaaactacttctgggaaaactcttctgggaaatgccttct




space_mi
gggaaatgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcg




nBIRC5
cgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcg





gccaagcttggcaatccggtactgttggtaaagccacc


 


187
PL6
STAT:S
ggcctaactggccggtaccactagtaattcttagaaataagaaattcttagaaatat



02
TAT_3b
cgaattcttagaaatagacaattcttagaaatactaaattcttagaaataactaatt




p
cttagaaatatgcgctcccgacatgccccgcggcgcgccattaaccgccagatttga




space_mi
gtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctc




nBIRC5
ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


188
PL6
SOX9_3
ggcctaactggccggtaccactagtaaaacaaaggatcctttgttttagaaaaacaa



03
bp
aggatcctttgtttttcgaaaacaaaggatcctttgttttgacaaaacaaaggatcc




space_mi
tttgtttttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagt




nBIRC5
cgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcgg





cggccaagcttggcaatccggtactgttggtaaagccacc


 


189
PL6
HNF4_3
ggcctaactggccggtaccactagtaaagtccaagtccaagaaaagtccaagtccat



04
bp
cgaaagtccaagtccagacaaagtccaagtccactaaaagtccaagtccaactaaag




space_mi
tccaagtccatgcgctcccgacatgccccgcggcgcgccattaaccgccagatttga




nBIRC5
gtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctc





ggcggccaagcttggcaatccggtactgttggtaaagccacc


 


190
PL6
STAT:S
ggcctaactggccggtaccactagtaattcttagaaataaattcttagaaataaatt



05
TAT_no
cttagaaataaattcttagaaataaattcttagaaataaattcttagaaataaattc




space_mi
ttagaaatatgcgctcccgacatgtcccgcggcgcgccattaaccgccagatttgag




nBIRC5
tcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcg




2 w extra
gcggccaagcttggcaatccggtactgttggtaaagccaccatcctcgaggatatca




insert
agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


191
PL6
HOXA1
ggcctaactggccggtaccactagtccaataaaaaccaataaaaaccaataaaaacc



16
3_no
aataaaaaccaataaaaaccaataaaaaccaataaaaaccaataaaaaccaataaaa




space_mi
atgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggga




nB
cccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


193
PL6
FOXM1_
ggcctaactggccggtaccactagttgtttacttatgtttacttatgtttacttatg



35
no
tttacttatgtttacttatgtttacttatgtttacttatgtttacttatgtttactt




space_co
atgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggga




reBIRC5
cccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


194
PL6
E2F2_no
ggcctaactggccggtaccactagtaaaatggcgccattttaaaatggcgccatttt



36
space_co
aaaatggcgccattttaaaatggcgccattttaaaatggcgccattttaaaatggcg




reBIRC5
ccatttttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtc





gcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggc





ggccaagcttggcaatccggtactgttggtaaagccacc


 


195
PL6
RUNX1_
ggcctaactggccggtaccactagttattgtggttatattgtggttatattgtggtt



37
no
atattgtggttatattgtggttatattgtggttatattgtggttatattgtggttat




space_co
gcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacc




reBIRC5
cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


196
PL6
SOX4_no
ggcctaactggccggtaccactagtgaacaattgcagtgttgaacaattgcagtgtt



38
space_co
gaacaattgcagtgttgaacaattgcagtgttgaacaattgcagtgttgaacaattg




reBIRC5
cagtgttgaacaattgcagtgtttgcgctcccgacatgccccgcggcgcgccattaa





ccgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatc





aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


197
PL6
RREB1_
ggcctaactggccggtaccactagtccccaaaccaccccccccccccccaaaccacc



39
no
ccccccccccccaaaccaccccccccccccccaaaccaccccccccccccccaaacc




space_co
acccccccccctgcgctcccgacatgccccgcggcgcgccattaaccgccagatttg




reBIRC5
agtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcct





cggcggccaagcttggcaatccggtactgttggtaaagccacc


 


198
PL6
ETV4_no
CACTAGTACCGGAAGTAACCGGAAGTAACCGGAAGTAACCGGAAGTAACCGGAAGTA



40
space_co
ACCGGAAGTAACCGGAAGTAACCGGAAGTAACCGGAAGTAtgcgctcccgacatgcc




reBIRC5
ccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtggg





ctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtact





gttggtaaagccacc


 


199
PL6
HES6_no
ggcctaactggccggtaccactagtggcacgtgttggcacgtgttggcacgtgttgg



41
space_co
cacgtgttggcacgtgttggcacgtgttggcacgtgttggcacgtgttggcacgtgt




reBIRC5
ttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggga





cccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


200
PL6
ASCL1_
ggcctaactggccggtaccactagtcgagcagctggtgcgagcagctggtgcgagca



42
no
gctggtgcgagcagctggtgcgagcagctggtgcgagcagctggtgcgagcagctgg




space_co
tgtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggg




reBIRC5
acccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggcca





agcttggcaatccggtactgttggtaaagccacc


 


201
PL6
TWIST1_
ggcctaactggccggtaccactagttccagatgtttccagatgtttccagatgtttc



43
no
cagatgtttccagatgtttccagatgtttccagatgtttccagatgtttgcgctccc




space_co
gacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca




reBIRC5
gaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaat





ccggtactgttggtaaagccacc


 


202
PL6
FOXA3_
ggcctaactggccggtaccactagtatagtaaacaatagtaaacaatagtaaacaat



44
no
agtaaacaatagtaaacaatagtaaacaatagtaaacaatagtaaacatgcgctccc




space_co
gacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca




reBIRC5
gaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaat





ccggtactgttggtaaagccacc


 


203
PL6
PITX2_no
ggcctaactggccggtaccactagttaatccctaatccctaatccctaatccctaat



45
space_co
ccctaatccctaatccctaatccctaatccctaatccctaatccctgcgctcccgac




reBIRC5
atgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagag





gtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccg





gtactgttggtaaagccacc


 


204
PL6
HOXB2_
ggcctaactggccggtaccactagtctaattaactaattaactaattaactaattaa



46
no
ctaattaactaattaactaattaactaattaactaattaactaattaatgcgctccc




space_co
gacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca




reBIRC5
gaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaat





ccggtactgttggtaaagccacc


 


205
PL6
EN2_no
ggcctaactggccggtaccactagtcccaattagccccaattagccccaattagccc



47
space_co
caattagccccaattagccccaattagccccaattagccccaattagctgcgctccc




reBIRC5
gacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca





gaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaat





ccggtactgttggtaaagccacc


 


206
PL6
DLX4_no
ggcctaactggccggtaccactagtcaattacaattacaattacaattacaattaca



48
space_co
attacaattacaattacaattacaattacaattacaattatgcgctcccgacatgcc




reBIRC5
ccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtggg





ctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtact





gttggtaaagccacc


 


207
PL6
GRHL1_
ggcctaactggccggtaccactagtaaaaccggttttaaaaccggttttaaaaccgg



49
no
ttttaaaaccggttttaaaaccggttttaaaaccggttttaaaaccggttttaaaac




space_co
cggtttttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtc




reBIRC5
gcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggc





ggccaagcttggcaatccggtactgttggtaaagccacc


 


208
PL6
FOXM1_
ggcctaactggccggtaccactagttgtttacttaagatgtttacttatcgtgttta



50
3bp
cttagactgtttacttactatgtttacttaacttgtttacttatgctgtttacttat




space_co
gcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacc




reBIRC5
cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


209
PL6
E2F2_3b
ggcctaactggccggtaccactagtaaaatggcgccatttttcgaaaatggcgccat



51
p
tttgacaaaatggcgccattttctaaaaatggcgccattttactaaaatggcgccat




space_co
ttttgcaaaatggcgccatttttgcgctcccgacatgccccgcggcgcgccattaac




reBIRC5
cgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatca





agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


210
PL6
RUNX1_
ggcctaactggccggtaccactagttattgtggttatcgtattgtggttagactatt



52
3bp
gtggttactatattgtggttaacttattgtggttatgctattgtggttatgcgctcc




space_co
cgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggc




reBIRC5
agaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaa





tccggtactgttggtaaagccacc


 


211
PL6
SOX4_3
ggcctaactggccggtaccactagtgaacaattgcagtgttgacgaacaattgcagt



53
bp
gttctagaacaattgcagtgttactgaacaattgcagtgtttgcgaacaattgcagt




space_co
gtttgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgg




reBIRC5
gacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


212
PL6
RREB1_
ggcctaactggccggtaccactagtccccaaaccaccccccccccgacccccaaacc



54
3bp
accccccccccctaccccaaaccaccccccccccactccccaaaccacccccccccc




space_co
tgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggac




reBIRC5
ccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaag





cttggcaatccggtactgttggtaaagccacc


 


213
PL6
ETV4_3
ggcctaactggccggtaccactagtaccggaagtaagaaccggaagtatcgaccgga



55
bp
agtagacaccggaagtactaaccggaagtaactaccggaagtatgcaccggaagtat




space_co
gcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacc




reBIRC5
cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


214
PL6
HES6_3
ggcctaactggccggtaccactagtggcacgtgttagaggcacgtgtttcgggcacg



56
bp
tgttgacggcacgtgttctaggcacgtgttactggcacgtgtttgcggcacgtgttt




space_co
gcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacc




reBIRC5
cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


215
PL6
ASCL1_
ggcctaactggccggtaccactagtcgagcagctggtgagacgagcagctggtgtcg



57
3bp
cgagcagctggtggaccgagcagctggtgctacgagcagctggtgactcgagcagct




space_co
ggtgtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcg




reBIRC5
ggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggc





caagcttggcaatccggtactgttggtaaagccacc


 


216
PL6
TWIST1_
ggcctaactggccggtaccactagttccagatgttagatccagatgtttcgtccaga



58
3bp
tgttgactccagatgttctatccagatgttacttccagatgtttgctccagatgttt




space_co
gcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacc




reBIRC5
cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


217
PLE
FOXA3_
ggcctaactggccggtaccactagtatagtaaacaagaatagtaaacatcgatagta



59
3bp
aacagacatagtaaacactaatagtaaacaactatagtaaacatgcatagtaaacat




space_co
gcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacc




reBIRC5
cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


218
PL6
PITX2_3
ggcctaactggccggtaccactagttaatcccagataatccctcgtaatcccgacta



60
bp
atcccctataatcccacttaatccctgctaatcccacttaatccctgctaatccctg




space_co
cgctcccgacatgccccgcggcgcgtcattaaccgccagatttgagtcgcgggaccc




reBIRC5
gttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagct





tggcaatccggtactgttggtaaagccacc


 


219
PLE
HOXB2_
ggcctaactggccggtaccactagtctaattaaagactaattaatcgctaattaaga



61
3bp
cctaattaactactaattaaactctaattaatgcctaattaaactctaattaatgcg




space_co
ctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgt




reBIRC5
tggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttg





gcaatccggtactgttggtaaagccacc


 


220
PL6
EN2_3bp
ggcctaactggccggtaccactagtcccaattagcagacccaattagctcgcccaat



62
space_co
tagcgaccccaattagcctacccaattagcactcccaattagctgccccaattagct




reBIRC5
gcgctcccgacatgccctgcggcgcgccattaaccgccagatttgagtcgcgggacc





cgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagc





ttggcaatccggtactgttggtaaagccacc


 


221
PL6
DLX4_3
ggcctaactggccggtaccactagtcaattaagacaattatcgcaattagaccaatt



63
bp
actacaattaactcaattatgccaattaactcaattatgccaattaagacaattatg




space_co
cgctcccgacatgccccgcggcgtgccattaaccgccagatttgagtcgcgggaccc




reBIRC5
gttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagct





tggcaatccggtactgttggtaaagccacc


 


222
PL6
GRHL1_
ggcctaactggccggtaccactagtaaaaccggttttagaaaaaccggtttttcgaa



64
3bp
aaccggttttgacaaaaccggttttctaaaaaccggttttactaaaaccggtttttg




space_co
caaaaccggtttttgcgctcccgacatgccccgcggcgcgccattaaccgccagatt




reBIRC5
tgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggc





ctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


223
PL6
FOSL1-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



69
5X_BIR
gggtgactcatgggtgactcatgtgcgctcccgacatgccccgcggcgcgccattaa




C5core
ccgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggatatc





aagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


224
PL6
FOSL1-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



72
11X_BI
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




RC5core
gtgactcatgggtgactcatgggtgactcatgtgcgctcccgacatgccccgcggcg





cgccattaaccgccagatttgagtcgcgggacccgttggcagaggtgggctagcctc





gaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaa





agccacc


 


225
PL6
FOSL1-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



73
7X_BIR
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgtgcgctcccgac




C5core
atgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagag





gtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccg





gtactgttggtaaagccacc


 


226
PL6
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



74
no
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




space_no
gtgactcatgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcag




p53_BIR
aggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatc




C5core
cggtactgttggtaaagccacc


 


227
PL6
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



75
TATATS
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




S_10bp
gtgactcatgcggtgctagctataaaaggccagcagcagcctgaccacatctcatcc




spacing
tcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgtt





ggtaaagccacc


 


228
PL6
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



76
TATATS
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




S_no
gtgactcatgtataaaaggccagcagcagcctgaccacatctcatcctcctcgagga




spacing
tatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagcca





CC


 


229
PL6
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



85
TATATS
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




S_25bp
gtgactcatgacatctttcagggaccggtgctagctataaaaggccagcagcagcct




spacing
gaccacatctcatcctcctcgaggatatcaagatctggcctcggcggccaagcttgg





caatccggtactgttggtaaagccacc


 


230
PL6
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



86
TATATS
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




S_50bp
gtgactcatgtggctattagcagtaccgcttagacacatctttcagggaccggtgct




spacing
agctataaaaggccagcagcagcctgaccacatctcatcctcctcgaggatatcaag





atctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


231
PL6
Forkhead_
ggcctaactggccggtaccactagtctgtttacctgtttacctgtttacctgtttac



89
7XFOS
ctgtttacggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtga




L1_BIR
ctcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgtgcgctc




C5core
ccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttgg





cagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggca





atccggtactgttggtaaagccacc


 


232
PL6
Forkhead_
ggcctaactggccggtaccactagtctgtttacagactgtttactcgctgtttacga



90
7XFOS
cctgtttacctactgtttacggtgactcatgggtgactcatgggtgactcatgggtg




L1_BIR
actcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgac




C5core
tcatgtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgc




3bp
gggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcgg





ccaagcttggcaatccggtactgttggtaaagccacc


 


233
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



25
10bp
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




spacer_c
gtgactcatgcataggcctctgaacaacgcgtcccgacatgccccgcggcgcgccat




oreBIRC
taaccgccagatttgagtcgcgggacccgttggcagaggtgggctagcctcgaggat




5
atcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccac





C


 


234
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



26
30bp
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




spacer_c
gtgactcatgcataggcctctgatagagctgcgatagaccaagacaacgcgtcccga




oreBIRC
catgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcaga




5
ggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatcc





ggtactgttggtaaagccacc


 


235
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



27
88bp
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




spacer_c
gtgactcatgcatagaaacgacgcaatatctccatagggttaacggcggaacttgac




oreBIRC
ggcgtccattagccacttggtcatgggacagggggggaaaacggacaacgcgtcccg




5
acatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcag





aggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatc





cggtactgttggtaaagccacc


 


236
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



28
Low_cor
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




eBIRC5
gtgactcatgcataccggaagtacttgcgcaatgaccggaagtacaacgcgtcccga





catgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcaga





ggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatcc





ggtactgttggtaaagccacc


 


237
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



29
Medium
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




coreBI
gtgactcatgcatttgcgcaacaggggcggggtgatgacacagcaattcgcttgcgt




RC5
gagaagagaccggaagtgagggactttccacatgacacagcaatacaacgcgtcccg





acatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcag





aggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatc





cggtactgttggtaaagccacc


 


238
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



30
High_cor
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




eBIRC5
gtgactcatgcatggggggggtgatgacacagcaattcgggactttccacgcttgc





gtgagaagagaccggaagtgaatgacacagcaattcgcttgcgtgagaagctgggac





tttcctaggggcggggttgggactttccacatgacacagcaatacaacgcgtcccga





catgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcaga





ggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatcc





ggtactgttggtaaagccacc


 


239
PL8
Low_cor
ggcctaactggccggtaccactagtaccggaagtacttgcgcaatgaccggaagtac



31
eBIRC5
aacgcgtcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggga





cccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


240
PL8
Medium_
ggcctaactggccggtaccactagtttgcgcaacaggggggggtgatgacacagca



32
coreBI
attcgcttgcgtgagaagagaccggaagtgagggactttccacatgacacagcaata




RC5
caacgcgtcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggg





acccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggcca





agcttggcaatccggtactgttggtaaagccacc


 


241
PL8
High_cor
ggcctaactggccggtaccactagtggggcggggtgatgacacagcaattcgggact



33
eBIRC5
ttccacgcttgcgtgagaagagaccggaagtgaatgacacagcaattcgcttgcgtg





agaagctgggactttcctaggggcggggttgggactttccacatgacacagcaatac





aacgcgtcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcggga





cccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


242
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



34
Tetramer
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




p53_core
gtgactcatgcatacaacgcgtcccgacatgccccgacatgcccatcgacatgcccc




BIRC5
gacatgcccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcag





aggtgggctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatc





cggtactgttggtaaagccacc


 


243
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



35
p53RE_c
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




oreBIRC
gtgactcatgcatgaattcggacatgcccgggcatgtccccagggacatgcccgggc




5
atgtccccagagacatgtccagacatgtccccaggaacatgtcccaacatgttgtcc





aggagacatgtccagacatgtccccaggaacatgtcccaacatgttgtactagtaca





acgcgtcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggac





ccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggcggccaag





cttggcaatccggtactgttggtaaagccacc


 


244
PL8
EN7R_F
ggcctaactggccggtacctgccactcaaagtggcacactccctgctcaggaggccg



36
OSL1_co
ggagggaggacacagccctggcaactcctctgccccggggggtcaggaaggggtcac




reBIRC5
cccacactccagaaccctacagaatgtggccttggcttttcccatcaagagctgggg





aaagccaggccccgacttcattaccccctgcccccgtcccatgctcagtgggcccca





tcgtgggtccatgccacactcccaactgagcagccccgcagccccgcgtgtcacaga





catggggcctcctaattgctgctgaggtcccaatccctggctggacgtgcctg


 


245
PL8
FOSL1_
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



58
CS6X-
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatga




BIRC5co
ctagtgtccccacccacacattcctgtccccacccacacattcctgtccccacccac




re
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc





cacacattcctgtgcgctcccgacatgccccgcggcgcgccattaaccgccagattt





gagtcgcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcc





tcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


246
PL8
pGL4.10-
ggcctaactggccggtaccaagacaggttgtcctcccaggggatgggggtccatcca



80
coreCEA
ccttgccgaaaagatttgtctgaggaactgaaaatagaagggaaaaaagaggaggga




CAM5_1
caaaagaggcagaaatgagaggggaggggacagaggacacctgaataaagaccacac





ccatgacccacgtgatgctgagaagtactcctgccctaggaagagactcagggcaga





gggaggaaggacagcagaccagacagtcacagcagccttgacaaaacgttcctggaa





ctaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaa





tccggtactgttggtaaagccacc


 


247
PL8
pGL4.10-
ggcctaactggccggtaccatgacccacgtgatgctgagaagtactcctgccctagg



81
coreCEA
aagagactcagggcagagggaggaaggacagcagaccagacagtcacagcagccttg




CAM5_2
acaaaacgttcctggaactaccggtgctagcctcgaggatatcaagatctggcctcg





gcggccaagcttggcaatccggtactgttggtaaagccacc


 


248
PL8
pGL4.10-
ggcctaactggccggtaccctggatgctcatcccgccaccgtcgcccaccccgccgc



82
coreFA
tgcagaaaggcagcaactgccacacacctaagcaacttggcgggctattcgccctgc




M111B_
agctgccgccagcgcgcggctcccgccagcgcgctggcaatcaaaagtcggagaaag




1
cgcgaaacctccaggcacctcccactccgcccagctaccgcgcagctcctccctagc





ctccactgggagacaggggacgcccatgagcgggaaagagcagggcggtgattgctt





agtttatcctgggacacgggaactggccgtggactgagtggtgccggggaggggatc





actgagaccgggaagggtcatccagacaaatagggagggtgggcgggttggcgcgca





gtaccctcggcccggccttcagacccacctgcgcgcgctgcgcgctcatccggtcct





tcccttcaatcactgtctggagtgatgataattggcttccacagtggatgagagatg





agtcatttacatccaatgagagaaaaacagcctccagagactcttcgtccattggcc





agcgagagtgtcagttcccaggctcctgccgcgcacgggcgagcccttctaggcggg





aaaagttcagctgagagatataaaagagcagtctttccagcacctgcaaatccagag





cggcgggcactgacgggcacttgcaccgtgtggacagactctccggttctgtgagtg





gtttttcttttcccgggtcggacctggagttcttagggggatggctgaaccggtgct





agcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgt





tggtaaagccacc


 


249
PL8
pGL4.10-
ggcctaactggccggtacctgagaccgggaagggtcatccagacaaatagggagggt



83
coreFA
gggcgggttggcgcgcagtaccctcggcccggccttcagacccacctgcgcgcgctg




M111B_
cgcgctcatccggtccttcccttcaatcactgtctggagtgatgataattggcttcc




2
acagtggatgagagatgagtcatttacatccaatgagagaaaaacagcctccagaga





ctcttcgtccattggccagcgagagtgtcagttcccaggctcctgccgcgcacgggc





gagcccttctaggcgggaaaagttcagctgagagatataaaagagcagtctttccag





cacctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggacagact





ctccggttctgtgagtggtttttcttttcccgggtcggacctggagttcttaggggg





atggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagct





tggcaatccggtactgttggtaaagccacc


 


250
PL8
pGL4.10-
ggcctaactggccggtaccgggaaaagttcagctgagagatataaaagagcagtctt



84
coreFA
tccagcacctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggac




M111B_
agactctccggttctgtgagtggtttttcttttcccgggtcggacctggagttctta




3
gggggatggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


251
PL8
pGL4.10-
ggcctaactggccggtaccctgctcctccttcttgcgggccgcgccctgccggcagt



85
coreCEP
gacgtgccccgccctgcagccgcgggattcaaactcccggaagcggcatccacacct




55
gatggtgtgactcggccgacgcgagcgccgcgcttcgcttcagctgctaaccggtgc





tagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactg





ttggtaaagccacc


 


252
PL8
pGL4.10-
ggcctaactggccggtaccggcccgccccctttccttacgcggattggtagctgcag



86
coreKIF2
gcttccctatctgattggccgaacgaacgcagcgcgtaatttaaaatattgtatctg




0A
taacaaagctgcacctcgtgggcggagttgtgctctgcggctgcgaaagtccagctt





cggcgactaggtgtgagtaagccagtatcccaggaggagcaagtggcacgtcttcgg





gtgagtgtgcggctgtgctggagcccgggttaccagctcttaccggtgctagcctcg





aggatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaa





gccacc


 


253
PL8
pGL4.10-
ggcctaactggccggtaccttgttttgacaggagcagggaagtattgtagaaaataa



87
coreAGR
tttttatcataatggagtatggcaggttatatgactgcgaggatcagaattgtgaat




2_1
catctcttgtgtgtcttcaagtaaataaaggcaatctgcccacggagcagaaaaaaa





atctacaaactacaaactctgtccaatcatgtaaagacaaatcagccttcaggcaaa





tcaaatgtcttcattcaaagtctacctggatttggcactctgcccatcgtttcaaaa





cctcttaacaatacgtttcacaaatagttaaaaacatgcatactgaaaagcatactt





ttgcaatgttatttttaaaaacaaggaactctttaacccagggaagataatcacttg





gggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagcactagtgggtgg





gattgaggtgtgccctggtgcataaatagagactcagctgtgctggcacactcagaa





gcttggaccgcatcctagccgccgactcacacaaggcaggtgggtgaggaaatccag





gtaaggctcctgacagcagctttagaagggtacttgctggagtgaattcgggcctct





gattaccggtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggc





aatccggtactgttggtaaagccacc


 


254
PL8
pGL4.10-
ggcctaactggccggtaccacctcttaacaatacgtttcacaaatagttaaaaacat



88
coreAGR
gcatactgaaaagcatacttttgcaatgttatttttaaaaacaaggaactctttaac




2_2
ccagggaagataatcacttggggaaaggaaggttcgtttctgagttagcaacaagta





aatgcagcactagtgggtgggattgaggtgtgccctggtgcataaatagagactcag





ctgtgctggcacactcagaagcttggaccgcatcctagccgccgactcacacaaggc





aggtgggtgaggaaatccaggtaaggctcctgacagcagctttagaagggtacttgc





tggagtgaattcgggcctctgattaccggtgctagcctcgaggatatcaagatctgg





cctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


255
PL8
pGL4.10-
ggcctaactggccggtacccagtgggtaggtctagcagtggcgcagcaatagagcgc



89
coreUBE
tccggagcgtctcattggctggatcaaacccaagcgagccattgattggtcgacgcc




2C
cccagagggttacaattcaaacgcgggcgggcgggcccgcagtcctgcagttgcagt





cgtgttctccgagttcctgtctctctgccgagctagcctcgaggatatcaagatctg





gcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


256
PL8
pGL4.10-
ggcctaactggccggtaccagtggtgggggagtgaaaagagagatggagaaagaggg



90
coreCST1
gatgggcagaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctgg





gctgccaaagcaggataaatgcacacctgcctgctggtctgggctccctgcctcggg





ctctcaccctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgag





gatatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagc





cacc


 


257
PL8
hTERT-
ggcctaactggccggtaccactagtcgggttaccccacagcctaggccgattcgacc



93
FLUC
tctctccgctggggccctcgctggcgtccctgcaccctgggagcgcgagcggcgcgc





gggcggggaagcgcggcccagacccccgggtccgcccggagcagctgcgctgtcggg





gccaggccgggctcccagtggattcgcgggcacagacgcccaggaccgcgcttccca





cgtggcggagggactggggacccgggcacccgtcctgccccttcaccttccagctcc





gcctcctccgcgcggaccccgccccgtcccgacccctcccgggtccccggcccagcc





ccctccgggccctcccagcccctccccttcctttccgcggccccgccctctcctcgc





ggcgcgagtttcaggcagcgctgcgtcctgctgcgcacgtgggaagccctggccccg





gccacccccgcgatgccgcgcgctcctagctatcctcgaggatatcaagatctggcc





tcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


258
PL8
pGL4.10-
ggcctaactggccggtaccctggcaggaagcctactgagatttattgaaaaggaaac



94
murine
cgaattatcagggcactcgtttgcaacgccaacctgggctgtgttcggggcatgccc




BIRC5-
agcctgctgtctgcagtgtgaagctctttagaagccactgcaaccacaggccgcccg




FLUC
acaggaacagagacactgaaaacgggcccgcagcaaggcaggctcagcagccaacag





tcacacccaggaagcagtatttttcttctgctcctggactctcttgcggtgtatggc





tgcttccctttggtctgagccaggccgatggtctcagaaatagacacccattgactt





tcttttccagcgctgggacatacagaccccgcctccatcccagggtgtctataggaa





ggatggcggctgctgcagggaggagggtctcctgtcttcctaagggcgcccctccac





cagcctgtgggtgggtccgaggcacttccattccgatatctagctggccaaatcctg





caaaccttgaggcaggaagaacctgcagagcacatgggacttgcagcggacatgctt





taaagaggtgccccaggcccgtccaccgccctcggccaccctccgtgtcctctgggg





agcagctgcggaagattcgagtcagaatagcaagaaggaaccgcagcagaaggtaca





actcccagcatgccctgcgcccgccacgcccacaaggccaggcgcagatgggcgtgg





ggcgggactttcccggctcgcctcgcgccgtccactcccagaaggcagcgggcgagg





gcgtggggccggggctctcccggcatgctctgcggcgcgcctccgcccgcgcgattt





gaatcctgcgtttgagtcgtcttggcggaggttgtggtgacgcgctagcctcgagga





tatcaagatctggcctcggcggccaagcttggcaatccggtactgttggtaaagcca





CC


 


259
PL8
pGL4.10-
ggcctaactggccggtaccactcccagaaggcagcgggcgagggcgtggggccgggg



95
murine
ctctcccggcatgctctgcggcgcgcctccgcccgcgcgatttgaatcctgcgtttg




coreBIR
agtcgtcttggcggaggttgtggtgacgcgctagctattctagcctcgaggatatca




C5-
agatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc




FLUC



 


260
PL9
PL-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



88
FOSL1-
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




coreCEA
gtgactcatggtgatcatgctagcctcgaggatatcaagatcggtaccatgacccac




CAM5_2
gtgatgctgagaagtactcctgccctaggaagagactcagggcagagggaggaagga





cagcagaccagacagtcacagcagccttgacaaaacgttcctggaactaccggtgct





agcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggtactgt





tggtaaagccacc


 


261
PL9
PL-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



89
FOSL1-
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




coreFA
gtgactcatggtgatcatcgggaaaagttcagctgagagatataaaagagcagtctt




M111B_
tccagcacctgcaaatccagagcggcgggcactgacgggcacttgcaccgtgtggac




3
agactctccggttctgtgagtggtttttcttttcccgggtcggacctggagttctta





gggggatggctgaaccggtgctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


262
PL9
PL-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



90
FOSL1-
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




coreKIF2
gtgactcatggtgatcatgctagcctcgaggatatcaagatcggtaccggcccgccc




0A
cctttccttacgcggattggtagctgcaggcttccctatctgattggccgaacgaac





gcagcgcgtaatttaaaatattgtatctgtaacaaagctgcacctcgtgggcggagt





tgtgctctgcggctgcgaaagtccagcttcggcgactaggtgtgagtaagccagtat





cccaggaggagcaagtggcacgtcttcgggtgagtgtgcggctgtgctggagcccgg





gttaccagctcttaccggtgctagcctcgaggatatcaagatctggcctcggcggcc





aagcttggcaatccggtactgttggtaaagccacc


 


263
PL9
PL-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



91
FOSL1-
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




coreCST
gtgactcatggtgatcatgctagcctcgaggatatcaagatcggtaccagtggtggg




1
ggagtgaaaagagagatggagaaagaggggatgggcagaaagaggaggaggagtcag





gggcagggcatggaggtgggtggggctgggctgccaaagcaggataaatgcacacct





gcctgctggtctgggctccctgcctcgggctctcaccctcctctcctgcagctccag





ctttgtgctctaccggtgctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


264
PL9
PL-
ggcctaactggccggtaccactagtgtccccacccacacattcctgtccccacccac



92
Canscript-
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc




coreCEA
cacacattcctgtccccacccacacattcctgaccggtgctagcctcgaggatatca




CAM5_2
agatcggtaccatgacccacgtgatgctgagaagtactcctgccctaggaagagact





cagggcagagggaggaaggacagcagaccagacagtcacagcagccttgacaaaacg





ttcctggaactaccggtgctagcctcgaggatatcaagatctggcctcggcggccaa





gcttggcaatccggtactgttggtaaagccacc


 


265
PL9
PL-
ggcctaactggccggtaccactagtgtccccacccacacattcctgtccccacccac



93
Canscript-
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc




coreFA
cacacattcctgtccccacccacacattcctgcgggaaaagttcagctgagagatat




M111B_
aaaagagcagtctttccagcacctgcaaatccagagcggcgggcactgacgggcact




3
tgcaccgtgtggacagactctccggttctgtgagtggtttttcttttcccgggtcgg





acctggagttcttagggggatggctgaaccggtgctagcctcgaggatatcaagatc





tggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


266
PL9
PL-
ggcctaactggccggtaccactagtgtccccacccacacattcctgtccccacccac



94
Canscript-
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc




coreKIF2
cacacattcctgtccccacccacacattcctgcggcccgccccctttccttacgcgg




0A
attggtagctgcaggcttccctatctgattggccgaacgaacgcagcgcgtaattta





aaatattgtatctgtaacaaagctgcacctcgtgggcggagttgtgctctgcggctg





cgaaagtccagcttcggcgactaggtgtgagtaagccagtatcccaggaggagcaag





tggcacgtcttcgggtgagtgtgcggctgtgctggagcccgggttaccagctcttac





cggtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccg





gtactgttggtaaagccacc


 


267
PL9
PL-
ggcctaactggccggtaccactagtgtccccacccacacattcctgtccccacccac



95
Canscript-
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc




coreAGR
cacacattcctgtccccacccacacattcctgaccggtgctagcctcgaggatatca




2_2
agatcggtaccacctcttaacaatacgtttcacaaatagttaaaaacatgcatactg





aaaagcatacttttgcaatgttatttttaaaaacaaggaactctttaacccagggaa





gataatcacttggggaaaggaaggttcgtttctgagttagcaacaagtaaatgcagc





actagtgggtgggattgaggtgtgccctggtgcataaatagagactcagctgtgctg





gcacactcagaagcttggaccgcatcctagccgccgactcacacaaggcaggtgggt





gaggaaatccaggtaaggctcctgacagcagctttagaagggtacttgctggagtga





attcgggcctctgattaccggtgctagcctcgaggatatcaagatctggcctcggcg





gccaagcttggcaatccggtactgttggtaaagccacc


 


268
PL9
PL-
ggcctaactggccggtaccactagtgtccccacccacacattcctgtccccacccac



96
Canscript-
acattcctgtccccacccacacattcctgtccccacccacacattcctgtccccacc




coreCST
cacacattcctgtccccacccacacattcctgaccggtgctagcctcgaggatatca




1
agatcggtaccagtggtgggggagtgaaaagagagatggagaaagaggggatgggca





gaaagaggaggaggagtcaggggcagggcatggaggtgggtggggctgggctgccaa





agcaggataaatgcacacctgcctgctggtctgggctccctgcctcgggctctcacc





ctcctctcctgcagctccagctttgtgctctaccggtgctagcctcgaggatatcaa





gatctggcctcggcggccaagcttggcaatccggtactgttggtaaagccacc


 


269
PL9
PL-
ggcctaactggccggtaccactagtggtgactcatgggtgactcatgggtgactcat



99
FOSL1-
gggtgactcatgggtgactcatgggtgactcatgggtgactcatgggtgactcatgg




coreAGR
gtgactcatggtgatcatgctagcctcgaggatatcaagatcggtaccacctcttaa




2_2
caatacgtttcacaaatagttaaaaacatgcatactgaaaagcatacttttgcaatg





ttatttttaaaaacaaggaactctttaacccagggaagataatcacttggggaaagg





aaggttcgtttctgagttagcaacaagtaaatgcagcactagtgggtgggattgagg





tgtgccctggtgcataaatagagactcagctgtgctggcacactcagaagcttggac





cgcatcctagccgccgactcacacaaggcaggtgggtgaggaaatccaggtaaggct





cctgacagcagctttagaagggtacttgctggagtgaattcgggcctctgattaccg





gtgctagcctcgaggatatcaagatctggcctcggcggccaagcttggcaatccggt





actgttggtaaagccacc


 


271
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



30
5XFOSL
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




1-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




coreBIR
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




C5-
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct




FLUC
accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGTGACTCATGGGTGACTCATGGGTGACT





CATGGGTGACTCATGGGTGACTCATGtgcgctcccgacatgccccgcggcgcgccat





taaccgccagatttgagtcgcgggacccgttggcagaggtgggaattcaccggtcga





cgctagc


 


273
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



31
7XFOSL
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




1-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




coreBIR
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




C5-
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct




FLUC
accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGTGACTCATGGGTGACTCATGGGTGACT





CATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGtgcgctccc





gacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca





gaggtgggaattcaccggtcgacgctagc


 


274
NP1
NP-
TCTGTAGTTTGAGGAGAATATTTGTTATATTGCACAATAAAATAAGTTTGCAAGTTT



03
AFP3-
TTTTTTTCTGCCCCAAAGAGCTCTGTGTCCTTGAACATAAAATACAAATAACCGCTA




FLUC
TGCTGTTAATTATTAACAAATGTCCCATTTTCAACCTAAGGAAATACCATAAAGTAA





CAGATATACCAACAAAAGGTTAATAATTAACAGGCATTGCCTGAAAAGAGTATAAAA





GGCTTTCAGCATGATTTTCCATATTGTGCTTCCACCACTGCCAATAACAAAccggtc





gacgctagc


 


278
NP1
NP-AFP-
gcccctcccccgtgccttccttgaccctggaaggtgccactcccactgtcctttcct



02
FLUC
aataaaatgaggaaattgcatcgcattgtctgagtaggtgtcattctattctggggg





gtggggtggggcaggacagcaagggggaggattgggaagacaatagcaggcatgctg





gggatgcggtgggctctatggcccgggacggccgctagcccgcctaatgagcgggct





tttttttggcttgttgtccacaaccgttaaaccttaaaagctttaaaagccttatat





attcttttttttcttataaaacttaaaaccttagaggctatttaagttgctgattta





tattaattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagta





cgttagccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgag





agcttagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctg





atccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacat





cttgttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgt





atctaccttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagg





gcgtgcccttgggctccccgggcgcgaCTAGTCTCGAGTCTTGTGTGCCTGGCATAT





GATAGGCATTTAATAGTTTTAAAGAATTAATGTATTTAGATGAATTGCATACCAAAT





CTGCTGTCTTTTCTTTATGGCTTCATTAACTTAATTTGAGAGAAATTAATTATTCTG





CAACTTAGGGACAAGTCATCTCTTTGAATATTCTGTAGTTTGAGGAGAATATTTGTT





ATATTTGCAAAATAAAATAAGTTTGCAAGTTTTTTTTTTCTGCCCCAAAGAGCTCTG





TGTCCTTGAACATAAAATACAAATAACCGCTATGCTGTTAATTATTGGCAAATGTCC





CATTTTCAACCTAAGGAAATACCATAAAGTAACAGATATACCAACAAAAGGTTACTA





GTTAACAGGCATTGCCTGAAAAGAGTATAAAAGAATTTCAGCATGATTTTCCATATT





GTGCTTCCACCACTGCCAATAACAAAATAACTAGCAGAGCTAGCCtcgaggctagc


 


279
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



88
coreAGR
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




2-FLUC
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc





acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgAATGCATACTAGTaacatttctctggcctaactgg





ccggtacCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAA





AGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGAT





AATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACT





AGTGGGTGGGATTGAGGTqTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCA





CACTCAGAAGCTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAG





GAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATT





CGGGCCTCTGATTAccggtcgacgctagc


 


281
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



85
coreCEA
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




CAM5-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgAATGCATACTAGTaacatttctctggcctaactgg





ccggtaccatgACCCACGTGATGCTGAGAAGTACTCCTGCCCTAGGAAGAGACTCAG





GGCAGAGGGAGGAAGGACAGCAGACCAGACAGTCACAGCAGCCTTGACAAAACGTTC





CTGGAACTaccggtcgacgctagc


 


282
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



89
coreCST-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




FLUC
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc





acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgAATGCATACTAGTaacatttctctggcctaactgg





ccggtaccAGTGGTGGGGGAGTGAAAAGAGAGATGGAGAAAGAGGGGATGGGCAGAA





AGAGGAGGAGGAGTCAGGGGCAGGGCATGGAGGTGGGTGGGGCTGGGCTGCCAAAGC





AGGATAAATGCACACCTGCCTGCTGGTCTGGGCTCCCTGCCTCGGGCTCTCACCCTC





CTCTCCTGCAGCTCCAGCTTTGTGCTCTccggtcgacgctagc


 


283
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



86
coreFA
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




M111B-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgAATGCATACTAGTaacatttctctggcctaactgg





ccggtacCGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTG





CAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGG





TTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCT





Gaaccggtcgacgctagc


 


284
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



87
coreKIF2
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




0A-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcAATGCATACTAGTaacatttctctggcctaactggc





cggtacCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCT





GATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGC





ACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGT





GTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGG





CTGTGCTGGAGCCCGGGTTACCAGCTCTTAAccggtcgacgctagc


 


285
NP4
NP-
gagagcaactgcataaggctatgaagagatacgccctggttcctggaacaattgctt



00
CREB3L
ttacagatgcacatatcgaggtggacatcacttacgctgagtacttcgaaatgtccg




1_v6-
ttcggttggcagaagctatgaaacgatatgggctgaatacaaatcacagaatcgtcg




coreBIR
tatgcagtgaaaactctcttcaattctttatgccggtgttgggcgcgttatttatcg




C5-
gagttgcagttgcgcccgcgaacgacatttataatgaacgtgaattgctcaacagta




FLUC
tgggcatttcgcagcctaccgtggtgttcgtttccaaaaaggggttgcaaaaaattt





tgaacgtgcaaaaaaagctcccaatcatccaaaaaattattatcatggattctaaaa





cggattaccagggatttcagtcgatgtacacgttcgtcacatctcatctacctcccg





gttttaatgaatacgattttgtgccagagtccttcgatagggacaagacaattgcac





tgatcatgaactcctctggatctactggtctgcctaaaggtgtcgctctgcctcata





gaactgcctgcgtgagattctcgcatgccagagatcctatttttggcaatcaaatca





ttccggatactgcgattttaagtgttgttccattccatcacggttttggaatgttta





ctacactcggatatttgatatgtggatttcgagtcgtcttaatgtatagatttgaag





aagagctgtttctgaggagccttcaggattacaagattcaaagtgcgctgctggtgc





caaccctattctccttcttcgccaaaagcactctgattgacaaatacgatttatcta





atttacacgaaattgcttctggtggcgctcccctctctaaggaagtcggggaagcgg





ttgccaagaggttccatctgccaggtatcaggcaaggatatgggctcactgagacta





catcagctattctgattacacccgagggggatgataaaccgggcgcggtcggtaaag





ttgttccattttttgaagcgaaggttgtggatctggataccgggaaaacgctgggcg





ttaatcaaagaggcgaactgtgtgtgagaggtcctatgattatgtccggttatgtaa





acaatccggaagcgaccaacgccttgattgacaaggatggatggctacattctggag





acatagcttactgggacgaagacgaacacttcttcatcgttgaccgcctgaagtctc





tgattaagtacaaaggctatcaggtggctcccgctgaattggaatccatcttgctcc





aacaccccaacatcttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtg





aacttcccgccgccgttgttgttttggagcacggaaagacgatgacggaaaaagaga





tcgtggattacgtcgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttg





tgtttgtggacgaagtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatca





gagagatcctcataaaggccaagaagggcggaaagatcgccgtgtaatgaatgcatg





aattcctgtgccttctagttgccagccatctgttgtttgcccctcccccgtgccttc





cttgaccctggaaggtgccactcccactgtcctttcctaataaaatgaggaaattgc





atcgcattgtctgagtaggtgtcattctattctggggggtggggtggggcaggacag





caagggggaggattgggaagacaatagcaggcatgctggggatgcggtgggctctat





ggcccgggacggccgctagcccgcctaatgagcgggcttttttttggcttgttgtcc





acaaccgttaaaccttaaaagctttaaaagccttatatattcttttttttcttataa





aacttaaaaccttagaggctatttaagttgctgatttatattaattttattgttcaa





acatgagagcttagtacgtgaaacatgagagcttagtacgttagccatgagagctta





gtacgttagccatgagggtttagttcgttaaacatgagagcttagtacgttaaacat





gagagcttagtacgtactatcaacaggttgaactgctgatccacgttgtggtagaat





tggtaaagagagtcgtgtaaaatatcgagttcgcacatcttgttgtctgattattga





tttttggcgaaaccatttgatcatatgacaagatgtgtatctaccttaacttaatga





ttttgataaaaatcattaggtacggccgcggtgccagggcgtgcccttgggctcccc





gggcgcgaCTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCACATCGGCTATGCT





GCTGCTAATGCCACGTCACCACATCGACATGCCACGTCACCATCATGCCATGCCACG





TCACCACTGCAAGATGCCACGTCACCACAGTATAATGCCACGTCACCAAGTTACTAT





GCCACGTCACCAggtacctgcgctcccgacatgccccgcggcgcgccattaaccgcc





agatttgagtcgcgggacccgttggcagaggtggaccggtcgacgctagc


 


289
NP4
NP-
cgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttgt



03
E4AD-
tgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatcta




AFP3-
ccttaacttaatgattttgataaaaatcattaggtacCACTAGTTATTAATAGTAAT




FLUC
CAATTACGGGGTCATTAGTTCATAGCCCATATATGGAGTTCCGCGTTACATAACTTA





CGGTAAATGGCCCGCCTTGACCGCCCAACGACCCCCGCCCATTGACGTCAATAATGA





CGTATGTTCCCATAGTAACGCCAATAGGGACTTTCCATTGACGTCAATGGGTGGAGT





ATTTACGGTAAACTGCCCACTTGGCAGTACATCAAGTGTATCATATGCCAAGTACGC





CCCCTATTGACGTCAATGACGGTAAATGGCCCGCCTGGCATTATGCCCAGTACATGA





CCTTATGGGACTTTCCTACTTGGCAGTACATCTACGTATTAGTCATCGCTATTACCA





TGGTGATGCGGTTTTGGCAGTACATCAATGGGCGTGGATAGCGGTTTGACTCACGGG





GATTTCCAAGTCTCCACCCCATTGACGTCAATGGGAGTTTGTTTTGGCACCAAAATC





AACGGGACTTTCCAAAATGTCGTAACAACTCCGCCCCATGGATCTCAGATTGAATTA





TTTGCCTGTCATACAGCTAATAATTGACCATAAGACAATTAGATTTAAATTAGTTTT





GAATCTTTCTAATACCAAAGTTCAGTTTACTGTTCCATGTTGCTTCTGAGTGGCTTC





ACAGACTTATGAAAAAGTAAACGGAATCAGAATTACATCAATGCAAAAGCATTGCTG





TGAACTCTGTACTTAGGACTAAACTTTGAGCAATAACACATATAGATTGAGGATTGT





TTGCTGTTAGTATACAAACTCTGGTTCAAAGCTCCTCTTTATTGCTTGTCTTGGAAA





ATTTGCTGTTCTTCATGGTTTCTCTTTTCACTGCTATCTATTTTTCTCAACCACTCA





CATGGCTACAATAACTGTCTGCAAGCTTATGATTCCCAAATATCTATCTCTAGCCTC





AATCTTGTTCCAGAAGATAAAAAGTAGTATTCAAATGCACATCAACGTCTCCACTTG





GAGGGCTTAAAGACGTTTCAACATACAAACCGGGGAGTTTTGCCTGGAATGTTTCCT





AAAATGTGTCCTGTAGCACATAGGGTCCTCTTGTTCCTTAAAATCTAATTACTTTTA





GCCCAGTGCTCATCCCACCTATGGGGAGATGAGAGTGAAAAGGGAGCCTGATTAATA





ATTACACTAAGTCAATAGGCATAGAGCCAGGACTGTTTGGGTAAACTGGTCACTTTA





TCTTAAACTAAATATATCCAAAACTGAACATGTACTTAGTTACTAAGTCTTTGACTT





TATCTCATTCATACCACTCAGCTTTATCCAGGCCACTTATTTGACAGTATTATTGCG





AAAACTTCCTACTAGTGTCATCTCTTTGAATATTCTGTAGTTTGAGGAGAATATTTG





TTATATTGCACAATAAAATAAGTTTGCAAGTTTTTTTTTTCTGCCCCAAAGAGCTCT





GTGTCCTTGAACATAAAATACAAATAACCGCTATGCTGTTAATTATTAACAAATGTC





CCATTTTCAACCTAAGGAAATACCATAAAGTAACAGATATACCAACAAAAGGTTAAT





AATTAACAGGCATTGCCTGAAAAGAGTATAAAAGGCTTTCAGCATGATTTTCCATAT





TGTGCTTCCACCACTGCCAATAACAAAccggtcgacgctagc


 


290
NP3
NP-
actggtctgcctaaaggtgtcgctctgcctcatagaactgcctgcgtgagattctcg



71
EN7R-
catgccagagatcctatttttggcaatcaaatcattccggatactgcgattttaagt




FOS-
gttgttccattccatcacggttttggaatgtttactacactcggatatttgatatgt




coreBIR
ggatttcgagtcgtcttaatgtatagatttgaagaagagctgtttctgaggagcctt




C5-
caggattacaagattcaaagtgcgctgctggtgccaaccctattctccttcttcgcc




FLUC
aaaagcactctgattgacaaatacgatttatctaatttacacgaaattgcttctggt





ggcgctcccctctctaaggaagtcggggaagcggttgccaagaggttccatctgcca





ggtatcaggcaaggatatgggctcactgagactacatcagctattctgattacaccc





gagggggatgataaaccgggcgcggtcggtaaagttgttccattttttgaagcgaag





gttgtggatctggataccgggaaaacgctgggcgttaatcaaagaggcgaactgtgt





gtgagaggtcctatgattatgtccggttatgtaaacaatccggaagcgaccaacgcc





ttgattgacaaggatggatggctacattctggagacatagcttactgggacgaagac





gaacacttcttcatcgttgaccgcctgaagtctctgattaagtacaaaggctatcag





gtggctcccgctgaattggaatccatcttgctccaacaccccaacatcttcgacgca





ggtgtcgcaggtcttcccgacgatgacgccggtgaacttcccgccgccgttgttgtt





ttggagcacggaaagacgatgacggaaaaagagatcgtggattacgtcgccagtcaa





gtaacaaccgcgaaaaagttgcgcggaggagttgtgtttgtggacgaagtaccgaaa





ggtcttaccggaaaactcgacgcaagaaaaatcagagagatcctcataaaggccaag





aagggcggaaagatcgccgtgtaatgaatgcatgaattcctgtgccttctagttgcc





agccatctgttgtttgcccctcccccgtgccttccttgaccctggaaggtgccactc





ccactgtcctttcctaataaaatgaggaaattgcatcgcattgtctgagtaggtgtc





attctattctggggggtggggtggggcaggacagcaagggggaggattgggaagaca





atagcaggcatgctggggatgcggtgggctctatggcccgggacggccgctagcccg





cctaatgagcgggcttttttttggcttgttgtccacaaccgttaaaccttaaaagct





ttaaaagccttatatattcttttttttcttataaaacttaaaaccttagaggctatt





taagttgctgatttatattaattttattgttcaaacatgagagcttagtacgtgaaa





catgagagcttagtacgttagccatgagagcttagtacgttagccatgagggtttag





ttcgttaaacatgagagcttagtacgttaaacatgagagcttagtacgtactatcaa





caggttgaactgctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaat





atcgagttcgcacatcttgttgtctgattattgatttttggcgaaaccatttgatca





tatgacaagatgtgtatctaccttaacttaatgattttgataaaaatcattaggtac





ggccgcggtgccagggcgtgcccttgggctccccgggcgcgaCTAGTAACATTTCTC





TGGCCTAACTGGCCGGTACCTGCCACTCAAAGTGGCACACTCCCTGCTCAGGAGGCC





GGGAGGGAGGACACAGCCCTGGCAACTCCTCTGCCCCGGGGGGTCAGGAAGGGGTCA





CCCCACACTCCAGAACCCTACAGAATGTGGCCTTGGCTTTTCCCATCAAGAGCTGGG





GAAAGCCAGGCCCCGACTTCATTACCCCCTGCCCCCGTCCCATGCTCAGTGGGCCCC





ATCGTGGGTCCATGCCACACTCCCAACTGAGCAGCCCCGCAGCCCCGCGTGTCACAG





ACATGGGGCCTCCTAATTGCTGCTGAGGTCCCAATCCCTGGCTGGACGTGCCTGATG


 


291
NP3
NP-
GAAGAGCCAGCTCTGGTCTCAGGGGGCTGGTTTGCAGGAGTCTCCACAGACCTGGCT



69
EN18-
CCAGCTTTGTGTCTTCAAATGAATACCCGGCCAAGATTGCAACTAAATTACCAGAAA




Canscript-
CACTTAGGTTTCCTCACAGACTCCACAACAGGGATGGAGAAGGAAGTCAGCTGACGA




FLUC
GGTTACGACGCTGTTCGAGGGAGTCTTTCTTGGGTCACAAGTGGTAAACTGTGTTCC





CTGAACAAAACCAGGAAGCTTTCAGTGTTTATTGTATGTACTAAGTGGAGGGAGGGG





CTTCAGATTCTGATAAAAATATCTCCCCATTCCCAGTGCCCAATGTGACATGAATAG





GAGGGCCCCTCCCTGAATTCCCAAGCAGATCTCCAGAGACAGCTTCAGAGAGCAGGG





AGCCCACGGTGGCTGGGGCTTTAGGGACTTTCTGGGTTGTGGGGAGGCTAGAGGCTG





GGCAGTCCCAGCAGGATTTGGCCTCTAGGGACCGGGCACTGTAGGGCTCAGGAGAGC





AGCTGCCGTCCCAGTATATAAGCATAGGTGGAATTATCTGGAAACATATTTCTGCGT





TTCACAGGCAGAGAAATCAGTCTATCCCTAAAGAATGGAAGAGCTACAGTAGCAGAC





CTACCACCCTCCACCCTCCCACAGGCAAAAGCCCCTGAGATTCAGGTTTGGGAAGAA





AAAGAAAATATCCCAAATATGTCATTTGAGAAAGCAGCTGCTAACCACAGGCGGCCC





CAGCTTTTCTCAAGATCCAGGATGTGGGTTCAGTGCCCTTACTAGGGCAGTGGGGGA





GGACGGTCAGTACCAGGACCCCAGGCACAGGCCTGGAGGACTTGCTCCCCCAAGCAA





CTCAGATCCACGCAGAACCCATGGTACCACTAGTGGTGACTCATGGGTGACTCATGG





GTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGT





GACTCATGGGTGACTCATGtgcgctcccgacatgccccgcggcgcgccattaaccgc





cagatttgagtcgcgggacccgttggcagaggtggaccggtcgacgctagc





cgattttgtgccagagtccttcgatagggacaagacaattgcactgatcatgaactc





ctctggatctactggtctgcctaaaggtgtcgctctgcctcatagaactgcctgcgt





gagattctcgcatgccagagatcctatttttggcaatcaaatcattccggatactgc





gattttaagtgttgttccattccatcacggttttggaatgtttactacactcggata





tttgatatgtggatttcgagtcgtcttaatgtatagatttgaagaagagctgtttct





gaggagccttcaggattacaagattcaaagtgcgctgctggtgccaaccctattctc





cttcttcgccaaaagcactctgattgacaaatacgatttatctaatttacacgaaat





tgcttctggtggcgctcccctctctaaggaagtcggggaagcggttgccaagaggtt





ccatctgccaggtatcaggcaaggatatgggctcactgagactacatcagctattct





gattacacccgagggggatgataaaccgggcgcggtcggtaaagttgttccattttt





tgaagcgaaggttgtggatctggataccgggaaaacgctgggcgttaatcaaagagg





cgaactgtgtgtgagaggtcctatgattatgtccggttatgtaaacaatccggaagc





gaccaacgccttgattgacaaggatggatggctacattctggagacatagcttactg





ggacgaagacgaacacttcttcatcgttgaccgcctgaagtctctgattaagtacaa





aggctatcaggtggctcccgctgaattggaatccatcttgctccaacaccccaacat





cttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtgaacttcccgccgc





cgttgttgttttggagcacggaaagacgatgacggaaaaagagatcgtggattacgt





cgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttgtgtttgtggacga





agtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatcagagagatcctcat





aaaggccaagaagggcggaaagatcgccgtgtaatgaatgcatgaattcctgtgcct





tctagttgccagccatctgttgtttgcccctcccccgtgccttccttgaccctggaa





ggtgccactcccactgtcctttcctaataaaatgaggaaattgcatcgcattgtctg





agtaggtgtcattctattctggggggtggggtggggcaggacagcaagggggaggat





tgggaagacaatagcaggcatgctggggatgcggtgggctctatggcccgggacggc





cgctagcccgcctaatgagcgggcttttttttggcttgttgtccacaaccgttaaac





cttaaaagctttaaaagccttatatattcttttttttcttataaaacttaaaacctt





agaggctatttaagttgctgatttatattaattttattgttcaaacatgagagctta





gtacgtgaaacatgagagcttagtacgttagccatgagagcttagtacgttagccat





gagggtttagttcgttaaacatgagagcttagtacgttaaacatgagagcttagtac





gtactatcaacaggttgaactgctgatccacgttgtggtagaattggtaaagagagt





cgtgtaaaatatcgagttcgcacatcttgttgtctgattattgatttttggcgaaac





catttgatcatatgacaagatgtgtatctaccttaacttaatgattttgataaaaat





cattaggtacggccgcggtgccagggcgtgcccttgggctccccgggcgcgACTAGT





CTTCTGCCCTGAGAAAGACCTATGATTGCATGACACAAAAGAGACTGTTCAAAGGGA





CACCATCATTCAGCAGGGCAAGCCTCCTTGCTGGGGGCAACCTGGTAGCTCCTGAGC





CTCCCTCATCTTCACTGAGCCCCTCCAACTCTCTGAGTTCCCATGCCCCTCACTGAA





CCTCCCTTCCCCCATGGCGAGCCTCCGCCAGCACCTTTGCACACACTCAGCCCCTTC





CCCCTACTGAGCCCCAGCACAGTCACTGAACAGCTCTTCTTCCCCTCTGACTGAGTC





ATCCTCCCAAGCCCTCCCCTTCCCCTCACTGAGTCTCCACCACCCCTGGTCACTGGG





CACCCTGCTTCTGACCTCCTCCCTCCCCCAACCCCTCCACCCTTCCTCTTCACTGAG





CCTGGCGCCTCTCACCCACCCGCCTTCCTCTCCCAGCCGCTTCTGAGCTGCCTCTTT





GGAGCCCAACTGTCTCGCCCACGAGTCCCCATCACTCAGTCTCACTCACTCTAAGAC





ACCTGAAAGCAGTTAGAGAACATGTGTTCATGGGGGGAGGATGAGGCTCTATCATCA





TCCTGCAAACTAGTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTC





CCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCT





GTCCCCACCCACACATTCCTGAccggtcgacgctagc


 


292
NP3
NP-
cgattttgtgccagagtccttcgatagggacaagacaattgcactgatcatgaactc



70
EN19-
ctctggatctactggtctgcctaaaggtgtcgctctgcctcatagaactgcctgcgt




Canscript-
gagattctcgcatgccagagatcctatttttggcaatcaaatcattccggatactgc




FLUC
gattttaagtgttgttccattccatcacggttttggaatgtttactacactcggata





tttgatatgtggatttcgagtcgtcttaatgtatagatttgaagaagagctgtttct





gaggagccttcaggattacaagattcaaagtgcgctgctggtgccaaccctattctc





cttcttcgccaaaagcactctgattgacaaatacgatttatctaatttacacgaaat





tgcttctggtggcgctcccctctctaaggaagtcggggaagcggttgccaagaggtt





ccatctgccaggtatcaggcaaggatatgggctcactgagactacatcagctattct





gattacacccgagggggatgataaaccgggcgcggtcggtaaagttgttccattttt





tgaagcgaaggttgtggatctggataccgggaaaacgctgggcgttaatcaaagagg





cgaactgtgtgtgagaggtcctatgattatgtccggttatgtaaacaatccggaagc





gaccaacgccttgattgacaaggatggatggctacattctggagacatagcttactg





ggacgaagacgaacacttcttcatcgttgaccgcctgaagtctctgattaagtacaa





aggctatcaggtggctcccgctgaattggaatccatcttgctccaacaccccaacat





cttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtgaacttcccgccgc





cgttgttgttttggagcacggaaagacgatgacggaaaaagagatcgtggattacgt





cgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttgtgtttgtggacga





agtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatcagagagatcctcat





aaaggccaagaagggcggaaagatcgccgtgtaatgaatgcatgaattcctgtgcct





tctagttgccagccatctgttgtttgcccctcccccgtgccttccttgaccctggaa





ggtgccactcccactgtcctttcctaataaaatgaggaaattgcatcgcattgtctg





agtaggtgtcattctattctggggggtggggtggggcaggacagcaagggggaggat





tgggaagacaatagcaggcatgctggggatgcggtgggctctatggcccgggacggc





cgctagcccgcctaatgagcgggcttttttttggcttgttgtccacaaccgttaaac





cttaaaagctttaaaagccttatatattcttttttttcttataaaacttaaaacctt





agaggctatttaagttgctgatttatattaattttattgttcaaacatgagagctta





gtacgtgaaacatgagagcttagtacgttagccatgagagcttagtacgttagccat





gagggtttagttcgttaaacatgagagcttagtacgttaaacatgagagcttagtac





gtactatcaacaggttgaactgctgatccacgttgtggtagaattggtaaagagagt





cgtgtaaaatatcgagttcgcacatcttgttgtctgattattgatttttggcgaaac





catttgatcatatgacaagatgtgtatctaccttaacttaatgattttgataaaaat





cattaggtacggccgcggtgccagggcgtgcccttgggctccccgggcgcgACTAGT





GAACATACACACCTGTGGGGGTGTCTAAGGGGCTCCCAGGGAGTTCTGGGGGGTCCT





GGGGAGCAGGACCCTCTTCACTCCCTCCTCCAGGGGAAGTGGCCCTGGGGCACCCCA





GGCTGTTCCCCCAGCTCTGTGGGGCCGAAGCCATCCACAGGGGGCTTTCCCCACCGG





ATGTGGTGCGGGCCGTGGTTAATCTCACTTGAGTTAGTCACCCAGGACAAACAGCTA





ACCGACACAATTCCTCCCAAGTCCAGGGGGCCGGAGGCGGGGTCAGCACCTGGCGGC





AGGAGACAGTGCTGCCCTGGGATGTGGCCGGGCCTCCCTCCATTCCCAATCCTGTTG





TCTCTGTGGCAATACCTGGCTGGGAGCTCCTATCAGGCCCGTGACCCCCGCCCTTTC





TCCAGTGCCCTCCTGTCTGCATTCACCTGTCAGATCCCGgGGAGAGAGGGGCACTGG





CGGCCGCCCAGGACCAGAGCTGTGGGGCCTCCCGCACCAGAGTGCAGTGAAGGTTTG





TGGGCTGCTAGTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCC





CACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGT





CCCCACCCACACATTCCTGAccggtcgacgctagc


 


293
NP3
NP-
gagagcaactgcataaggctatgaagagatacgccctggttcctggaacaattgctt



99
ETV4-
ttacagatgcacatatcgaggtggacatcacttacgctgagtacttcgaaatgtccg




coreBIR
ttcggttggcagaagctatgaaacgatatgggctgaatacaaatcacagaatcgtcg




C5-
tatgcagtgaaaactctcttcaattctttatgccggtgttgggcgcgttatttatcg




FLUC
gagttgcagttgcgcccgcgaacgacatttataatgaacgtgaattgctcaacagta





tgggcatttcgcagcctaccgtggtgttcgtttccaaaaaggggttgcaaaaaattt





tgaacgtgcaaaaaaagctcccaatcatccaaaaaattattatcatggattctaaaa





cggattaccagggatttcagtcgatgtacacgttcgtcacatctcatctacctcccg





gttttaatgaatacgattttgtgccagagtccttcgatagggacaagacaattgcac





tgatcatgaactcctctggatctactggtctgcctaaaggtgtcgctctgcctcata





gaactgcctgcgtgagattctcgcatgccagagatcctatttttggcaatcaaatca





ttccggatactgcgattttaagtgttgttccattccatcacggttttggaatgttta





ctacactcggatatttgatatgtggatttcgagtcgtcttaatgtatagatttgaag





aagagctgtttctgaggagccttcaggattacaagattcaaagtgcgctgctggtgc





caaccctattctccttcttcgccaaaagcactctgattgacaaatacgatttatcta





atttacacgaaattgcttctggtggcgctcccctctctaaggaagtcggggaagcgg





ttgccaagaggttccatctgccaggtatcaggcaaggatatgggctcactgagacta





catcagctattctgattacacccgagggggatgataaaccgggcgcggtcggtaaag





ttgttccattttttgaagcgaaggttgtggatctggataccgggaaaacgctgggcg





ttaatcaaagaggcgaactgtgtgtgagaggtcctatgattatgtccggttatgtaa





acaatccggaagcgaccaacgccttgattgacaaggatggatggctacattctggag





acatagcttactgggacgaagacgaacacttcttcatcgttgaccgcctgaagtctc





tgattaagtacaaaggctatcaggtggctcccgctgaattggaatccatcttgctcc





aacaccccaacatcttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtg





aacttcccgccgccgttgttgttttggagcacggaaagacgatgacggaaaaagaga





tcgtggattacgtcgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttg





tgtttgtggacgaagtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatca





gagagatcctcataaaggccaagaagggcggaaagatcgccgtgtaatgaatgcatg





aattcctgtgccttctagttgccagccatctgttgtttgcccctcccccgtgccttc





cttgaccctggaaggtgccactcccactgtcctttcctaataaaatgaggaaattgc





atcgcattgtctgagtaggtgtcattctattctggggggtggggtggggcaggacag





caagggggaggattgggaagacaatagcaggcatgctggggatgcggtgggctctat





ggcccgggacggccgctagcccgcctaatgagcgggcttttttttggcttgttgtcc





acaaccgttaaaccttaaaagctttaaaagccttatatattcttttttttcttataa





aacttaaaaccttagaggctatttaagttgctgatttatattaattttattgttcAA





ACATGAGAGCTTAGTACGTGaaacatgagagcttagtacgtgaaacatgagagctta





gtacgttagccatgagagcttagtacgttagccatgagggtttagttcgttaaacat





gagagcttagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactg





ctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgca





catcttgttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatg





tgtatctaccttaacttaatgattttgataaaaatcattaggtacggccgcggtgcc





agggcgtgcccttgggctccccgggcgcgaCTAGTAACATTTCTCTGGCCTAACTGG





CCGGTACCACTAGTACCGGAAGTAAGAACCGGAAGTATCGACCGGAAGTAGACACCG





GAAGTACTAACCGGAAGTAACTACCGGAAGTATGCACCGGAAGTAtgcgctcccgac





atgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagag





gtggaccggtcgacgctagc


 


301
NP3
NP-FOS-
tcaaacatgagagcttagtacgtgaaaCATGAGAGCTTAGTACGTTAGCcatgagag



91
coreAGR
cttagtacgttagccatgagagcttagtacgttagccatgagggtttagttcgttaa




2-FLUC
acatgagagcttagtacgttaaacatgagagcttagtacgtactatcaacaggttga





actgctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagtt





cgcacatcttgttgtctgattattgatttttggcgaaaccatttgatcatatgacaa





gatgtgtatctaccttaacttaatgattttgataaaaatcattaggtacggccgcgg





tgccagggcgtgcccttgggctccccgggcgcgaATGCATACTAGTAACATTTCTCT





GGCCTAACTGGCCGGTACCGATCTTGATATCCTCGAGGCTAGCATGATCACCATGAG





TCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTC





ACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGTACCACCTCTTAA





CAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATG





TTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGG





AAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGG





TgTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTGGAC





CGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCT





CCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATTAccg





gtcgacgctagc


 


302
NP4
NP-FOS-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



04
coreCEA
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




CAM-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgAATGCATaCTAGTGGTGACTCATGGGTGACTCATG





GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGG





TGACTCATGGGTGACTCATGGTGATCATGCTAGCCTCGAGGATATCAAGATCGGTAC





CATGACCCACGTGATGCTGAGAAGTACTCCTGCCCTAGGAAGAGACTCAGGGCAGAG





GGAGGAAGGACAGCAGACCAGACAGTCACAGCAGCCTTGACAAAACGTTCCTGGAAC





Taccggtcgacgctagc


 


303
NP3
NP-FOS-
aattttattgttcaaacatgagagcttagtacgtgaaaCATGAGAGCTTAGTACGTT



92
coreCST-
AGCcatgagagcttagtacgttagccatgagagcttagtacgttagccatgagggtt




FLUC
tagttcgttaaacatgagagcttagtacgttaaacatgagagcttagtacgtactat





caacaggttgaactgctgatccacgttgtggtagaattggtaaagagagtcgtgtaa





aatatcgagttcgcacatcttgttgtctgattattgatttttggcgaaaccatttga





tcatatgacaagatgtgtatctaccttaacttaatgattttgataaaaatcattagg





tacggccgcggtgccagggcgtgcccttgggctccccgggcgcgAATGCATACTAGT





AACATTTCTCTGGCCTAACTGGCCGGTACCGATCTTGATATCCTCGAGGCTAGCATG





ATCACCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTC





ACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGTA





CCAGTGGTGGGGGAGTGAAAAGAGAGATGGAGAAAGAGGGGATGGGCAGAAAGAGGA





GGAGGAGTCAGGGGCAGGGCATGGAGGTGGGTGGGGCTGGGCTGCCAAAGCAGGATA





AATGCACACCTGCCTGCTGGTCTGGGCTCCCTGCCTCGGGCTCTCACCCTCCTCTCC





TGCAGCTCCAGCTTTGTGCTCTaccggtcgacgctagc


 


304
NP3
NP-FOS-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



90
coreFA
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




M111B-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTAACATTTCTCTGGCCTAACTGGCCGGTAC





CACTAGTGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC





TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGTGATCAT





GCTAGCCTCGAGGATATCAAGATCGGTACCGGGAAAAGTTCAGCTGAGAGATATAAA





AGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGC





ACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACC





TGGAGTTCTTAGGGGGATGGCTGaaccggtcgacgctagc


 


305
NP4
NP-FOS-
ataccgggaaaacgctgggcgttaatcaaagaggcgaactgtgtgtgagaggtccta



05
coreKIF-
tgattatgtccggttatgtaaacaatccggaagcgaccaacgccttgattgacaagg




FLUC
atggatggctacattctggagacatagcttactgggacgaagacgaacacttcttca





tcgttgaccgcctgaagtctctgattaagtacaaaggctatcaggtggctcccgctg





aattggaatccatcttgctccaacaccccaacatcttcgacgcaggtgtcgcaggtc





ttcccgacgatgacgccggtgaacttcccgccgccgttgttgttttggagcacggaa





agacgatgacggaaaaagagatcgtggattacgtcgccagtcaagtaacaaccgcga





aaaagttgcgcggaggagttgtgtttgtggacgaagtaccgaaaggtcttaccggaa





aactcgacgcaagaaaaatcagagagatcctcataaaggccaagaagggcggaaaga





tcgccgtgtaatgaatgcatgaattcctgtgccttctagttgccagccatctgttgt





ttgcccctcccccgtgccttccttgaccctggaaggtgccactcccactgtcctttc





ctaataaaatgaggaaattgcatcgcattgtctgagtaggtgtcattctattctggg





gggtggggtggggcaggacagcaagggggaggattgggaagacaatagcaggcatgc





tggggatgcggtgggctctatggcccgggacggccgctagcccgcctaatgagcggg





cttttttttggcttgttgtccacaaccgttaaaccttaaaagctttaaaagccttat





atattcttttttttcttataaaacttaaaaccttagaggctatttaagttgctgatt





tatattaattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttag





tacgttagccatgagagcttagtacgttagccatgagggtttagttcgttaaacatg





agagcttagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgc





tgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcac





atcttgttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgt





gtatctaccttaacttaatgattttgataaaaatcattaggtacggccgcggtgcca





gggcgtgcccttgggctccccgggcgcgAATGCATaCTAGTGGTGACTCATGGGTGA





CTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACT





CATGGGTGACTCATGGGTGACTCATGGTGATCATGCTAGCCTCGAGGATATCAAGAT





CGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCT





GATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGC





ACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGT





GTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGG





CTGTGCTGGAGCCCGGGTTACCAGCTCTTccggtcgacgctagc


 


310
NP4
NP-FOS-
cttataaaacttaaaaccttagaggctatttaagttgctgatttatattaattttat



64
FOS-
tgttcaaacatgagagcttagtacgtgaaaCATGAGAGCTTAGTACGTTAGCcatga




coreAGR
gagcttagtacgttagccatgagagcttagtacgttagccatgagggtttagttcgt




2-FLUC
taaacatgagagcttagtacgttaaacatgagagcttagtacgtactatcaacaggt





tgaactgctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcga





gttcgcacatcttgttgtctgattattgatttttggcgaaaccatttgatcatatga





caagatgtgtatctaccttaacttaatgattttgataaaaatcattaggtacggccg





cggtgccagggcgtgcccttgggctccccgggcgcgaATGCATACTAGTAACATTTC





TCTGGCCTAACTGGCCGGTACCGATCTTGATATCCTCGAGGCTAGCATGATCACCAT





GAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGA





GTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGTACCGATTCT





TGATATCCTCGAGGCTAGCATGATCACCATGAGTCACCCATGAGTCACCCATGAGTC





ACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCAC





CCATGAGTCACCACTAGTGGTACCACCTCTTAACAATACGTTTCACAAATAGTTAAA





AACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCT





TTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAAC





AAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAGA





CTCAGCTGTGCTGGCACACTCAGAAGCTTGGACCGCATCCTAGCCGCCGACTCACAC





AAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTA





CTTGCTGGAGTGAATTCGGGCCTCTGATTAccggtcgacgctagc


 


311
NP4
NP-FOS-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



06
FOS-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreCEA
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




CAM-
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




FLUC
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgAATGCATaCTAGTAACATTTCTCTGGCCTAACTGG





CCGGTACCACTAGTGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCAT





GGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGG





TGATCATGCTAGCCTCGAGGATATCAAGATCGGTACCACTAGTGGTGACTCATGGGT





GACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGA





CTCATGGGTGACTCATGGGTGACTCATGGTGATCATGCTAGCCTCGAGGATATCAAG





ATCGGTACCATGACCCACGTGATGCTGAGAAGTACTCCTGCCCTAGGAAGAGACTCA





GGGCAGAGGGAGGAAGGACAGCAGACCAGACAGTCACAGCAGCCTTGACAAAACGTT





CCTGGAACTaccggtcgacgctagc


 


312
NP4
NP-FOS-
cttataaaacttaaaaccttagaggctatttaagttgctgatttatattaattttat



63
FOS-
tgttcaaacatgagagcttagtacgtgaaaCATGAGAGCTTAGTACGTTAGCcatga




FOS-
gagcttagtacgttagccatgagagcttagtacgttagccatgagggtttagttcgt




coreAGR
taaacatgagagcttagtacgttaaacatgagagcttagtacgtactatcaacaggt




2-FLUC
tgaactgctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcga





gttcgcacatcttgttgtctgattattgatttttggcgaaaccatttgatcatatga





caagatgtgtatctaccttaacttaatgattttgataaaaatcattaggtacggccg





cggtgccagggcgtgcccttgggctccccgggcgcgaATGCATACTAGTAACATTTC





TCTGGCCTAACTGGCCGGTACCGATCTTGATATCCTCGAGGCTAGCATGATCACCAT





GAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGTACCGATC





TTGATATCCTCGAGGCTAGCATGATCACCATGAGTCACCCATGAGTCACCCATGAGT





CACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCA





CCCATGAGTCACCACTAGTGGTACCGATTCTTGATATCCTCGAGGCTAGCATGATCA





CCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCC





ATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGTACCAC





CTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTT





TGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGG





GGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGG





ATTGAGGTgTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAG





CTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGG





TAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTG





ATTAccggtcgacgctagc


 


315
NP4
NP-FOS-
ctgggacgaagacgaacacttcttcatcgttgaccgcctgaagtctctgattaagta



59
TATA-
caaaggctatcaggtggctcccgctgaattggaatccatcttgctccaacaccccaa




TSS-
catcttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtgaacttcccgc




FLUC-
cgccgttgttgttttggagcacggaaagacgatgacggaaaaagagatcgtggatta




3′OIPR
cgtcgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttgtgtttgtgga





cgaagtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatcagagagatcct





cataaaggccaagaagggcggaaagatcgccgtgtaatgaattgggATCTTCacaca





gcagGTaaggttgcGGGCCGGGCCTGGGCCGGGTCCGGGCCGGGgcccgcctaatga





gcgggcttttttttggcttgttgtccacaaccgttaaaccttaaaagctttaaaagc





cttatatattcttttttttcttataaaacttaaaaccttagaggctatttaagttgc





tgatttatattaattttattgttcaaacatgagagcttagtacgtgaaacatgagag





cttagtacgttagccatgagagcttagtacgttagccatgagggtttagttcgttaa





acatgagagcttagtacgttaaacatgagagcttagtacgtactatcaacaggttga





actgctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagtt





cgcacatcttgttgtctgattattgatttttggcgaaaccatttgatcatatgacaa





gatgtgtatctaccttaacttaatgattttgataaaaatcattaccgcaCTGACccc





tggtgttgcTTTTTTTTTTTAGgccgcaagCTGAAGcgtgtccctgtgccttctagt





tgccagccatctgttgtttgcccctcccccgtgccttccttgaccctggaaggtgcc





actcccactgtcctttcctaataaaatgaggaaattgcatcgcattgtctgagtagg





tgtcattctattctggggggtggggtggggcaggacagcaagggggaggattgggaa





gacaatagcaggcatgctggggatgcggtgggctctatggggtaccatgcatactag





tGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGG





GTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGCGGTGCTAGCTATA





AAAGGCCAGCAGCAGCCTGACCACATCTCATCCTCctcgaggatatcaagatctggc





ctcggcggccagaattcaccggtcacc


 


318
NP3
NP-
ggccgctagcccgcctaatgagcgggcttttttttggcttgttgtccacaaccgtta



14
FOSL1-
aaccttaaaagctttaaaagccttatatattcttttttttcttataaaacttaaaac




Canscript-
cttagaggctatttaagttgctgatttatattaattttattgttcaaacatgagagc




coreBIR
ttagtacgtgaaacatgagagcttagtacgttagccatgagagcttagtacgttagc




C5-
catgagggtttagttcgttaaacatgagagcttagtacgttaaacatgagagcttag




FLUC
tacgtactatcaacaggttgaactgctgatccacgttgtggtagaattggtaaagag





agtcgtgtaaaatatcgagttcgcacatcttgttgtctgattattgatttttggcga





aaccatttgatcatatgacaagatgtgtatctaccttaacttaatgattttgataaa





aatcattaggtacCACTAGTGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTG





ACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGACTAGT





GTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATT





CCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACAC





ATTCCTGtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtc





gcgggacccgttggcagaggtgggctagcctcgaggatatcaagatctggcctcggc





ggccaagcttgctagc


 


319
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



08
FOSL1-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreBIR
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




C5-
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




FLUC
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGTGACTCATGGGTGACTCATGGGTGACT





CATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCA





TGGGTGACTCATGtgcgctcccgacatgccccgcggcgcgccattaaccgccagatt





tgagtcgcgggacccgttggcagaggtggaccggtcgacgctagc


 


324
NP3
NP-
gacggccgctagcccgcctaatgagcgggcttttttttggcttgttgtccacaaccg



34
FOSL1-
ttaaaccttaaaagctttaaaagccttatatattcttttttttcttataaaacttaa




High-
aaccttagaggctatttaagttgctgatttatattaattttattgttcAAACATGAG




FLUC
AGCTTAGTACGTGaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt





agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct





tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc





acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGTGACTCATGGGTGACTCATGGGTGACT





CATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCA





TGGGTGACTCATGcatGGGGGGGGGtgATGACACAGCAATtcGGGACTTTCCacGCT





TGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGG





GACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacaAcgcGtcc





cgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggc





agaggtgggaattcaccggtcgacgctagc


 


325
NP3
NP-
tttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgttagc



32
FOSL1-
catgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagcttag




Low-
tacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatccacg




FLUC
ttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttgttg





tctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatctacc





ttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgtgcc





cttgggctccccgggcgcgaCTAGTGGTGACTCATGGGTGACTCATGGGTGACTCAT





GGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGG





GTGACTCATGcatACCGGAAGTacTTGCGCAAtgACCGGAAGTacaAcgcGtcccga





catgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcaga





ggtgggaattcaccggtcgacgctagc


 


326
NP3
NP-
taattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgt



33
FOSL1-
tagccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagc




Med-
ttagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatc




FLUC
cacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatctt





gttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatc





taccttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcg





tgcccttgggctccccgggcgcgaCTAGTGGTGACTCATGGGTGACTCATGGGTGAC





TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTC





ATGGGTGACTCATGcatTTGCGCAAcaGGGGGGGGGtgATGACACAGCAATtcGCTT





GCGTGAGAAGagACCGGAAGTgaGGGACTTTCCacATGACACAGCAATacaAcgcGt





cccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg





gcagaggtgggaattcaccggtcgacgctagc


 


328
NP3
NP-
gcccgcctaatgagcgggcttttttttggcttgttgtccacaaccgttaaaccttaa



15
FOSL1-
aagctttaaaagccttatatattcttttttttcttataaaacttaaaaccttagagg




TATA-
ctatttaagttgctgatttatattaattttattgttcaaacatgagagcttagtacg




TSS-
tgaaacatgagagcttagtacgttagccatgagagcttagtacgttagccatgaggg




FLUC
tttagttcgttaaacatgagagcttagtacgttaaacatgagagcttagtacgtact





atcaacaggttgaactgctgatccacgttgtggtagaattggtaaagagagtcgtgt





aaaatatcgagttcgcacatcttgttgtctgattattgatttttggcgaaaccattt





gatcatatgacaagatgtgtatctaccttaacttaatgattttgataaaaatcatta





ggtacCACTAGTGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGG





GTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGCGG





TGCTAGCTATAAAAGGCCAGCAGCAGCCTGACCACATCTCATCCTCctcgaggatat





caagatctggcctcggcggccaagcttgctagc


 


329
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



96
HIGH-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreAGR
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




2-FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGGGGGGGGtgATGACACAGCAATtcGGG





ACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATtcGCTTGC





GTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAA





TacagtacCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAA





AAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGA





TAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCAC





TAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGC





ACACTCAGAAGCTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGA





GGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAAT





TCGGGCCTCTGATTAccggtcgacgctagc


 


330
NP3
NP-
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACC



35
HIGH-
GGAAGTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCG




coreBIR
GGGttGGGACTTTCCacATGACACAGCAATacaAcgcGtcccgacatgccccgcggc




C5-
gcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtgggaattcac




FLUC
cggtcgacgctagc


 


331
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



93
HIGH-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreCEA
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




CAM-
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




FLUC
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGGGGGGGGtgATGACACAGCAATtcGGG





ACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATtcGCTTGC





GTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAA





TacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCATGACCCACGTGATGCTG





AGAAGTACTCCTGCCCTAGGAAGAGACTCAGGGCAGAGGGAGGAAGGACAGCAGACC





AGACAGTCACAGCAGCCTTGACAAAACGTTCCTGGAACtaccggtcgacgctagc


 


332
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



97
HIGH-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreCST-
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




FLUC
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg





ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGGGGGGGGtgATGACACAGCAATtcGGG





ACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATtcGCTTGC





GTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAA





TacactagtaacatttctctggcctaactggccggtaccAGTGGTGGGGGAGTGAAA





AGAGAGATGGAGAAAGAGGGGATGGGCAGAAAGAGGAGGAGGAGTCAGGGGCAGGGC





ATGGAGGTGGGTGGGGCTGGGCTGCCAAAGCAGGATAAATGCACACCTGCCTGCTGG





TCTGGGCTCCCTGCCTCGGGCTCTCACCCTCCTCTCCTGCAGCTCCAGCTTTGTGCT





CTaccggtcgacgctagc


 


333
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



94
HIGH-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreFA
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




M111B-
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




FLUC
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGGGGGGGGtgATGACACAGCAATtcGGG





ACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATtcGCTTGC





GTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAA





TacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCGGGAAAAGTTCAGCTGAG





AGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACG





GGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCG





GGTCGGACCTGGAGTTCTTAGGGGGATGGCTGAaccggtcgacgctagc


 


334
NP4
NP-
AGgccgcaagCTGAAGcgtgtccctgtgccttctagttgccagccatctgttgtttg



65
High-
cccctcccccgtgccttccttgaccctggaaggtgccactcccactgtcctttccta




coreFA
ataaaatgaggaaattgcatcgcattgtctgagtaggtgtcattctattctgggggg




M111B-
tggggtggggcaggacagcaagggggaggattgggaagacaatagcaggcatgctgg




FLUC-
ggatgcggtgggctctatggggtaccatgcataCTAGTGGGGCGGGGtgATGACACA




3′OIPR
GCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCA





ATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGttGGGACTTTCCacAT





GACACAGCAATacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCGGGAAAAG





TTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCG





GGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTT





TCTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTGAagaattcaccggtc





acc


 


335
NP3
NP-
aattttattgttcaaacatgagagcttagtacgtgaaacatgagagcttagtacgtt



95
HIGH-
agccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagct




coreKIF2
tagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatcc




0A-
acgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatcttg




FLUC
ttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatct





accttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcgt





gcccttgggctccccgggcgcgaCTAGTGGGGGGGGGtgATGACACAGCAATtcGGG





ACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATtcGCTTGC





GTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAA





TacactagtaacatttctctggcctaactggccggtacCGGCCCGCCCCCTTTCCTT





ACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGT





AATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTG





CGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGG





AGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGC





TCTTAaccggtcgacgctagc


 


342
NP4
NP-
gagagcaactgcataaggctatgaagagatacgccctggttcctggaacaattgctt



01
HOXA1_
ttacagatgcacatatcgaggtggacatcacttacgctgagtacttcgaaatgtccg




v8-
ttcggttggcagaagctatgaaacgatatgggctgaatacaaatcacagaatcgtcg




coreBIR
tatgcagtgaaaactctcttcaattctttatgccggtgttgggcgcgttatttatcg




C5-
gagttgcagttgcgcccgcgaacgacatttataatgaacgtgaattgctcaacagta




FLUC
tgggcatttcgcagcctaccgtggtgttcgtttccaaaaaggggttgcaaaaaattt





tgaacgtgcaaaaaaagctcccaatcatccaaaaaattattatcatggattctaaaa





cggattaccagggatttcagtcgatgtacacgttcgtcacatctcatctacctcccg





gttttaatgaatacgattttgtgccagagtccttcgatagggacaagacaattgcac





tgatcatgaactcctctggatctactggtctgcctaaaggtgtcgctctgcctcata





gaactgcctgcgtgagattctcgcatgccagagatcctatttttggcaatcaaatca





ttccggatactgcgattttaagtgttgttccattccatcacggttttggaatgttta





ctacactcggatatttgatatgtggatttcgagtcgtcttaatgtatagatttgaag





aagagctgtttctgaggagccttcaggattacaagattcaaagtgcgctgctggtgc





caaccctattctccttcttcgccaaaagcactctgattgacaaatacgatttatcta





atttacacgaaattgcttctggtggcgctcccctctctaaggaagtcggggaagcgg





ttgccaagaggttccatctgccaggtatcaggcaaggatatgggctcactgagacta





catcagctattctgattacacccgagggggatgataaaccgggcgcggtcggtaaag





ttgttccattttttgaagcgaaggttgtggatctggataccgggaaaacgctgggcg





ttaatcaaagaggcgaactgtgtgtgagaggtcctatgattatgtccggttatgtaa





acaatccggaagcgaccaacgccttgattgacaaggatggatggctacattctggag





acatagcttactgggacgaagacgaacacttcttcatcgttgaccgcctgaagtctc





tgattaagtacaaaggctatcaggtggctcccgctgaattggaatccatcttgctcc





aacaccccaacatcttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtg





aacttcccgccgccgttgttgttttggagcacggaaagacgatgacggaaaaagaga





tcgtggattacgtcgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttg





tgtttgtggacgaagtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatca





gagagatcctcataaaggccaagaagggcggaaagatcgccgtgtaatgaatgcatg





aattcctgtgccttctagttgccagccatctgttgtttgcccctcccccgtgccttc





cttgaccctggaaggtgccactcccactgtcctttcctaataaaatgaggaaattgc





atcgcattgtctgagtaggtgtcattctattctggggggtggggtggggcaggacag





caagggggaggattgggaagacaatagcaggcatgctggggatgcggtgggctctat





ggcccgggacggccgctagcccgcctaatgagcgggcttttttttggcttgttgtcc





acaaccgttaaaccttaaaagctttaaaagccttatatattcttttttttcttataa





aacttaaaaccttagaggctatttaagttgctgatttatattaattttattgttcAA





ACATGAGAGCTTAGTACGTGaaacatgagagcttagtacgtgaaacatgagagctta





gtacgttagccatgagagcttagtacgttagccatgagggtttagttcgttaaacat





gagagcttagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactg





ctgatccacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgca





catcttgttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatg





tgtatctaccttaacttaatgattttgataaaaatcattaggtacggccgcggtgcc





agggcgtgcccttgggctccccgggcgcgaCTAGTAACATTTCTCTGGCCTAACTGG





CCggtaccCGATGTAGCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTA





TACGTCGCCTAAATCGAGATGCTGTACTGATCTATAAGGATCGGTAATGACGTAATG





ACGTAATGACGTAATGACGTAATGACGTAATGAcggtacctgcgctcccgacatgcc





ccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtgga





ccggtcgacgctagc


 


343
NP4
NP-
aactgcataaggctatgaagagatacgccctggttcctggaacaattgcttttacag



02
HOXC10_
atgcacatatcgaggtggacatcacttacgctgagtacttcgaaatgtccgttcggt




v24-
tggcagaagctatgaaacgatatgggctgaatacaaatcacagaatcgtcgtatgca




coreBIR
gtgaaaactctcttcaattctttatgccggtgttgggcgcgttatttatcggagttg




C5-
cagttgcgcccgcgaacgacatttataatgaacgtgaattgctcaacagtatgggca




FLUC
tttcgcagcctaccgtggtgttcgtttccaaaaaggggttgcaaaaaattttgaacg





tgcaaaaaaagctcccaatcatccaaaaaattattatcatggattctaaaacggatt





accagggatttcagtcgatgtacacgttcgtcacatctcatctacctcccggtttta





atgaatacgattttgtgccagagtccttcgatagggacaagacaattgcactgatca





tgaactcctctggatctactggtctgcctaaaggtgtcgctctgcctcatagaactg





cctgcgtgagattctcgcatgccagagatcctatttttggcaatcaaatcattccgg





atactgcgattttaagtgttgttccattccatcacggttttggaatgtttactacac





tcggatatttgatatgtggatttcgagtcgtcttaatgtatagatttgaagaagagc





tgtttctgaggagccttcaggattacaagattcaaagtgcgctgctggtgccaaccc





tattctccttcttcgccaaaagcactctgattgacaaatacgatttatctaatttac





acgaaattgcttctggtggcgctcccctctctaaggaagtcggggaagcggttgcca





agaggttccatctgccaggtatcaggcaaggatatgggctcactgagactacatcag





ctattctgattacacccgagggggatgataaaccgggcgcggtcggtaaagttgttc





cattttttgaagcgaaggttgtggatctggataccgggaaaacgctgggcgttaatc





aaagaggcgaactgtgtgtgagaggtcctatgattatgtccggttatgtaaacaatc





cggaagcgaccaacgccttgattgacaaggatggatggctacattctggagacatag





cttactgggacgaagacgaacacttcttcatcgttgaccgcctgaagtctctgatta





agtacaaaggctatcaggtggctcccgctgaattggaatccatcttgctccaacacc





ccaacatcttcgacgcaggtgtcgcaggtcttcccgacgatgacgccggtgaacttc





ccgccgccgttgttgttttggagcacggaaagacgatgacggaaaaagagatcgtgg





attacgtcgccagtcaagtaacaaccgcgaaaaagttgcgcggaggagttgtgtttg





tggacgaagtaccgaaaggtcttaccggaaaactcgacgcaagaaaaatcagagaga





tcctcataaaggccaagaagggcggaaagatcgccgtgtaatgaatgcatgaattcc





tgtgccttctagttgccagccatctgttgtttgcccctcccccgtgccttccttgac





cctggaaggtgccactcccactgtcctttcctaataaaatgaggaaattgcatcgca





ttgtctgagtaggtgtcattctattctggggggtggggtggggcaggacagcaaggg





ggaggattgggaagacaatagcaggcatgctggggatgcggtgggctctatggcccg





ggacggccgctagcccgcctaatgagcgggcttttttttggcttgttgtccacaacc





gttaaaccttaaaagctttaaaagccttatatattcttttttttcttataaaactta





aaaccttagaggctatttaagttgctgatttatattaattttattgttcaaacatga





gagcttagtacgtgaaaCATGAGAGCTTAGTACGTTAGCcatgagagcttagtacgt





tagccatgagagcttagtacgttagccatgagggtttagttcgttaaacatgagagc





ttagtacgttaaacatgagagcttagtacgtactatcaacaggttgaactgctgatc





cacgttgtggtagaattggtaaagagagtcgtgtaaaatatcgagttcgcacatctt





gttgtctgattattgatttttggcgaaaccatttgatcatatgacaagatgtgtatc





taccttaacttaatgattttgataaaaatcattaggtacggccgcggtgccagggcg





tgcccttgggctccccgggcgcgaCTAGTAACATTTCTCTGGCCTAACTGGCCggta





ccAGCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTATACGTCGCCTAA





ATCGAGATGCTGTACTGATCTATAAGTCGTAAACTGTCGTAAACTGTCGTAAACTGT





CGTAAACTGTCGTAAACTGTCGTAAACTggtacctgcgctcccgacatgccccgcgg





cgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtggaccggtc





gacgctagc
















TABLE 1B







Sequences of Synthetic Response Elements (SREs) according to the disclosure









SEQ




ID




NO:
Name
Sequence





377
SRE001
Cggagtactgtcctccgagcggagtactgtcctccgagcggagtactgtcctccgagcgga




gtactgtcctccgagcggagtactgtcctccgag


 


378
SRE002
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC




TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATG


 


379
SRE003
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGG




ACTTTCCacATGACACAGCAATac


 


380
SRE004
AATAGGTACCACTAGTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCC




CACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCC




ACCCACACATTCCTGACCGGTGctagcctcgag


 


381
SRE005
CTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTTTGATGTACGCAACTCCT




TTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGT




CCGTAAATCCTTTGATGTGACgatcttgatatc


 


382
SRE006
TACCTGATCAAACATGCCCGGACATGTCGTAAGACATAAACATGCCCGGACATGTCCTCGC




AATCTAACATGCCCGGACATGTCCTCGCAATCTAACATGCCCGGACATGTCTGCAAGCTAC




AACATGCCCGGACATGTC


 


383
SRE007
GGGGGGGGGTGATGACACAGCAATTCGGGACTTTCCACGCTTGCGTGAGAAGAGACCGGAA




GTGAATGACACAGCAAT


 


384
SRE008
GCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGC




AATac


 


385
SRE009
GGTGACTCATGGGTGACTCATGGGTGACTCATGCTaCgTgTgAcGGTGACTCATGGGTGAC




TCATGGGTGACTCATGaagTcgcaGattGGTGACTCATGGGTGACTCATGGGTGACTCATG


 


386
SRE010
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGACGTGTGACATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




G


 


387
SRE011
GGGAGGAAGTCGTAAAACTTGGGAGGAAGTCGTAAAAAATGGGAGGAAGTCGTAAAATGCG




GGAGGAAGTCGTAAAAGAAGGGAGGAAGTCGTAAAAATCGGGAGGAAGTCGTAAAA


 


388
SRE012
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTA


 


389
SRE013
ACATCAAAGGATTTACGGACATCAAAGGATGTACCTACATCAAAGGAATCCTTAACATCAA




AGGACGCATAGACATCAAAGGAGTTGCGTACATCAAAGGA


 


390
SRE014
CACTTCCGGTTTACTTCCACTTCCGGTTTACTAGCACTTCCGGTTTACGCTCACTTCCGGT




TTACGATCACTTCCGGTTTACAGACACTTCCGGTTTAC


 


391
SRE015
GCGTCCGCCCGAGTCCCCGCCTCGCCGCCAACGCCAAtgcTcatGCGTCCGCCCGAGTCCC




CGCCTCGCCGCCAACGCCAtcatgcctGCGTCCGCCCGAGTCCCCGCCTCGCCGCCAACGC




CA


 


392
SRE016
CAACATGGCGGCGCCCAACATGGCGGCTACCAACATGGCGGCCTCCAACATGGCGGCAGGC




AACATGGCGGCTGCCAACATGGCGGC


 


393
SRE017
TGGTTGCTGACTAATTGAGATGCATGCTTTGCATACTTCTGCCTGCTGGGGAGCCTGGGGA




CTTTCCACAC


 


394
SRE018
GCTCACTCACTCACTCACTGAGGCCTGCAGAGCAAAGCTCTGCAGTCTGGGGACCTTTGGT




CCCCAGGCCTCAGTGAGTGAGTGAGTGAGCAGAGAGGGAGTGGCCAACTCCATCACTAGGG




GTTCCT


 


395
SRE019
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGCTaCgTGGTGACTCATG




GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATG


 


396
SRE020
AGTATAGTGCACAGTGACTGCAGCAGGGTGACTCATGATGATGCCACGTCACCAATGCCAC




GTCACCAGGTGACTCATGGGTGACTCATGATGCCACGTCACCAATGCCACGTCACCAGGTG




ACTCATGGGTGACTCATG


 


397
SRE021
TAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTCCTTTGATGT




ACGCAACTCCTTTGATGTCTATGCGTAATTGCTGAGTCATAATCGAGATGTAATTGCTGAG




TCATGTCCGACGCATCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATAATTGCTGAG




TCATTCTAACTCGCTAATTGCTGAGTCATCATCTCGACCTCCTTTGATGTCCGTAAATCCT




TTGATGT
















TABLE 1C







Sequences of Synthetic Response Sensors (SRSs) according to the disclosure









SEQ




ID




NO:
Name
Sequence





398
SRS002
ACTAGTGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATG




GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGtgcgctcccgacatgcc




ccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtgg


 


399
SRS003
agcttgcatgcctgcaggtcggagtactgtcctccgagcggagtactgtcctccgagcgga




gtactgtcctccgagcggagtactgtcctccgagcggagtactgtcctccgagcggtgcgc




tcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggca




gaggtggg


 


400
SRS004
ctcgaggctagcATGATCACCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTC




ACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACT




AGTGGTACCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAAAGC




ATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACT




TGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGA




TTGAGGTGTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTGG




ACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCC




TGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


401
SRS005
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC




TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGTGATCATGCTAGCCTCGAGGAT




ATCAAGATCGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGT




TCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTGa


 


402
SRS006
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC




TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGTGATCATGCTAGCCTCGAGGAT




ATCAAGATCGGTACCATGACCCACGTGATGCTGAGAAGTACTCCTGCCCTAGGAAGAGACT




CAGGGCAGAGGGAGGAAGGACAGCAGACCAGACAGTCACAGCAGCCTTGACAAAACGTTCC




TGGAACT


 


403
SRS007
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC




TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGTGATCATGCTAGCCTCGAGGAT




ATCAAGATCGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGC




ACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGA




GTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTG




GAGCCCGGGTTACCAGCTCTT


 


404
SRS008
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC




TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGCGGTGCTAGCTATAAAAGGCCAG




CAGCAGCCTGACCACATCTCATCCTCctcgaggatatcaagatctggcctcggcggccaaa




ttca


 


405
SRS009
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGG




ACTTTCCacATGACACAGCAATacaAcgcGtcccgacatgccccgcggcgcgccattaacc




gccagatttgagtcgcgggacccgttggcagaggtgg


 


406
SRS010
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGG




ACTTTCCacATGACACAGCAATacagtacCACCTCTTAACAATACGTTTCACAAATAGTTA




AAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTT




AACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAA




ATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAGACTCAGCTGTG




CTGGCACACTCAGAAGCTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTG




AGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCG




GGCCTCTGATT


 


407
SRS011
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGG




ACTTTCCacATGACACAGCAATacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCG




GGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCG




GCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTT




CTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTGA


 


408
SRS012
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGG




ACTTTCCacATGACACAGCAATacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCA




TGACCCACGTGATGCTGAGAAGTACTCCTGCCCTAGGAAGAGACTCAGGGCAGAGGGAGGA




AGGACAGCAGACCAGACAGTCACAGCAGCCTTGACAAAACGTTCCTGGAACt


 


409
SRS013
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGG




ACTTTCCacATGACACAGCAATacactagtaacatttctctggcctaactggccggtacCG




GCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAAC




GAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGT




TGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCA




GGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAG




CTCTTA


 


410
SRS014
TCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGT




CCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGtg




cgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttg




gcagaggtgg


 


411
SRS015
GGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGAC




TCATGGGTGACTCATGGGTGACTCATGACTAGTGTCCCCACCCACACATTCCTGTCCCCAC




CCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACCCACACATTCCTGTCCCCACC




CACACATTCCTGTCCCCACCCACACATTCCTGtgcgctcccgacatgccccgcggcgcgcc




attaaccgccagatttgagtcgcgggacccgttggcagaggtgg


 


412
SRS016
CTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTTTGATGTACGCAACTCCT




TTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGT




CCGTAAATCCTTTGATGTGACGTCTACGTACATACTGAAAAGCATACTTTTGCAATGTTAT




TTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCG




TTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTG




CATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTGGACCGCATCCTAGCCGCCG




ACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAG




GGTACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


413
SRS017
CTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTTTGATGTACGCAACTCCT




TTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGT




CCGTAAATCCTTTGATGTGACgatcttgatatcctcgaggctagcATGATCACCATGAGTC




ACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCAT




GAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGTACCACCTCTTAACAATACGTTT




CACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAAC




AAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTT




AGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTqTGCCCTGGTGCATAAATAGA




GACTCAGCTGTGCTGGCACACTCAGAAGCTTGGACCGCATCCTAGCCGCCGACTCACACAA




GGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCT




GGAGTGAATTCGGGCCTCTGATTA


 


414
SRS018
CTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATTCCTTTGATGTACGCAACTCCT




TTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGT




CCGTAAATCCTTTGATGTGACGTCTACGTATCTACCTGATCAAACATGCCCGGACATGTCG




TAAGACATAAACATGCCCGGACATGTCCTCGCAATCTAACATGCCCGGACATGTCCTCGCA




ATCTAACATGCCCGGACATGTCTGCAAGCTACAACATGCCCGGACATGTCTACAATATACG




TATCTACCTGATCAAACATGCCCGGACATGTCGTAAGACATAAACATGCCCGGACATGTCC




TCGCAATCTAACATGCCCGGACATGTCCTCGCAATCTAACATGCCCGGACATGTCTGCAAG




CTACAACATGCCCGGACATGTCTACGTACATACTGAAAAGCATACTTTTGCAATGTTATTT




TTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTT




TCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCA




TAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTGGACCGCATCCTAGCCGCCGAC




TCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGG




TACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


415
SRS019
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACG




CGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAA




AATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAA




GTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTC




TTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


416
SRS020
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGGAAAAGTTCAGCTGAGAGA




TATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTT




GCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTG




GAGTTCTTAGGGGGATGGCTG


 


417
SRS021
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGGGTGACTCATGGGTGA




CTCATGCTaCgTgTgAcGGTGACTCATGGGTGACTCATGGGTGACTCATGaagTcgcaGat




tGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTACCGGCCCGCCCCCTTTCCTTACG




CGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAA




AATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAA




GTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTC




TTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


418
SRS022
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGCCCGCCCCCTTTCCTTAC




GCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTA




AAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAA




AGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGT




CTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


419
SRS023
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGGAGGAAGTCGTAAAACTTGGGAGGA




AGTCGTAAAAAATGGGAGGAAGTCGTAAAATGCGGGAGGAAGTCGTAAAAGAAGGGAGGAA




GTCGTAAAAATCGGGAGGAAGTCGTAAAAGGTACCGGCCCGCCCCCTTTCCTTACGCGGAT




TGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATAT




TGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCA




GCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGG




GTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


420
SRS024
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGGGTGACTCATGGGTGA




CTCATGCTaCgTgTgAcGGTGACTCATGGGTGACTCATGGGTGACTCATGaagTcgcaGat




tGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAGA




TATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTT




GCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTG




GAGTTCTTAGGGGGATGGCTG


 


421
SRS025
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAG




ATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACT




TGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCT




GGAGTTCTTAGGGGGATGGCTG


 


422
SRS026
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGA




TTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCG




TGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGC




CAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCC




GGGTTACCAGCTCTT


 


423
SRS027
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCCATACTGAAAAGCATACTTTT




GCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAA




GGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTA




TGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTGGACCGCATC




CTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCA




GCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


424
SRS028
ACATCAAAGGATTTACGGACATCAAAGGATGTACCTACATCAAAGGAATCCTTAACATCAA




AGGACGCATAGACATCAAAGGAGTTGCGTACATCAAAGGAGCTAGTAAGCTTGGGGCGGGG




tgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGAC




ACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTT




CCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGT




AGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTA




TCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTT




CGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGA




GTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


425
SRS029
GGTGACTCATGGGTGACTCATGGGTGACTCATGCTaCgTgTgAcGGTGACTCATGGGTGAC




TCATGGGTGACTCATGaagTcgcaGattGGTGACTCATGGGTGACTCATGGGTGACTCATG




ACTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAG




AAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCC




taGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCCC




CCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAG




CGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCT




GCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGC




AAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


426
SRS030
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCC




CCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCA




GCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTC




TGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAG




CAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


427
SRS031
CACTTCCGGTTTACTTCCACTTCCGGTTTACTAGCACTTCCGGTTTACGCTCACTTCCGGT




TTACGATCACTTCCGGTTTACAGACACTTCCGGTTTACGCTAGTAAGCTTGGGGCGGGGtg




ATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACAC




AGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCC




acATGACACAGCAATacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAG




CTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATC




TGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCG




GCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGT




GTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


428
SRS032
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAA




ATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTG




AGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTG


 


429
SRS033
ACATCAAAGGATTTACGGACATCAAAGGATGTACCTACATCAAAGGAATCCTTAACATCAA




AGGACGCATAGACATCAAAGGAGTTGCGTACATCAAAGGAGCTAGTAAGCTTGGGGCGGGG




tgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGAC




ACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTT




CCacATGACACAGCAATacCTCGAGGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGA




GCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGT




GGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTA




GGGGGATGGCTG


 


430
SRS034
GGTGACTCATGGGTGACTCATGGGTGACTCATGCTaCgTgTgAcGGTGACTCATGGGTGAC




TCATGGGTGACTCATGaagTcgcaGattGGTGACTCATGGGTGACTCATGGGTGACTCATG




ACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAG




AAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCC




taGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGGAAAAGT




TCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCAC




TGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCC




GGGTCGGACCTGGAGTTCTTAGGGGGATGGCTG


 


431
SRS035
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGGAAAAG




TTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCA




CTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCC




CGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTG







AGTGCTAGTAAACCGGAAGTGGAAGTAAACCGGAAGTGACTAGTAAGCTTGGGGGGGGGtg


 









432
SRS036
GTAAACCGGAAGTGTCTGTAAACCGGAAGTGATCGTAAACCGGAAGTGAGCGTAAACCGGA




AGTGCTAGTAAACCGGAAGTGGAAGTAAACCGGAAGTGACTAGTAAGCTTGGGGGGGGGtg




ATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACAC




AGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCC




acATGACACAGCAATacCTCGAGGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGAGC




AGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGG




ACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAGG




GGGATGGCTG


 


433
SRS037
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCGTCCGCCCGAGTCCCCGCCTCGCCGCCAACGCCAAt




gcTcatGCGTCCGCCCGAGTCCCCGCCTCGCCGCCAACGCCAtcatgcctGCGTCCGCCCG




AGTCCCCGCCTCGCCGCCAACGCCAGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGG




GGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCC




ACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCqTgTgAcATGCCAC




GTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGCCCGCCCCCT




TTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGC




GTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCG




GCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAG




TGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


434
SRS038
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtqATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGA




CTCATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACT




CATGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTG




ATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTC




GTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAG




CCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCC




CGGGTTACCAGCTCTT


 


435
SRS039
ACATCAAAGGATTTACGGACATCAAAGGATGTACCTACATCAAAGGAATCCTTAACATCAA




AGGACGCATAGACATCAAAGGAGTTGCGTACATCAAAGGAGCTAGTAAGCTTGGGGCGGGG




tgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGAC




ACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTT




CCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACCAATGCCACG




TCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCCACGTC




ACCAGGTGACTCATGGGTGACTCATGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGG




TAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGT




ATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCT




TCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTG




AGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


436
SRS040
CACTTCCGGTTTACTTCCACTTCCGGTTTACTAGCACTTCCGGTTTACGCTCACTTCCGGT




TTACGATCACTTCCGGTTTACAGACACTTCCGGTTTACGCTAGTAAGCTTGGGGGGGGGtg




ATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACAC




AGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCC




acATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACCAATGCCACGTC




ACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCAC




CAGGTGACTCATGGGTGACTCATGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTA




GCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTAT




CTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTC




GGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAG




TGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


437
SRS041
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCCAACATGGCGGCGCCCAACATGGCGGCTACCAACATGG




CGGCCTCCAACATGGCGGCAGGCAACATGGCGGCTGCCAACATGGCGGCGGATCCGCTTGC




GTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacC




TCGAGGGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGT




GACTCATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGA




CTCATGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATC




TGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACC




TCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTA




AGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAG




CCCGGGTTACCAGCTCTT


 


438
SRS042
GGGGGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCTCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTC




CTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGAT




GTGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacAT




GACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCA




GGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGG




TGACTCATGGGTGACTCATGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTG




CAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGT




AACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCG




ACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTG




CGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


439
SRS043
TAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTAATTGCTGAG




TCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTGAGTCATTCTAACT




CGCTAATTGCTGAGTCATGTCGACGCTAGCGGTGACTCATGATGATGCCACGTCACCAATG




CCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCC




ACGTCACCAGGTGACTCATGGGTGACTCATGACTAGTAAGCTTGGGGGGGGGtgATGACAC




AGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATG




GATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGAC




ACAGCAATacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGG




CTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACA




AAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTA




GGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGC




TGTGCTGGAGCCCGGGTTACCAGCTCTT


 


440
SRS044
TAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTCCTTTGATGT




ACGCAACTCCTTTGATGTCTATGCGTAATTGCTGAGTCATAATCGAGATGTAATTGCTGAG




TCATGTCCGACGCATCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATAATTGCTGAG




TCATTCTAACTCGCTAATTGCTGAGTCATcatCtcgAcCTCCTTTGATGTCCGTAAATCCT




TTGATGTGTCGACGCTAGCGGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCA




GGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGG




TGACTCATGGGTGACTCATGACTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGG




ACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGC




GTGAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacC




TCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCT




GATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCT




CGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAA




GCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGC




CCGGGTTACCAGCTCTT


 


441
SRS045
TAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTAATTGCTGAG




TCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTGAGTCATTCTAACT




CGCTAATTGCTGAGTCATGTCGACACTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATt




CGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGC




TTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGttGGGACTTTCCacATGACACAGCAA




TacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGC




ACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGA




GTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTG




GAGCCCGGGTTACCAGCTCTT


 


442
SRS046
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTGAATTCTAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTAT




CCTCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTAATTGCTGAGTCATAATCGAGA




TGTAATTGCTGAGTCATGTCCGACGCATCCTTTGATGTTAAGGATTCCTTTGATGTAGGTA




CATAATTGCTGAGTCATTCTAACTCGCTAATTGCTGAGTCATcatCtcgAcCTCCTTTGAT




GTCCGTAAATCCTTTGATGTGTCGACACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAA




TtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCC




GCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGC




AATacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCC




CTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCT




GCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGT




GAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGC




TGGAGCCCGGGTTACCAGCTCTT


 


443
SRS047
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGTCGACGCTAGCGGTGACTCA




TGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgT




gAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGACTAGTAA




GCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACC




GGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCG




GGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCCCCCTTTCCT




TACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAAT




TTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGC




GAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCA




CGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


444
SRS048
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTGAATTCGACTCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGAT




GTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGTCGA




CACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCC




CCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCA




GCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTC




TGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAG




CAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


445
SRS049
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtqATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCGT




ATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGT




TACCAGCTCTTA


 


446
SRS050
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCtgcgctcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgc




gggacccgttggcagaggtgg


 


447
SRS051
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGGAAAAG




TTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCGTATCCCAGGAGGAGCAAG




TGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTTA


 


448
SRS052
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCtgcgctcc




cgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagag




gtgg


 


449
SRS053
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGGGAGGAA




GTCGTAAAACTTGGGAGGAAGTCGTAAAAAATGGGAGGAAGTCGTAAAATGCGGGAGGAAG




TCGTAAAAGAAGGGAGGAAGTCGTAAAAATCGGGAGGAAGTCGTAAAAGGATCCGCTTGCG




TGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCT




CGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTG




ATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTC




GTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAG




CCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCC




CGGGTTACCAGCTCTT


 


450
SRS054
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCTCCTTTGA




TGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGT




ACATCCTTTGATGTCCGTAAATCCTTTGATGTGGATCCGCTTGCGTGAGAAGctGGGACTT




TCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCG




CCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACG




CAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGC




TCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGG




AGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


451
SRS055
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCTTTTACGACTTCCTCCCGATTTTTA




CGACTTCCTCCCTTCTTTTACGACTTCCTCCCGCATTTTACGACTTCCTCCCATTTTTTAC




GACTTCCTCCCAAGTTTTACGACTTCCTCCCGGATCCGCTTGCGTGAGAAGctGGGACTTT




CCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGC




CCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGC




AGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCT




CTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGA




GCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


452
SRS056
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCTCCTTTGATGTACGCAACTCCTTTG




ATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGTCCG




TAAATCCTTTGATGTGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGttG




GGACTTTCCacATGACACAGCAATacCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCG




GATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAA




TATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGT




CCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTT




CGGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


453
SRS057
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCTATAAAAGGCCAGCAGCAGCCTGACCACATCTCATCC


 


454
SRS058
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCTATAAAAG




GCCAGCAGCAGCCTGACCACATCTCATCC


 


455
SRS059
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAAAGC




ATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACT




TGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGA




TTGAGGTgTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAAGAAGCTTG




GACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTC




CTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATT


 


456
SRS060
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGaCgTgTgAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGA




GAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTC




CtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTCGAGGGTACCACCTCTTA




ACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTA




TTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTC




GTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGT




GCATAAATAGAGACTCAGCTGTGCTGGCACACTCAAGAAGCTTGGACCGCATCCTAGCCGC




CGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGA




AGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATT


 


457
SRS061
TAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTAATTGCTGAG




TCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTGAGTCATTCTAACT




CGCTAATTGCTGAGTCATGTCGACGCTAGCGGTGACTCATGATGATGCCACGTCACCAATG




CCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCC




ACGTCACCAGGTGACTCATGGGTGACTCATGACTAGTTCCTTTGATGTACGCAACTCCTTT




GATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGATGTAGGTACATCCTTTGATGTCC




GTAAATCCTTTGATGTCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGC




TGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCT




GTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGG




CGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTG




TGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


458
SRS062
TAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTAATTGCTGAG




TCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTGAGTCATTCTAACT




CGCTAATTGCTGAGTCATGTCGACGCTAGCGGTGACTCATGATGATGCCACGTCACCAATG




CCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAATGCC




ACGTCACCAGGTGACTCATGGGTGACTCATGACTAGTCAACATGGCGGCGCCCAACATGGC




GGCTACCAACATGGCGGCCTCCAACATGGCGGCAGGCAACATGGCGGCTGCCAACATGGCG




GCCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTA




TCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTGTAACAAAGCTGCA




CCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGCGACTAGGTGTGAG




TAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGG




AGCCCGGGTTACCAGCTCTT


 


459
SRS063
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGTCGACGCTAGCGGTGACTCA




TGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgT




gAcATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCATGACTAGTTA




ATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTATCCTAATTGCTGAGTC




ATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTGAGTCATTCTAACTCG




CTAATTGCTGAGTCATCTCGAGGGTACCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGC




TGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCT




GTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGG




CGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTG




TGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT


 


460
SRS064
AcgcGtcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgt




tggcagaggtgg


 


461
SRS065
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCACCTCTTAACAATACGTTTC




ACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACA




AGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAG




ACTCAGCTGTGCTGGCACACTCAAAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACC




GTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTT




CTTAGGGGGATGGCTGAAgaattcA


 


462
SRS066
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCACCTCTTAACAATACGTTTC




ACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACA




AGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAG




ACTCAGCTGTGCTGGCACACTCAAGAAGCTTGGACCGCATCCTAGCCGCCGACTCACACAA




GGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCT




GGAGTGAATTCGGGCCTCTGATTA


 


463
SRS067
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCACCTCTTAACAATACGTTTC




ACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACA




AGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAG




ACTCAGCTGTGCTGGCACACTCAAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGA




GTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTTAA


 


464
SRS068
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCACCTCTTAACAATACGTTTC




ACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACA




AGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAG




ACTCAGCTGTGCTGGCACACTCAACACTCGCGCTGCCATCACTCTTCCGCCGTCTTCGCCG




CCATCCTCGGCGCGACTCGCTTCTTTCGGTTCTACCAGGTAGAGTCCGCCGCCATCCTCA


 


465
SRS069
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTqTqAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCACCTCTTAACAATACGTTTC




ACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACA




AGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAG




ACTCAGCTGTGCTGGCACACTCAACtttttccgtgctacctgcagaggggtccatacggcg




ttgttctggattca


 


466
SRS070
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCACCTCTTAACAATACGTTTC




ACAAATAGTTAAAAACATGCATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACA




AGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTGGTGCATAAATAGAG




ACTCAGCTGTGCTGGCACACTCAAcggcggcgcagatcgcccggcgcggctccgccccctg




cgccggtcacgtgggggcgccggctgcgcctgcggagaagcggtggccgccgagcgggatc




tgtgcggggagccggaaatggttgtggactacgtctgtgcggctgcgtggggctcggccgc




gcggactgaaggagactgaaggtgctggggggaccctgatgtggA


 


467
SRS071
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAG




ATATAAAAGAGCAGTCTTTCCAGCACCTGCGAAGCTTGGACCGCATCCTAGCCGCCGACTC




ACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTA




CTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


468
SRS072
GGGGGGGGGTGATGACACAGCAATTCGGGACTTTCCACGCTTGCGTGAGAAGAGACCGGAA




GTGAATGACACAGCAATGGATCCGCTTGCGTGAGAAGCTGGGACTTTCCTAGGGGGGGGGT




TGGGACTTTCCACATGACACAGCAATACCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGACGTGTGACATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAG




ATATAAAAGAGCAGTCTTTCCAGCACCTGCGTATCCCAGGAGGAGCAAGTGGCACGTCTTC




GGGTGAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTTAA


 


469
SRS073
GGGGGGGGGTGATGACACAGCAATTCGGGACTTTCCACGCTTGCGTGAGAAGAGACCGGAA




GTGAATGACACAGCAATGGATCCGCTTGCGTGAGAAGCTGGGACTTTCCTAGGGGGGGGT




TGGGACTTTCCACATGACACAGCAATACCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGACGTGTGACATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAG




ATATAAAAGAGCAGTCTTTCCAGCACCTGCCACTCGCGCTGCCATCACTCTTCCGCCGTCT




TCGCCGCCATCCTCGGCGCGACTCGCTTCTTTCGGTTCTACCAGGTAGAGTCCGCCGCCAT




CCTCA


 


470
SRS074
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAG




ATATAAAAGAGCAGTCTTTCCAGCACCTGCCtttttccgtgctacctgcagaggggtccat




acggcgttgttctggattc


 


471
SRS075
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAG




ATATAAAAGAGCAGTCTTTCCAGCACCTGCcggcggcgcagatcgcccggcgcggctccgc




cccctgcgccggtcacgtgggggcgccggctgcgcctgcggagaagcggtggccgccgagc




gggatctgtgcggggagccggaaatggttgtggactacgtctgtgcggctgcgtggggctc




ggccgcgcggactgaaggagactgaaggtgctggggggaccctgatgtgg


 


472
SRS076
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCCGGCCCGCCCCCTTTCCTTA




CGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTT




AAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGA




AAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAAAATCCAGAGCGGCGGGCACTGACGG




GCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCG




GACCTGGAGTTCTTAGGGGGATGGCTGAAgaattc


 


473
SRS077
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCCGGCCCGCCCCCTTTCCTTA




CGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTT




AAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGA




AAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGAAGCTTGGACCGCATCCTAGCCGCC




GACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAA




GGGTACTTGCTGGAGTGAATTCGGGCCTCTGATT


 


474
SRS078
GGGGGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCCGGCCCGCCCCCTTTCCTTA




CGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTT




AAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGA




AAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCACACTCGCGCTGCCATCACTCTTCCGC




CGTCTTCGCCGCCATCCTCGGCGCGACTCGCTTCTTTCGGTTCTACCAGGTAGAGTCCGCC




GCCATCCTC


 


475
SRS079
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCCGGCCCGCCCCCTTTCCTTA




CGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTT




AAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGA




AAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCACtttttccgtgctacctgcagagggg




tccatacggcgttgttctggattc


 


476
SRS080
GGGGCGGGGtgATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAA




GTgaATGACACAGCAATGGATCCGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGCGGGGt




tGGGACTTTCCacATGACACAGCAATacCTCGAGGGTGACTCATGATGATGCCACGTCACC




AATGCCACGTCACCAGGTGACTCATGGGTGACTCATGaCgTgTgAcATGCCACGTCACCAA




TGCCACGTCACCAGGTGACTCATGGGTGACTCATGGGTACCCGGCCCGCCCCCTTTCCTTA




CGCGGATTGGTAGCTGCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTT




AAAATATTGTATCTGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGA




AAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAcggcggcgcagatcgcccggcgcggc




tccgccccctgcgccggtcacgtgggggcgccggctgcgcctgcggagaagcggtggccgc




cgagcgggatctgtgcggggagccggaaatggttgtggactacgtctgtgcggctgcgtgg




ggctcggccgcgcggactgaaggagactgaaggtgctggggggaccctgatgtgg


 


477
SRS081
AGTATAGTGCACAGTGACTGCAGCAGGGTGACTCATGATGATGCCACGTCACCAATGCCAC




GTCACCAGGTGACTCATGGGTGACTCATGATGCCACGTCACCAATGCCACGTCACCAGGTG




ACTCATGGGTGACTCATGGGTACCTATAAAAGGCCAGCAGCAGCCTGACCACATCTCATCC


 


478
SRS082
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTAAGCTTAACTCGCAATCTAGC




ATCGTCCGACGCAACGCCTTACACCATCAGAATCTGCTAGCGGTGACTCATGGGTGACTCA




TGGGTGACTCATGGGTGACTCATGCTaCgTGGTGACTCATGGGTGACTCATGGGTGACTCA




TGGGTGACTCATGGGTGACTCATGGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGAG




CAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTG




GACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAG




GGGGATGGCTGa


 


479
SRS083
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTAAGCTTGGTACAACTTCTCAC




GGAGGCTTCTAACTCGCAATCTAGCATCGTCCGACGCAACGCCTTACACCATCAGAATCTG




CTAGCGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGCTaCgTGGTGAC




TCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTGACTCATGGGTACCGGGAAA




AGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGG




CACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTT




CCCGGGTCGGACCTGGAGTTCTTAGGGGGATGGCTGa


 


480
SRS084
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACgattcttgatatcctcga




ggctagcATGATCACCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCA




TGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGG




TACCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGAAAAGCATACT




TTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCACTTGGGG




AAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAG




GTgTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTGGACCGC




ATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTCCTGACA




GCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


481
SRS085
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACgatcttgatatcctcgag




gctagcATGATCACCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCAT




GAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGT




ACCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCAtACTAGTGGGGGGGGGt




gATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACA




CAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacA




TGACACAGCAATacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCGGGAAAAGTTC




AGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTG




ACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGG




GTCGGACCTGGAGTTCTTAGGGGGATGGCTG


 


482
SRS086
TCCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTG




ATGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACgatcttgatatcctcgag




gctagcATGATCACCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCAT




GAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCCATGAGTCACCACTAGTGGT




ACCACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCAtACTAGTGGGGGGGGGt




gATGACACAGCAATtcGGGACTTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACA




CAGCAATtcGCTTGCGTGAGAAGctGGGACTTTCCtaGGGGGGGGttGGGACTTTCCacA




TGACACAGCAATacacTAGTAACATTTCTCTGGCCTAACTGGCCGGTACCGGGAAAAGTTC




AGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACCTGCAAATCCAGAGCGGCGGGCACTG




ACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGG




GTCGGACCTGGAGTTCTTAGGGGGATGGCTGAA


 


483
SRS087
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGCGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACcatgcataCTAGTCTGAGCGACAGTATAGTGCACAGTGACTGCAGCAGTCATT




CCTTTGATGTACGCAACTCCTTTGATGTCTATGCGTCCTTTGATGTTAAGGATTCCTTTGA




TGTAGGTACATCCTTTGATGTCCGTAAATCCTTTGATGTGACGTCTACGTATCTACCTGAT




CAAACATGCCCGGACATGTCGTAAGACATAAACATGCCCGGACATGTCCTCGCAATCTAAC




ATGCCCGGACATGTCCTCGCAATCTAACATGCCCGGACATGTCTGCAAGCTACAACATGCC




CGGACATGTCTACAATATACGTATCTACCTGATCAAACATGCCCGGACATGTCGTAAGACA




TAAACATGCCCGGACATGTCCTCGCAATCTAACATGCCCGGACATGTCCTCGCAATCTAAC




ATGCCCGGACATGTCTGCAAGCTACAACATGCCCGGACATGTCTACGTACATACTGAAAAG




CATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAACCCAGGGAAGATAATCAC




TTGGGGAAAGGAAGGTTCGTTTCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGG




ATTGAGGTgTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAGAAGCTTG




GACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCCAGGTAAGGCTC




CTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


484
SRS088
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGGGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACCACTAGTGTCATCTCTTTGAATATTCTGTAGTTTGAGGAGAATATTTGTTATA




TTGCACAATAAAATAAGTTTGCAAGTTTTTTTTTTCTGCCCCAAAGAGCTCTGTGTCCTTG




AACATAAAATACAAATAACCGCTATGCTGTTAATTATTAACAAATGTCCCATTTTCAACCT




AAGGAAATACCATAAAGTAACAGATATACCAACAAAAGGTTAATAATTAACAGGCATTGCC




TGAAAAGAGTATAAAAGGCTTTCAGCATGATTTTCCATATTGTGCTTCCACCACTGCCAAT




AACAAA


 


485
SRS089
ATGACTCAGCAATTAGCGAGTTAGAATGACTCAGCAATTATGCGTCGGACATGACTCAGCA




ATTACATCTCGATTATGACTCAGCAATTAGGATAGGCATATGACTCAGCAATTACATAGCA




GCAATGACTCAGCAATTAGCTAGTAAGCTTGGGGGGGGGtgATGACACAGCAATtcGGGAC




TTTCCacGCTTGCGTGAGAAGagACCGGAAGTgaATGACACAGCAATGGATCCGCTTGCGT




GAGAAGctGGGACTTTCCtaGGGGCGGGGttGGGACTTTCCacATGACACAGCAATacCTC




GAGGGTACcagcttgcatgcctgcaggtcggagtactgtcctccgagcggagtactgtcct




ccgagcggagtactgtcctccgagcggagtactgtcctccgagcggagtactgtcctccga




gcggagactctagagggtatataatggatcc


 


486
SRS090
TCTGTAGTTTGAGGAGAATATTTGTTATATTGCACAATAAAATAAGTTTGCAAGTTTTTTT




TTTCTGCCCCAAAGAGCTCTGTGTCCTTGAACATAAAATACAAATAACCGCTATGCTGTTA




ATTATTAACAAATGTCCCATTTTCAACCTAAGGAAATACCATAAAGTAACAGATATACCAA




CAAAAGGTTAATAATTAACAGGCATTGCCTGAAAAGAGTATAAAAGGCTTTCAGCATGATT




TTCCATATTGTGCTTCCACCACTGCCAATAACAAA


 


556
SRS091
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGACGTGTGACATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTGAATTCTAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTAT




CCTAATTGCTGAGTCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTG




AGTCATTCTAACTCGCTAATTGCTGAGTCATGTCGACACTAGTAAGCTTGGGGGGGGGTGA




TGACACAGCAATTCGGGACTTTCCACGCTTGCGTGAGAAGAGACCGGAAGTGAATGACACA




GCAATGGATCCGCTTGCGTGAGAAGCTGGGACTTTCCTAGGGGGGGGGTTGGGACTTTCCA




CATGACACAGCAATACCTCGAGGGTACCGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCA




GTCTTTCCAGCACCTGCGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCG




GCTGTGCTGGAGCCCGGGTTACCAGCTCTTAA


 


557
SRS092
GGTGACTCATGATGATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTC




ATGACGTGTGACATGCCACGTCACCAATGCCACGTCACCAGGTGACTCATGGGTGACTCAT




GACTAGTGAATTCTAATTGCTGAGTCATTGCTGCTATGTAATTGCTGAGTCATATGCCTAT




CCTAATTGCTGAGTCATAATCGAGATGTAATTGCTGAGTCATGTCCGACGCATAATTGCTG




AGTCATTCTAACTCGCTAATTGCTGAGTCATGTCGACACTAGTAAGCTTGGGGGGGGGTGA




TGACACAGCAATTCGGGACTTTCCACGCTTGCGTGAGAAGAGACCGGAAGTGAATGACACA




GCAATGGATCCGCTTGCGTGAGAAGCTGGGACTTTCCTAGGGGGGGGGTTGGGACTTTCCA




CATGACACAGCAATACCTCGAGGGTACGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCT




GCAGGCTTCCCTATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTG




TAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAAAGTCCAGCTTCGGC




GACTAGGTGTGAGTAAGCCAGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGCAGTG




TGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT
















TABLE 1D







coreBIRC5 H1299


















SEQ




Expression
Fold
Barcode

ID



Construct
Score
Change
Support
Motif
NO:
Spacer
















TRPS1_v22
2.20
1.95
5
TATTTTATCTTT
129
7


 


MNX1_v18
2.05
1.81
5
GTCATTAT

7


 


TWIST1_v3
1.87
1.66
5
ATTCCAGATGTTT
131
3


 


Control-1_FOSL1_v1
1.64
1.45
27





 


HOXAI_v10
1.47
1.30
5
GTCATTAC

7


 


TWIST1_v4
1.41
1.25
5
ATTCCAGATGTTT
131
0


 


ETV4_v2
1.40
1.24
6
ACCGGAAGTG
132
7


 


GATAI_v1
1.39
1.23
6
TTCTAATCTAT
133
10


 


ETV4_v14
1.38
1.22
6
ACCGGAAATG
134
7


 


FOSL2_v1
1.37
1.21
5
GGATGACTCAT
135
10


 


NFIC_v15
1.33
1.18
6
TTCTTGGCAGA
136
3


 


EN2_v7
1.33
1.18
5
CGCAATTA

3


 


ETV4_v6
1.33
1.18
6
ACCGGAAGCG
137
7


 


SOX11_v2
1.32
1.17
6
GAGAACAAAGGA
138
7


 


ETV6_v6
1.32
1.17
5
ACCGGAAGTG
132
7


 


TRPS1_v20
1.31
1.16
6
TAACTTATCTTT
139
0


 


TFDP1_v6
1.31
1.16
6
GGGCGGGAACG
140
7


 


TCF7_v9
1.30
1.15
5
TCCTTTGATAT
141
10


 


TRPS1_v10
1.29
1.14
6
TAGCTTATCTTT
142
7


 


PITX2_v22
1.29
1.14
5
TTAATCCA

7


 


TCF7L1_v8
1.26
1.12
6
AAACATCAAAGG
143
0


 


CREB3L1_v6
1.25
1.11
6
ATGCCACGTCACCA
144
7


 


E2F8_v21
1.24
1.10
5
TTCGCGCTAAAA
146
10


 


ZBTB7B_v6
1.23
1.09
6
GCGACCACCAAA
192
7


 


ZBTB7B_v21
1.23
1.09
5
GCAACCACCGAA
270
10


 


TCF7_v23
1.22
1.08
6
TCCTTTGAACT
272
3


 


HOXC10_v10
1.22
1.08
6
GTCGTTAAAT
275
7


 


ETV6_v15
1.22
1.08
6
AGAGGAAGTG
276
3


 


VENTX_v9
1.22
1.08
6
AGCGATTAG

10


 


NFIC_v1
1.22
1.08
6
TACTTGGCAGA
277
10


 


NFIC_v21
1.21
1.07
5
TACTTGGCAAA
280
10


 


FOXN1_v17
1.21
1.07
6
AGAAGC

10


 


PITX2_v24
1.21
1.07
5
TTAATCCA

0


 


E2F4_v7
1.21
1.07
6
TTTTGGCGCCCTTT
286
3


 


TCF7_v14
1.20
1.07
6
TCCTTTGATTT
287
7


 


EN2_v16
1.20
1.07
6
CTCAATTA

0


 


DMBX1_v19
1.20
1.06
6
TGAACAGGATTAATGTA
288
3


 


CREB3L1_v18
1.20
1.06
5
ATGCCACGTAATCA
294
7


 


SOX11_v7
1.20
1.06
6
GAGAACAAAGAA
295
3


 


ETV6_v10
1.20
1.06
6
ATCGGAAGTG
296
7


 


FOSL2_v9
1.20
1.06
5
GGGTGACTCAT
297
10


 


ZBTB7B_v4
1.20
1.06
5
GCGACCACCGAA
298
0


 


FOXNI_v6
1.19
1.06
5
GGAAGC

7


 


SIX4_v16
1.19
1.06
5
GAAATCTGAGC
299
0


 


TCF7_v3
1.19
1.05
5
TCCTTTGATGT
300
3


 


NFIC_v9
1.19
1.05
6
TACTTGGCATA
306
10


 


ETV4_v5
1.19
1.05
6
ACCGGAAGCG
137
10


 


FOSL2_v17
1.19
1.05
6
GGATGACTCAC
307
10


 


ETV6_v14
1.19
1.05
5
AGAGGAAGTG
276
7


 


GATA1_v13
1.19
1.05
6
TTCTAATCTCT
308
10
















TABLE 1E







TATA-TSS H1299


















SEQ




Expression
Fold
Barcode

ID



Construct
Score
Change
Support
Motif
NO:
Spacer
















Control-1_FOSL1_v1
3.19
4.84
27





 


FOSL2_v4
2.22
3.37
5
GGATGACTCAT
135
0


 


CREB3L1_v18
1.87
2.85
5
ATGCCACGTAATCA
294
7


 


Control-1_FOSL1_v2
1.52
2.31
24





 


FOSL2_v22
1.46
2.22
6
GGGTGACTCAC
309
7


 


CREB3L1_v6
1.46
2.22
6
ATGCCACGTCACCA
144
7


 


FOSL2_v17
1.35
2.04
6
GGATGACTCAC
307
10


 


Control-1_FOSL1_v3
1.32
2.00
26





 


FOSL2_v7
1.28
1.94
6
GGATGACTCAG
313
3


 


FOSL2_v1
1.28
1.94
6
GGATGACTCAT
135
10


 


NPAS2_v11
1.21
1.84
6
GACACGTGTC
314
3


 


FOSL2_v11
1.20
1.82
5
GGGTGACTCAT
297
3


 


HES6_v11
1.11
1.69
6
GGCACGTGTA
316
3


 


HES6_v7
1.09
1.66
5
GGCACGTGTC
317
3


 


CREB3L1_v14
1.03
1.57
6
ATGCCACGTCAACA
320
7


 


HES6_v3
0.98
1.49
6
GGCACGTGTT
321
3


 


ASCL1_v23
0.96
1.45
5
GGCACGTGCC
322
3


 


TWIST1_v3
0.95
1.43
5
ATTCCAGATGTTT
131
3


 


FOSL2_v8
0.94
1.43
5
GGATGACTCAG
313
0


 


TRPS1_v22
0.92
1.40
5
TATTTTATCTTT
129
7


 


GRHL1_v10
0.90
1.36
6
AAAACCGGTTCT
323
7


 


FOSL2_v9
0.87
1.32
6
GGGTGACTCAT
297
10


 


ETV4_v14
0.83
1.27
6
ACCGGAAATG
134
7


 


TWIST1_v2
0.82
1.25
6
ATTCCAGATGTTT
131
7


 


SOX11_v2
0.82
1.24
6
GAGAACAAAGGA
138
7


 


ZNF354A_v15
0.80
1.21
5
ATAAATAAAAATGGACTAATT
327
3


 


ZBTB7B_v4
0.79
1.20
5
GCGACCACCGAA
298
0


 


ZBTB7B_v21
0.78
1.18
5
GCAACCACCGAA
270
10


 


ETV6_v6
0.78
1.18
5
ACCGGAAGTG
132
7


 


ETV4_v12
0.77
1.18
5
ACCGGATGTG
336
0


 


ETV4_v6
0.77
1.17
6
ACCGGAAGCG
137
7


 


TFDP1_v21
0.76
1.16
6
GGGCGGGACCG
337
10


 


SOX11_v7
0.76
1.15
6
GAGAACAAAGAA
295
3


 


FOSL2_v18
0.75
1.14
6
GGATGACTCAC
307
7


 


ETV6_v10
0.74
1.13
6
ATCGGAAGTG
296
7


 


FOSL2_v14
0.74
1.12
6
GGGTGACTCAG
338
7


 


NFIC_v2
0.74
1.12
5
TACTTGGCAGA
277
7


 


MGA_v17
0.73
1.11
5
AGGTGCGA

10


 


TRPS1_v20
0.73
1.11
6
TAACTTATCTTT
139
0


 


IRF6_v23
0.73
1.10
6
GCCGATACT

3


 


ETV4_v10
0.72
1.10
5
ACCGGATGTG
336
7


 


ETV4_v7
0.72
1.10
6
ACCGGAAGCG
137
3


 


ZBTB7B_v24
0.72
1.09
6
GCAACCACCGAA
270
0


 


SIX2_v17
0.72
1.09
6
AACTGAAACTTGATAC
339
10


 


TWIST1_v23
0.72
1.09
6
ATTGCAGATGTTT
340
3


 


SIX2_v5
0.71
1.08
5
AACTGTAACCTGATAC
341
10


 


ETV4_v2
0.71
1.08
6
ACCGGAAGTG
132
7


 


E2F7_v3
0.71
1.08
5
TTTTCCCGCCAAAA
487
3


 


CUX1_v21
0.71
1.07
5
TGATCAATAA
488
10


 


SIX_4_v6
0.71
1.07
5
GAAACATGAGC
489
7
















TABLE 1F







coreBIRC5 PDX430


















SEQ




Expression

Barcode

ID



Construct
Score
Fold Change
Support
Motif
NO:
Spacer
















TCF7_v2
4.37
3.90
6
TCCTTTGATGT
300
7


 


TCF7_v3
3.76
3.35
5
TCCTTTGATGT
300
3


 


TCF7L1_v19
3.61
3.22
6
AGACATCAAAGG
490
3


 


ETV4_v14
3.58
3.19
6
ACCGGAAATG
134
7


 


TCF7L1_v5
3.10
2.76
6
AAACATCAAAGG
143
10


 


TCF7L1_v8
3.06
2.73
6
AAACATCAAAGG
143
0


 


ETV4_v2
3.01
2.68
6
ACCGGAAGTG
132
7


 


ETV4_v6
2.96
2.64
6
ACCGGAAGCG
137
7


 


ETV4_v10
2.92
2.61
5
ACCGGATGTG
336
7


 


ETV4_v13
2.73
2.43
6
ACCGGAAATG
134
10


 


TWIST1_v3
2.67
2.38
5
ATTCCAGATGTTT
131
3


 


TCF7L1_v24
2.61
2.33
6
AAACTTCAAAGG
491
0


 


TCF7_v23
2.54
2.27
6
TCCTTTGAACT
272
3


 


ETV4_v8
2.53
2.26
5
ACCGGAAGCG
137
0


 


DLX1_v24
2.47
2.20
6
GTCATTAC

0


 


TCF7_v7
2.41
2.15
5
TCCTTTGATCT
492
3


 


ETV6_v6
2.29
2.04
5
ACCGGAAGTG
132
7


 


ETV4_v5
2.29
2.04
6
ACCGGAAGCG
137
10


 


ETV4_v7
2.14
1.91
6
ACCGGAAGCG
137
3


 


TWIST1_v2
2.10
1.88
6
ATTCCAGATGTTT
131
7


 


TRPS1_v22
2.05
1.83
5
TATTTTATCTTT
129
7


 


SIX2_v5
2.05
1.83
5
AACTGTAACCTGATAC
341
10


 


HOXA1_v8
2.01
1.79
6
GTAATGAC

0


 


HOXC10_v24
1.97
1.75
6
GTCGTAAACT
493
0


 


HOXA1_v12
1.95
1.74
6
GTCATTAC

0


 


HOXB9_v18
1.94
1.73
6
GTCGTAAAGT
494
7


 


ETV4_v16
1.90
1.70
5
ACCGGAAATG
134
0


 


HOXC10_v14
1.85
1.65
6
GTCGTAAATT
495
7


 


ETV6_v8
1.84
1.64
6
ACCGGAAGTG
132
0


 


ETV4_v1
1.82
1.63
6
ACCGGAAGTG
132
10


 


MYCN_v22
1.80
1.60
5
GTCCACGTGGCC
496
7


 


SP3_v8
1.79
1.59
5
GGCCCCGCCCACC
497
0


 


HOXC10_v15
1.78
1.58
6
GTCGTAAATT
495
3


 


TCF7_v18
1.72
1.54
5
TCCTTTGAAGT
498
7


 


TCF7_v22
1.72
1.53
5
TCCTTTGAACT
272
7


 


ETV4_v23
1.72
1.53
6
AGCGGAAGTG
499
3


 


ZNF281_v13
1.71
1.52
5
GGGGGAAGGGAG
500
10


 


HOXC10_v4
1.71
1.52
6
GTCGTAAAAT
501
0


 


FOSL2_v1
1.70
1.51
5
GGATGACTCAT
135
10


 


PAX8_v19
1.64
1.46
5
GTCATGCATGACTGC
502
3


 


E2F2_v23
1.62
1.45
6
GTTTGGGCGCCATTTC
503
3


 


SP3_v19
1.61
1.43
5
GGACCCGCCCACC
504
3


 


SIX4_v4
1.60
1.43
5
GAAACCTGAGC
505
0


 


SIX4_v10
1.58
1.41
5
GAAACTTGAGC
506
7


 


NFIC_v10
1.56
1.39
5
TACTTGGCATA
306
7


 


HOXC9_v15
1.56
1.39
6
GTCGTAAACT
493
3


 


PAX7_v15
1.55
1.38
5
ATTAATCGATTATTT
507
3


 


RUNX1_v17
1.52
1.36
5
GTCTGTGGCTT
508
10


 


DLX1_v8
1.52
1.36
6
GTAATTAC

0


 


RREB1_v14
1.52
1.35
6
CCCCAAACCACCACCCCCCC
509
7
















TABLE 1G







TATA-TSS PDX430


















SEQ




Expression

Barcode

ID



construct
Score
Fold Change
Support
Motif
NO:
Spacer
















TCF7_v2
5.12
11.18
6
TCCTTTGATGT
300
7


 


TCF7L1_v19
4.35
9.49
6
AGACATCAAAGG
490
3


 


TCF7_v7
3.21
7.00
5
TCCTTTGATCT
492
3


 


TCF7_v19
2.78
6.07
5
TCCTTTGAAGT
498
3


 


TCF7_v3
2.78
6.06
5
TCCTTTGATGT
300
3


 


ETV4_v14
2.54
5.54
6
ACCGGAAATG
134
7


 


TCF7L1_v5
2.44
5.32
6
AAACATCAAAGG
143
10


 


ETV4_v2
2.37
5.17
6
ACCGGAAGTG
132
7


 


ETV4_v6
2.36
5.15
6
ACCGGAAGCG
137
7


 


ETV4_v10
2.29
5.00
5
ACCGGATGTG
336
7


 


ETV6_v6
2.18
4.75
5
ACCGGAAGTG
132
7


 


HOXC10_v24
2.07
4.51
6
GTCGTAAACT
493
0


 


HOXC10_v4
2.01
4.38
6
GTCGTAAAAT
501
0


 


ETV4_v8
1.94
4.23
5
ACCGGAAGCG
137
0


 


TCF7L1_v4
1.91
4.16
5
AAAGATCAAAGG
510
0


 


TCF7_v23
1.87
4.09
6
TCCTTTGAACT
272
3


 


ZNF354A_v7
1.80
3.94
5
ATAAATATAAAAGGACTAATT
511
3


 


TCF7_v18
1.80
3.93
5
TCCTTTGAAGT
498
7


 


TCF7L1_v11
1.69
3.70
6
AGAGATCAAAGG
512
3


 


DLX1_v24
1.65
3.61
6
GTCATTAC

0


 


FOSL2_v4
1.64
3.58
5
GGATGACTCAT
135
0


 


ZNF384_v14
1.63
3.55
5
TTGAAAAAAAAA
513
7


 


HNF1A_v13
1.62
3.54
5
AGTTAATTATTAACT
514
10


 


SIX4_v6
1.59
3.48
5
GAAACATGAGC
489
7


 


ETV4_v13
1.58
3.46
6
ACCGGAAATG
134
10


 


PAX7_v3
1.54
3.37
5
ATTAATCAATTATTT
515
3


 


TCF7L1_v24
1.53
3.35
6
AAACTTCAAAGG
491
0


 


SP3_v24
1.50
3.28
6
GGCCCCGCCTACC
516
0


 


HOXB9_v4
1.47
3.21
5
GTCGTAAAAT
501
0


 


TCF7L1_v23
1.44
3.14
6
AAACTTCAAAGG
491
3


 


TCF7L1_v8
1.44
3.13
6
AAACATCAAAGG
143
0


 


E2F3_v20
1.43
3.12
5
ATTTTGGCGCGAAAAT
517
0


 


HOXA1_v8
1.42
3.09
6
GTAATGAC

0


 


RORB_v4
1.38
3.00
6
AATTAGGTCAC
518
0


 


PAX7_v12
1.37
3.00
5
ATTAATCAATTTTTT
519
0


 


HOXB9_v13
1.37
2.99
6
GTCGTAAACT
493
10


 


TCF7_v22
1.36
2.97
5
TCCTTTGAACT
272
7


 


SP3_v12
1.35
2.95
6
GGACACGCCCACC
520
0


 


HOXA1_v4
1.35
2.95
6
GTAATTAC

0


 


HOXB9_v17
1.34
2.92
6
GTCGTAAAGT
494
10


 


HOXB9_v18
1.34
2.92
6
GTCGTAAAGT
494
7


 


HOXC10_v15
1.33
2.91
6
GTCGTAAATT
495
3


 


HOXC9_v15
1.33
2.91
6
GTCGTAAACT
493
3


 


ETV4_v1
1.32
2.89
6
ACCGGAAGTG
132
10


 


SP3_v11
1.32
2.89
6
GGACACGCCCACC
520
3


 


ETV4_v19
1.32
2.88
5
ACCGGAAGGG
521
3


 


ETV4_v16
1.32
2.88
5
ACCGGAAATG
134
0


 


HOXC10_v14
1.31
2.87
6
GTCGTAAATT
495
7


 


TWIST1_v3
1.31
2.85
5
ATTCCAGATGTTT
131
3


 


DLX4_v3
1.29
2.82
6
CCAATTAC

3
















TABLE 1H







coreBIRC5 PDX586


















SEQ




Expression
Fold
Barcode

ID



Construct
Score
Change
Support
Motif
NO:
Spacer
















TRPS1_v22
2.22
1.85
5
TATTTTATCTTT
129
7


 


TP53_v21
1.80
1.50
5
AACATGCCTGGGCATGTC
522
10


 


TP53_v5
1.76
1.47
6
AACATGCCCGGACATGTC
523
10


 


TWIST1_v3
1.75
1.46
5
ATTCCAGATGTTT
131
3


 


MYCN_v13
1.70
1.42
5
GCCCACGTGGCC
524
10


 


MNX1_v18
1.66
1.38
5
GTCATTAT

7


 


TP53_v1
1.65
1.37
6
AACATGCCCGGGCATGTC
525
10


 


TP53_v10
1.59
1.32
5
AACATGTCCGGGCATGTC
526
7


 


HOXB9_v5
1.57
1.31
6
GTCGTAAATT
495
10


 


SIX2_v5
1.57
1.31
5
AACTGTAACCTGATAC
341
10


 


TP63_v3
1.56
1.30
5
AACATGTTGGGACATGTC
527
3


 


SIX4_v16
1.55
1.29
5
GAAATCTGAGC
299
0


 


HOXB9_v15
1.51
1.26
6
GTCGTAAACT
493
3


 


SOX11_v16
1.50
1.25
5
GAGAACAAAGCA
528
0


 


E2F8_v21
1.50
1.25
5
TTCGCGCTAAAA
146
10


 


HOXA1_v12
1.49
1.24
6
GTCATTAC

0


 


TP53_v6
1.48
1.23
6
AACATGCCCGGACATGTC
523
7


 


CREB3L1_v1
1.46
1.22
5
ATGCCACGTCATCA
529
10


 


TFDP1_v6
1.45
1.21
6
GGGCGGGAACG
140
7


 


ETV4_v14
1.44
1.20
6
ACCGGAAATG
134
7


 


SURV_v9
1.43
1.20
6
GGGCGTGCGCTCCCGACAAGCCC
530
0


 


TP53_v16
1.41
1.18
6
AACATGCCCAGGCATGTC
531
0


 


TP53_v8
1.41
1.18
5
AACATGCCCGGACATGTC
523
0


 


FOXE1_v3
1.40
1.17
5
CCTAAATAAACAAA
532
3


 


EN1_v23
1.40
1.17
6
GCAATTAG

3


 


ZBTB7B_v21
1.40
1.17
5
GCAACCACCGAA
270
10


 


TRPS1_v20
1.40
1.16
6
TAACTTATCTTT
139
0


 


TP53_v22
1.39
1.16
6
AACATGCCTGGGCATGTC
522
7


 


SP3_v8
1.39
1.16
5
GGCCCCGCCCACC
497
0


 


SIX2_v20
1.38
1.15
5
AACTGAAACTTGATAC
339
0


 


TP53_v7
1.38
1.15
5
AACATGCCCGGACATGTC
523
3


 


TWIST1_v1
1.37
1.15
5
ATTCCAGATGTTT
131
10


 


MYBL2_v4
1.37
1.15
5
AACCGTTAAACGGTC
533
0


 


SIX2_v17
1.37
1.14
6
AACTGAAACTTGATAC
339
10


 


TP53_v24
1.36
1.14
6
AACATGCCTGGGCATGTC
522
0


 


TRPS1_v11
1.36
1.13
5
TAGCTTATCTTT
142
3


 


Control-0_Filler_v3
1.36
1.13
26





 


TP53_v20
1.35
1.13
6
AACATGTCCGGACATGTC
534
0


 


GATA1_v1
1.35
1.12
6
TTCTAATCTAT
133
10


 


SHOX2_v16
1.34
1.12
5
CCAATTAG

0


 


TP53_v9
1.33
1.11
6
AACATGTCCGGGCATGTC
526
10


 


HOXB7_v16
1.33
1.11
6
GGTAATTGAC
535
0


 


E2F4_v9
1.32
1.10
5
TTTTGGCGCCTTTT
536
10


 


E2F2_v12
1.31
1.09
5
GTTTTGGCGCCTTTTC
537
0


 


SIX4_v21
1.30
1.09
5
GAAATTTGAGC
538
10


 


SURV_v3
1.30
1.09
5
GGGCAAGCGCTCCCGACATGCCC
539
0


 


DLX4_v12
1.30
1.08
6
CAAATTAC

0


 


BARX1_v11
1.29
1.08
6
GCGATTAG

3


 


NR2F6_v4
1.29
1.08
5
GAGGTCAAAGGTCA
540
0


 


TFDP1_v7
1.29
1.07
5
GGGCGGGAACG
140
3
















TABLE 1I







TATA-TSS PDX586


















SEQ




Expression
Fold
Barcode

ID



Construct
Score
Change
Support
Motif
NO:
Spacer
















TP53_v5
2.73
5.63
6
AACATGCCCGGACATGTC
523
10


 


NPAS2_v11
2.59
5.34
6
GACACGTGTC
314
3


 


HES6_v11
2.52
5.21
6
GGCACGTGTA
316
3


 


SURV_v3
2.41
4.97
6
GGGCAAGCGCTCCCGACATGCCC
539
0


 


TP53_v22
1.93
3.97
6
AACATGCCTGGGCATGTC
522
7


 


HES6_v3
1.82
3.76
6
GGCACGTGTT
321
3


 


TP53_v10
1.79
3.69
6
AACATGTCCGGGCATGTC
526
7


 


TP53_v13
1.79
3.69
5
AACATGCCCAGGCATGTC
531
10


 


TP53_v18
1.74
3.60
5
AACATGTCCGGACATGTC
534
7


 


TP53_v16
1.74
3.59
6
AACATGCCCAGGCATGTC
531
0


 


SURV_v15
1.73
3.57
6
GGGCTAGCGCTCCCGACATGCCC
541
0


 


HES6_v7
1.71
3.53
5
GGCACGTGTC
317
3


 


ASCL1_v23
1.66
3.43
5
GGCACGTGCC
322
3


 


TFDP1_v4
1.59
3.27
6
GGGCGGGAAGG
542
0


 


FOSL2_v4
1.57
3.25
5
GGATGACTCAT
135
0


 


TFDP1_v19
1.57
3.23
5
GGGCGGGACGG
543
3


 


TP53_v1
1.55
3.19
6
AACATGCCCGGGCATGTC
525
10


 


Control-1_FOSL1_v1
1.54
3.18
27





 


MYC_v22
1.46
3.01
6
GGACACGTGCCC
544
7


 


TP53_v6
1.45
2.99
6
AACATGCCCGGACATGTC
523
7


 


SP3_v24
1.45
2.98
6
GGCCCCGCCTACC
516
0


 


CREB3L1_v18
1.42
2.92
5
ATGCCACGTAATCA
294
7


 


ETV4_v10
1.41
2.90
5
ACCGGATGTG
336
7


 


CREB3L1_v6
1.37
2.82
6
ATGCCACGTCACCA
144
7


 


SOX11_v17
1.33
2.75
6
GGGAACAAAGAA
545
10


 


SP3_v12
1.32
2.73
6
GGACACGCCCACC
520
0


 


TP53_v24
1.31
2.70
6
AACATGCCTGGGCATGTC
522
0


 


SP3_v20
1.30
2.69
6
GGACCCGCCCACC
504
0


 


HOXC9_v15
1.30
2.68
6
GTCGTAAACT
493
3


 


ETV4_v14
1.28
2.65
6
ACCGGAAATG
134
7


 


HOXC10_v14
1.28
2.64
6
GTCGTAAATT
495
7


 


SP3_v22
1.28
2.64
5
GGCCCCGCCTACC
516
7


 


HES6_v6
1.27
2.61
6
GGCACGTGTC
317
7


 


CREB3L1_v14
1.26
2.61
6
ATGCCACGTCAACA
320
7


 


SURV_v6
1.25
2.58
6
GGGCATGCGCTCCCGACATGCCC
546
0


 


FOSL2_v7
1.25
2.57
6
GGATGACTCAG
313
3


 


HOXC10_v15
1.24
2.57
6
GTCGTAAATT
495
3


 


HOXA1_v8
1.23
2.54
6
GTAATGAC

0


 


BARX1_v7
1.23
2.53
5
GCCATTAG

3


 


HES6_v10
1.22
2.51
5
GGCACGTGTA
316
7


 


ETV6_v6
1.21
2.50
5
ACCGGAAGTG
132
7


 


CREB3L1_v12
1.21
2.50
5
ATGCCACGTCAGCA
547
0


 


DLX1_v24
1.21
2.50
6
GTCATTAC

0


 


TP53_v8
1.20
2.48
6
AACATGCCCGGACATGTC
523
0


 


SP3_v1
1.20
2.48
6
GGCCACGCCCACC
548
10


 


ZNF281_v15
1.20
2.48
5
GGGGGAAGGGAG
500
3


 


RREB1_v21
1.19
2.46
5
CCCCAAAACAACCCCCCCCC
549
10


 


MYCN_v3
1.19
2.45
5
GGCCACGTGGCC
550
3


 


TWIST1_v22
1.18
2.44
5
ATTGCAGATGTTT
340
7


 


NPAS2_v1
1.17
2.41
5
GGCACGTGTC
317
10
















TABLE 1J







Core Promoter Sequences









SEQ ID




NO:
Name
Sequence





558
PR181
CATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAA




CTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTT




TCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGG




TATGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAG




AAGCTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGT




GAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTT




GCTGGAGTGAATTCGGGCCTCTGATTA


 


559
PR180
ACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTGA




AAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAAC




CCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTTA




GCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCTG




GTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAAGAAGCTTGG




ACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAAT




CCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGT




GAATTCGGGCCTCTGATT


 


560
PR179
CCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATC




TGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCG




AAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAcggcggcgcagategc




ccggcgcggctccgccccctgcgccggtcacgtgggggcgccggctgcgcctgcggagaagcggtggccgc




cgagcgggatctgtgcggggagccggaaatggttgtggactacgtctgtgcggctgcgtggggctcggccgcgc




ggactgaaggagactgaaggtgctggggggaccctgatgtggA


 


561
PR178
CCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATC




TGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCG




AAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCACtttttccgtgctacctgc




agaggggtccatacggcgttgttctggattcACCGGTa


 


562
PR177
CCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATC




TGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCG




AAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCACACTCGCGCTG




CCATCACTCTTCCGCCGTCTTCGCCGCCATCCTCGGCGCGACTCGCTT




CTTTCGGTTCTACCAGGTAGAGTCCGCCGCCATCCTCA


 


563
PR176
CCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATC




TGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCG




AAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGAAGCTTGGAC




CGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGTGAGGAAATCC




AGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTTGCTGGAGTGA




ATTCGGGCCTCTGATTA


 


564
PR175
CCGGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCT




ATCTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATC




TGTAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCG




AAAGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAAAATCCAGAGC




GGCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCGGTT




CTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAGGGG




GATGGCTGAAgaattcA


 


565
PR174
CACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTG




AAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAA




CCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTT




AGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCT




GGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAAcggcggcgcaga




tcgcccggcgcggctccgccccctgcgccggtcacgtgggggcgccggctgcgcctgcggagaagcggtggc




cgccgagcgggatctgtgcggggagccggaaatggttgtggactacgtctgtgcggctgcgtggggctcggccg




cgcggactgaaggagactgaaggtgctggggggaccctgatgtggA


 


566
PR173
CACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTG




AAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAA




CCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTT




AGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCT




GGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAACtttttccgtgcta




cctgcagaggggtccatacggogttgttctggattca


 


567
PR172
CACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTG




AAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAA




CCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTT




AGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCT




GGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAACACTCGCG




CTGCCATCACTCTTCCGCCGTCTTCGCCGCCATCCTCGGCGCGACTCG




CTTCTTTCGGTTCTACCAGGTAGAGTCCGCCGCCATCCTCA


 


568
PR171
CACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTG




AAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAA




CCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTT




AGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCT




GGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAAGTATCCCA




GGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGA




GCCCGGGTTACCAGCTCTTAA


 


569
PR170
CACCTCTTAACAATACGTTTCACAAATAGTTAAAAACATGCATACTG




AAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAACTCTTTAA




CCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTTTCTGAGTT




AGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGGTgTGCCCT




GGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAAAAATCCAG




AGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGACAGACTCTCCG




GTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCTGGAGTTCTTAG




GGGGATGGCTGAAgaattcA


 


570
PR169
CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGCcggcggcgcagatcgcccggcgcggctccgccccctgcgccggtcacgtgggggcgccggctgcg




cctgcggagaagcggtggccgccgagcgggatctgtgcggggagccggaaatggttgtggactacgtctgtgc




ggctgcgtggggctcggccgcgcggactgaaggagactgaaggtgctggggggaccctgatgtggA


 


571
PR168
CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGCCtttttccgtgctacctgcagaggggtccatacggcgttgttctggattca


 


572
PR167
CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGCCACTCGCGCTGCCATCACTCTTCCGCCGTCTTCGCCGCCATCCT




CGGCGCGACTCGCTTCTTTCGGTTCTACCAGGTAGAGTCCGCCGCCAT




CCTCA


 


573
PR166
CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGCGTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGC




GGCTGTGCTGGAGCCCGGGTTACCAGCTCTTAA


 


574
PR165
CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGCGAAGCTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGG




TGGGTGAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGG




TACTTGCTGGAGTGAATTCGGGCCTCTGATTA


 


575
PR159
agcttgcatgcctgcaggtcggagtactgtcctccgagcggagtactgtcctccgagcggagtactgtcctccgag




cggagtactgtcctccgagcggagtactgtcctccgagcggtgcgctcccgacatgccccgcggcgcgccattaa




ccgccagatttgagtcgcgggacccgttggcagaggtggg


 


576
PR156
AGTGGTGGGGGAGTGAAAAGAGAGATGGAGAAAGAGGGGATGGGC




AGAAAGAGGAGGAGGAGTCAGGGGCAGGGCATGGAGGTGGGTGGG




GCTGGGCTGCCAAAGCAGGATAAATGCACACCTGCCTGCTGGTCTGG




GCTCCCTGCCTCGGGCTCTCACCCTCCTCTCCTGCAGCTCCAGCTTTG




TGCTCT


 


577
PR155
CATACTGAAAAGCATACTTTTGCAATGTTATTTTTAAAAACAAGGAA




CTCTTTAACCCAGGGAAGATAATCACTTGGGGAAAGGAAGGTTCGTT




TCTGAGTTAGCAACAAGTAAATGCAGCACTAGTGGGTGGGATTGAGG




TGTGCCCTGGTGCATAAATAGAGACTCAGCTGTGCTGGCACACTCAG




AAGCTTGGACCGCATCCTAGCCGCCGACTCACACAAGGCAGGTGGGT




GAGGAAATCCAGGTAAGGCTCCTGACAGCAGCTTTAGAAGGGTACTT




GCTGGAGTG


 


578
PR154
GGCCCGCCCCCTTTCCTTACGCGGATTGGTAGCTGCAGGCTTCCCTAT




CTGATTGGCCGAACGAACGCAGCGCGTAATTTAAAATATTGTATCTG




TAACAAAGCTGCACCTCGTGGGCGGAGTTGTGCTCTGCGGCTGCGAA




AGTCCAGCTTCGGCGACTAGGTGTGAGTAAGCCAGTATCCCAGGAGG




AGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCTGTGCTGGAGCCCG




GGTTACCAGCTCTT


 


579
PR153
GGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCACC




TGCAAATCCAGAGCGGCGGGCACTGACGGGCACTTGCACCGTGTGGA




CAGACTCTCCGGTTCTGTGAGTGGTTTTTCTTTTCCCGGGTCGGACCT




GGAGTTCTTAGGGGGATGGCTGa


 


580
PR152
ACCCACGTGATGCTGAGAAGTACTCCTGCCCTAGGAAGAGACTCAGG




GCAGAGGGAGGAAGGACAGCAGACCAGACAGTCACAGCAGCCTTGA




CAAAACGTTCCTGGAAC


 


581
PR151
TATAAAAGGCCAGCAGCAGCCTGACCACATCTCATCC


 


582
PR150
CACTCCCAGAAGGCAGCGGGCGAGGGCGTGGGGCCGGGGCTCTCCC




GGCATGCTCTGCGGCGCGCCTCCGCCCGCGCGATTTGAATCCTGCGTT




TGAGTCGTCTTGGCGGAGGTTGTGGTGACGC


 


583
PR131
tcccgacatgccccgcggcgcgccattaaccgccagatttgagtcgcgggacccgttggcagaggtg


 


584

GTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGT


 


585

CGGGAAAAGTTCAGCTGAGAGATATAAAAGAGCAGTCTTTCCAGCAC




CTGC


 


586

GTATCCCAGGAGGAGCAAGTGGCACGTCTTCGGGTGAGTGTGCGGCT




GTGCTGGAGCCCGGGTTACCAGCTCTTAA


 


587

CAGTGTGCGGCTGTGCTGGAGCCCGGGTTACCAGCTCTT









In some embodiments, the sequence of any of the core promoters listed in Table 1J can further comprise, at the 5′ end, any of SEQ ID NOs: 377-397 listed in Table 1B, or reverse complements thereof. In some embodiments, the sequence of any of the core promoters listed in Table 1J can further comprise, at the 5′ end, any of SEQ ID NOs: 377-397 listed in Table 1B, or reverse complements thereof, in a vector. In some embodiments, the sequence of any of the core promoters listed in Table UJ can further comprise, at the 5′ end, any of SEQ ID NOs: 377-397 listed in Table 1B, or reverse complements thereof, in a nanoplasmid. In some embodiments, the sequence of any of the core promoters listed in Table UJ can further comprise, at the 5′ end, any of SEQ ID NOs: 377-397 listed in Table 1B, or reverse complements thereof, in a linked double-stranded DNA.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, optionally in a vector, further optionally, in a nanoplasmid or linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012 and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012 and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012 and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In an embodiment, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, SRE012, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012, SRE007, and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector.
In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector.
In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA.
In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE007 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE007, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE008 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE008 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE008 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE008, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector.. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE010 and SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE010, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a vector. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a nanoplasmid. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, PR181 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR180 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR179 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR178 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR177 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR176 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR175 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR174 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR173 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR172 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR171 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR170 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR169 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR168 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR167 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR166 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR165 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR159 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR156 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR155 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR154 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR153 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR152 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR151 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR150 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, PR131 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 584 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 585 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 586 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, SEQ ID NO: 587 can further comprise, at the 5′ end, a sequence comprising SRE012, or a reverse complement thereof, in a linked double-stranded DNA. In some embodiments, any of these named elements can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a nucleic acid having any of these named elements and any of SEQ ID NOs: 584-587 can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
In some embodiments, the disclosure provides for a nucleic acid comprising any of the sequences described herein separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, the nucleic acid can comprise any of the sequences listed in Table 1B or any one of the sequences listed in Table 1J separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments, a sequence comprising any of nucleic acid sequences listed in Table 1B and any one of the core promoter sequences listed in Table 1J can be separated by a linker of variable length, wherein the linker can comprise a sequence of 1, 2, 5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
EXAMPLES
These examples are provided for illustrative purposes only and not to limit the scope of the claims provided herein.
Example 1: Development of a High-Throughput Screening Platform for Novel Cancer-Activated Promoters
In this example, a high-throughput screening (HTS) platform to design and test synthetic sequence elements that can drive cancer specific expression of a report gene or a gene of interest. Synthetic promoters described herein comprise a core promoter and one or more response elements. Response elements can be designed by tiling binding sites for putative transcription factor candidates identified through transcriptomics and proteomics. Using Massively Parallel Reporter Assay (MPRA) method, 1,800 unique synthetic response elements placed in front of (5′ end of) the two different core promoters were screened. Synthetic promoters were able to drive expression up to 80 times higher than the previously described FOS-coreBIRC5 synthetic promoter. In addition, TF tiles for TCF7 (a downstream target of the WNT signaling pathway) and TPS3 (a tumor suppressor that is mutated in many cancers) that can drive expression 100 times or more within a specific lung cancer cell line that represents a specific pathway dysregulation were identified. The MPRA platform allows simultaneously testing thousands of hypotheses from the multi-omics identification of key transcription factors in cancer combined with different design strategies for a functioning response element, as demonstrated in this example. Low-throughput validation demonstrated that the MPRA accurately identifies winning candidates from thousands of test sequences. This MPRA pipeline is a key component of the workflow to develop and test hypotheses for cancer-regulated gene expression at a massive, highly parallelized scale. The MPRA can be performed by assembling a pooled library of reporter plasmids that interrogate the function of a candidate DNA sequence through an expressed barcode. The pool of reporter plasmids can be transfected into mammalian cell lines and then harvested for RNA. The barcodes from the mRNA and the input DNA can be sequenced using Next Generation sequencing techniques. The input DNA barcode can be used to normalize the mRNA barcode to get the final expression level for each candidate DNA sequence.
Genes are highly regulated by a complex collaboration between the transcription factors downstream of signaling pathways and the DNA regulatory elements they interact with. These DNA regulatory elements include promoters, 5′ and 3′UTRs, and distal and proximal enhancers. Cancer is marked by aberrant molecular signaling leading to highly active transcription factors and functional signaling cascades that might normally only be found in early development or in other disease states, leading to hallmark cancer phonotypes such as uncontrolled growth and invasion/metastasis. The regulatory elements of these dysregulated genes can be re-used in exogenous vectors to drive expression that is restricted to cancer cells. For example, the promoters for Survivin and hTERT have been used exogenously to drive tumor specific expression. Although endogenous promoters can be used as cancer-activated regulatory elements, by having highly complex logic and interplay of multiple transcription factor binding sites, they can be unpredictable and have higher basal activity than desired. Endogenous promoters also rarely drive very high signal even in the correct cell-state or genomic profile to activate TFs, as few natural promoters have been naturally evolved to have the high level of expression observed in the constitutive viral-origin promoters often used in gene therapy.
A stronger, and more predictably activated promoter can be engineered by bringing together diverse regulatory elements that respond to a variety of signaling pathways that might not be found in a single regulatory element. For these reasons, a synthetic approach has been developed to construct novel cancer-activated promoters, as further described in Example 2.
Synthetic promoters were constructed by combining a small core promoter from a gene upregulated in cancer with synthetic response elements to particular dysregulated TFs. These response elements comprise a series of repeated binding sites for the desired TFs. Various “-omics” based approaches have been used to identify TFs that are enriched in tumor targets, and hundreds of possible candidate TFs have been identified. Each of those TFs has many possible binding sites and configurations that can create the most efficacious response element. As testing each individual candidate element in series can be costly in labor and time, a high-throughput approach was used to test thousands of synthetic promoter elements simultaneously.
The screening assay that most closely aligns with the vector design and transient delivery platform described herein is the MPRA (Massively Parallel Reporter Assay). In this assay, short oligos containing a sequence of interest coupled with a unique barcode was synthesized and cloned as a pool into a reporter plasmid. This plasmid pool was transfected into a cell line and the expression of each sequence of interest was measured in parallel through targeted barcode sequencing of the RNA and plasmid DNA. MPRAs have been used to identify endogenous human enhancers, determine the role of genetic variation on gene expression, and characterize sequence determinants of gene regulation. This screening assay is an ideal method to simultaneously test and identify synthetic promoters that drive strong expression in relevant cancer models.
A high-throughput screening platform (MPRA) to identify novel synthetic promoters that can drive cancer-activated expression is described in this example.
High-Throughput Screening (HTS) Methodology
Overview
The MPRA was performed by assembling a pooled library of reporter plasmids that interrogate the function of a candidate DNA sequence through an expressed barcode. The pool of reporter plasmids was transfected into mammalian cell lines and then harvested for RNA. The barcodes from the mRNA and the input DNA were sequenced using Next Generation sequencing (NGS) techniques. The input DNA barcode was used to normalize the mRNA barcode to get the final expression level for each candidate DNA sequence.
Homotypic TF Tile Library Design
A computational pipeline that systematically creates synthetic DNA sequences that contain repeated TF binding sites (TF tiles) was developed using the following parameters:

    
    
        1. Total Length: The full length of the synthetic DNA sequence. A length of 140 bp was used.
        2. Total Number of Binding Sites in a Tile: The number of repeated binding sites that make up the homotypic TF tile. 6 repeated binding sites were used.
        3. Spacing: The number of nucleotides between each of the TF binding sites. 0, 3, 7, and 10 bp spacing were used.
        4. Binding Site Sequence: The binding site sequences for each tile were chosen using the TF's position frequency matrix (PFM) from either the HOMER or JASPAR database. The pipeline used the frequency of each nucleotide at each position and chose the most frequent nucleotide or nucleotides based on a user defined frequency cut off. Once a nucleotide was chosen for one position all other positions were assigned the most frequent nucleotide. The pipeline used a 10% cut off and focused on the positions at the core of the motif. For example, if at the center position the frequency of A, T, C, G is 5%, 5%, 30%, 60%, respectively, then two binding sites were chosen. One would have a C and the other would have a G and all other positions would have the highest frequency nucleotide.
    
    


In addition, the pipeline has the following features:

    
    
        1. Length Consistency: For TF tiles that were shorter than the total length, a small filler sequence was added to the 5′ end. This short sequence was randomly chosen from a 1 kb filler sequence that was manually curated to reduce strong binding site for characterized TFs. This created synthetic DNA sequences that were the same length with little to no effect on the overall expression.
        2. Restriction Enzyme Check: Each synthetic DNA sequence was checked for restriction enzyme cut sites used in the cloning method. In this example, the KpnI and XbaI cut sites were used and checked.
        3. Addition of Cloning Sequences: Primer sites and restriction enzyme sites were added to facilitate the cloning workflow.
        4. Addition of Barcodes: A unique barcode was added to each synthetic DNA sequence. These barcodes were created using the DNABarcodes R package. This package created large numbers of barcodes that were different enough from each other that when mutations were introduced during the sequencing and library preparation the barcodes were still distinguishable.
    
    


Using the pipeline described above, homotypic TF Tiles for 77 Lung adenocarcinoma (LUAD) specific TFs were designed. These TF were computationally identified using various multiomic data sets, including RNA-seq and proteomics (see Example 2). A full list of TFs can be found in Table 1D-1I. 24 TF tiles were designed for each TF (6 binding site variations each with 4 different spacing variants: 0, 3, 7, 10 bp). Each tile was assigned 6 barcodes for a total of 144 DNA sequences for each TF. Additionally, positive expression controls and controls for the baseline core promoter expression were included. The positive expression controls include FOSL and Canscript (see Example 2), and 90 barcodes were assigned to each. Baseline expression controls comprised 5 different 140 bp segments of the filler sequence (curated to remove all strong TF binding sites) that were assigned 30 barcodes for a total of 150. An oligo pool of ˜12,000 oligos containing the synthetic TF tile, the assigned barcode, and necessary sequences for cloning was ordered from a vendor (TWIST BIOSICENCES).
FIG. 13 (top) shows each synthetic DNA sequence that was designed as a series of repeated transcription factor (TF) binding sites derived from the consensus binding motif for the TF of interest (blue). To test the impact of the different relative positioning of these sites around the helical nature of the double stranded DNA (one helical turn is equivalent to ˜10.5 base pairs), the repeated binding sites were separated by a variable length of nucleic acid spacer sequences (FIG. 13, yellow). Lastly, the synthetic DNA sequence contained a short filler sequence (FIG. 13, grey) to maintain consistent total length of the candidate enhancer sequence block.
Building the MPRA Library
Base Plasmid
A base plasmid that contains the key features necessary for cloning, mammalian expression, and transfection efficiency monitoring was constructed. The plasmid has SfiI restriction enzyme sites for cloning in synthetic oligos, and a reverse selection cassette for removing undesired cloning products. For mammalian expression, the plasmid has a strong polyA termination site downstream of (or 3′ to) where the final expression cassette will be located. There is an additional polyA termination site upstream of (or 5′ to) the final expression cassette that reduces errant transcripts that might be produced by the bacterial components of the plasmid. Lastly, a constitutively expressed GFP cassette was added to monitor the transfection efficiency either visually under a fluorescent microscope or using FACS.
Cloning Round 1: Oligo Pool
The single stranded oligo pool was PCR amplified to create a pool of double stranded DNA fragments. To maintain the integrity of the library (size and complexity), an emulsion PCR with a limited number of cycles ranging from 12-20 cycles was used. Next the base plasmid and double stranded DNA pool were digested with the SfiI restriction enzyme. The base plasmid was gel extracted using the QIAGEN® II Gel Extraction Kit, a standard gel extraction kit. The double stranded DNA pool was purified using the Monarch® PCR and DNA Cleanup Kit, a standard DNA cleanup kit. The digested products were ligated overnight using a T4 DNA ligase and electroporated into bacteria at a recovery efficiency of at least 100 times the complexity (number of unique DNA sequences) of the oligo library. The integrity of the library was validated by performing Sanger sequencing on 40 individual clones. All clones that were Sanger sequenced contained a unique sequence from the oligo pool, indicating that the library's complexity was maintained. In addition, there was only 1 sequenced clone that contained a large variation in the sequence, indicating an estimated error rate of less than 3%, which met the tolerated criteria. The bacteria pool was cultured overnight at 30° C., and a plasmid prep was done using the ZymoPURE™ II Plasmid Maxiprep Kit, a standard plasmid purification kit. The product was a plasmid pool containing the library of synthetic sequences. Each of these sequences contained the XbaI and KpnI restriction enzyme sites. These sites were used in the next round of cloning to add in the core promoter and luciferase expression.
Cloning Round 2:
The plasmid pool from the Round 1 cloning was serially digested with KpnI and XbaI. Each digestion was purified using the Monarch® PCR and DNA Cleanup Kit, a standard DNA cleanup kit. The final digested product was treated with CIP to dephosphorylate the overhangs. Additionally, plasmids containing the coreBIRC5-Fluc or the TATA-TSS-Fluc cassette were digested with KpnI and XbaI, and gel extracted using a standard kit. The digested plasmid pool and core promoters were ligated overnight and electroporated into bacteria at a recovery efficiency of at least 100 times the complexity of the oligo library. 10 single clones were Sangar sequenced to validate the integrity of the library and expression cassette. Each of the clones sequenced had an intact core promoter-luciferase expression cassette and the expected TF tile-barcode combination. The pools of bacteria were cultured, and the plasmid libraries were extracted using a standard maxiprep kit.
Transfections and Library Preparation
Cell Line Transfections
Each library was transfected independently at least 3 times (3 replicates) in various lung cancer model cell lines, including the well-studied H1299 and several patient-derived xenografts (PDXs) from human lung tumors. Cells for each line were seeded at appropriate densities on 6-well plates. The total number of cells seeded was at least 100 times the complexity of the library and scaled for the typical transfection efficiency of the relevant cell line. For example, with the library complexity of 12,000 and a cell line of a transfection efficiency of 75%, 1.6e6 cells total were seeded for each replicate. Cells were transfected using the commercial product Lipofectamine™ 3000, a transfection agent comprising DOSPA (2,3-dioleoyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propaniminium trifluoroacetate) and DOPE (dioleoyl phosphatidylethanolamine), and harvested after 24 or 48 hours depending on the cell viability. Before harvesting, the transfection efficiency was evaluated by visual inspection of GFP expression using a fluorescent microscope. If the transfection efficiency was lower than expected, it was repeated.
NGS Tag-Seq Library Prep
Total RNA was extracted using a standard Trizol™ (a standard nucleic acid isolation reagent) prep method. Briefly, cells from each replicate were resuspended in Trizol™, chloroform was added, and the mixtures were phase-separated using centrifugation. Then, the aqueous layer was removed, and total RNA was recovered using ethanol precipitation. Next, mRNA was isolated using a commercial polyA magnet bead kit (Dynabeads™ mRNA Purification Kit), followed by a commercially available Turbo DNase treatment to remove all DNA fragments, including the transfected plasmid. To ensure that samples did not contain residual plasmid DNA, a pre-NGS PCR was performed using 30-50 ng of mRNA for 26 cycles and the result was visualized on a gel. Samples that had a visual band underwent additional DNase treatments. Next, cDNA production was done using the commercially available Superscript IV™, a standard reverse transcriptase. 400-600 ng of mRNA was used with a poly-dT primer. Targeted PCR amplification was performed to produce an Illumina compatible NGS sequencing library that contained the TF tile associated barcodes. In parallel, NGS sequencing libraries was also produced from the input plasmid DNA library. Indexed libraries were pooled, and paired end sequenced on an Illumina sequencing platform.
Data Processing and Analysis
Barcodes were matched to their respective synthetic TF tiles using the DNABarcodes R package. All libraries had greater than 95% of the sequenced barcodes matched to it synthetic TF tile. To determine the expression scores for our screens, the MPRAnalyze R package was used. Briefly, this package uses a graphical model to relate the barcode counts from the RNA to barcode counts from the input plasmid DNA. It supports the use of multiple barcodes per sequence, multiple replicates, and multiple conditions (i.e., cell line).
Luciferase Assay
For the low throughput validation, cells were transfected using Lipofectamine™ 3000, a transfection agent comprising DOSPA (2,3-dioleoyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propaniminium trifluoroacetate) and DOPE (dioleoyl phosphatidylethanolamine), according to the manufacturer's instructions. Briefly, for each well, 100 ng of plasmid DNA was mixed with 0.2 μL of P3000™ reagent, a neutral/helper co-lipid, and 0.2 μL of Lipofectamine™ 3000 and 2 ng of control DNA in 100 μL Opti-MEM™ medium, a serum-reduced minimal essential medium, and the mixture was incubated at room temperature for 20 minutes. The transfection mixture was added to the cells in a 96-well plate and incubated for 24 hours. Approximately 24 hours after transfection, the firefly luciferase and renilla luciferase levels were measured from each well using the Promega Dual-Glo® Luciferase System (E2940) with a working volume of 50 μL.
Results
Study Design and Synthetic TF Tile Construction
A high-throughput MPRA screen for identifying synthetic regulatory elements that drive strong expression in lung cancer has been developed and validated. In the first high-throughput screen, the focus was on screening synthetic enhancer elements intended to serve as response elements to TFs that play a role in non-small cell lung cancer (NSCLC). A multi-omics approach to NSCLC identified more than 100 TFs that are dysregulated in lung adenocarcinoma (LUAD). Based on the strength of the multi-omics and evidence, and with the filter of DNA binding site characterization, 77 TFs were selected for this library. For each TF, 24,140 bp homotypic tiles that varied in the binding site motif and the spacing between the binding sites were designed. Each binding site motif was tiled 6 times. 6 different binding site motifs with 4 spacing variants (0, 3, 7, and 10 bp) were chosen. 6 barcodes were assigned, and 4 different control TF tiles were also included (FOSL1, TTF, MYC-MAX, Cansript). As a result, a total of 1,850 unique synthetic sequences were designed and constructed.
These unique enhancer sequences were placed in front of (e.g., upstream of or 5′ end of) two core promoters and screened. The two core promoters included the minimal TATA-TSS that drives little to no expression of a reporter gene or a gene of interest, and coreBIRC5 that drives cancer specific expression of a reporter gene or a gene of interest (see Example 1). Additionally, 5 control sequences were included. The control sequences were selected from random sequences and known not to contain TF binding sites and served as negative control, when combined with the core promoters, and the measurement of expression from control sequences were used as the baseline expression. Several positive control TF tiles were also used. These positive control TF tiles had been previously characterized (i.e., FOSL2) (see Example 2). To add redundancy and allow for statistical significance, each TF tile was assigned 6 barcodes for a total screening library size of 12,000.
The coreBIRC5 and TATA-TSS libraries were screened in four lung cancer cell line models: H1299 and three human patient derived xenograft (PDX) tumor cell lines (LXFA586, LXFL1121, and LXFL430). At least 3 biological replicates were performed for each cell line. To measure the activity of the synthetic TF tiles, the detected barcode levels in the RNA were normalized to the DNA input, to calculate an expression score (as described in the Methods above).
High-Throughput Screen Identifies Active Synthetic TF Tiles
In both first two screening libraries, synthetic enhancers were found to drive expression in cancer cell line models with both the TATA-TSS and coreBIRC5 core promoters. The expression score distribution varied between cell lines, with the PDX LXFL430 having the widest distribution and the highest expression scores (FIG. 14).
Next, the fold change for each unique synthetic sequence was calculated using the baseline core promoter expression score to normalize. With the TATA-TSS core promoter driving low levels of expression, these TF tiles had a higher fold change compared to the coreBIRC5 promoter. The positive control FOSL2 tile was strongly active in the H1299 cell line for both core promoters tested, suggesting that there are no candidates that are stronger than the FOS motif for H1299s in this library of dysregulated TFs. Other synthetic response elements were discovered in this approach that were highly active in all cell lines. These include CREB3L1, TWIST, and a set of HOX variants (MNX1, HOXC10, HOXB9).
Other tiles were much more specific for particular genetic backgrounds across different cell lines. For example, the TCF7 and TCF7L1 TF tiles ranked at the top of the list in the LXFL430 cell line but not in any other cell lines. Similarly, the TP53 TF tiles rank highly only in the LXFA586 cell line.
Some TF tiles were found to have a core promoter preference. For example, the TWIST_v3 tile is at the top of the ranked list for the coreBIRC5 promoter but is not highly ranked for the TATA-TSS promoter. Additionally, this TWIST_v3 tile is ranked highly in all cell lines. HOXC10, MNX1, and CREB3L1 tile variants were also ranked higher for two or more cell lines (Table 1D-1I).
Synthetic TF Tile Validation
To establish the validity of the screening strategy and qualify candidates for further testing, a set of high-scoring and low-scoring candidates from the screen was constructed using the coreBIRC5 core sequence in the PDX430 lung cancer cell line. The candidates were cloned into the luciferase reporter plasmid and the expression of the luciferase was measured. Most of the high-scoring enhancer sequences were also found to have expression level that is higher than the core sequence alone, with some candidates approaching levels of internal positive control promoters, FOS-TATA-TSS and High-coreBIRC5 (FIG. 29). In PDX-derived cell line LXFL430, 10 out of 11 TF tiles tested from the top of the list drove significantly higher expression than coreBIRC5 alone (FIG. 29), while only 1 out of 9 sequences tested from the bottom of the list drove expression higher than coreBIRC5.
In summary, more than seven unique TFs were identified as candidates for synthetic enhancers that can drive cancer-regulated gene expression through the two screens described in this example. Some of the candidates appear to be stronger than the previous favorite FOSL2-enhancer element and will be studied further. As shown in FIG. 15, new synthetic promoters comprising coreBIRC5, that responds to HOXC10, MNX1, and CREB3L1, drive stronger expression of the reporter gene than the FOS-coreBIRC5 promoter.
Conclusion
MPRA high-throughput has been successfully implemented to screen 1,800 unique TF tiles in combination with two separate TF tile libraries, one using the TATA-TSS promoter and the other using the coreBIRC5 promoter. These libraries were screened in five different lung cancer cell lines. As expected, most candidate response elements drove expression of a reporter gene similar to the baseline expression of the core promoter alone, supporting the importance of approaching this testing in a highly parallel manner. However, a subset of synthetic promoter elements that drive expression well above the core promoter baseline was identified, as demonstrated by the screening data and low-throughput validation. Synthetic response elements particularly responding to HOXC10, CREB3L1 and MNX1 were found to drive expression across multiple lung cancer cell lines. For example, the HOXC10 element drove the expression of a reporter gene up to 80 times higher than FOS-coreBIRC5 synthetic promoter.
In addition, synthetic response elements that uniquely drive expression in only specific genetic contexts were identified. The screen identified that multiple variations of elements responding to TCF7 or TP53 drove strong expression in only LXFL430 or LXFA586, respectively. Low-throughput validation confirmed the results and have led to designing and testing of combining multiple pathway-sensitive synthetic promoter elements into a single regulatory element. TCF7 is the downstream target of the B-cat/Wnt signaling pathway, which is well-studied in primary & metastatic lung cancer. TP53 is also a well-studied for its role, particularly in mutated form, within non-small cell lung cancer.
Overall, the screening platform successfully identified synthetic promoters that (1) drive expression of a gene broadly across lung cancer models due to universal changes in proliferation and de-differentiation and (2) are downstream of signaling pathways and drive expression in specific lung cancer models. The MPRA developed is a core feature in designing and constructing synthetic promoters, given the vast amount of sequence space to cover when designing completely new promoter sequences from scratch. As demonstrated here, it allows simultaneously testing thousands of hypotheses from the multi-omics identification of key TFs in cancer combined with different design strategies for a functioning response element. The MPRA accurately brings the best candidates to the top, as demonstrated by the low-throughput validation results, and thus can greatly accelerate designing novel synthetic promoters. This MPRA platform, now optimized and fully-developed, can also be applied to test any series of large hypotheses that can result in stronger expression of a gene in any models of choice, such as mutations to UTR sequences, ideal codon optimization, or screening a library of endogenous enhancer sequences.
Example 2: Design and Construction of Synthetic Promoters
In this example, the general strategy of synthetic promoter engineering to combine specific response elements in dysregulated pathways in cancer is described. The modular components (response element, signal element and core promoter) can be individually and synchronously engineered for improved sensitivity, specificity and signal strength in both low-throughput and high-throughput approaches. Response of synthetic promoters to distinct TF upregulation is demonstrated, which indicates that synthetic promoters described herein can establish highly predictable activity in new cell lines.
The cancer-activated promoter is a key component within cancer-activated DNA constructs to drive expression of a synthetic biomarker in cancer cells. Cancer is notably characterized by aberrant molecular signaling, which is a result of dysregulated expression of highly active transcription factors (TFs) and functional signaling cascades that can normally only be found in early development or in other disease states. Synthetic promoters described herein can function directly as response elements or sensors for known dysregulated transcription factors. Synthetic promoters can perform as protein sensors by responding predictably to the presence of phosphorylated TF in the nucleus. This can allow estimating sensitivity and specificity using available in silico data for cancer and normal patients, without having to create and test in empirical models. Empirical testing can follow to demonstrate the responsiveness of a synthetic promoter comprising TF binding sequences to the TF, which allows extrapolating known expression data for that TF in large datasets like The Cancer Genome Atlas (TCGA) or Clinical Proteomic Tumor Analysis Consortium (CPTAC). In addition, as there are no common models for benign tissues, proteomics and transcriptomics of benign lung disease can be studied to determine whether a TF is present, which can be helpful for predicting whether a synthetic promoter comprising the TF binding sequence can activate in those cell states.
The approach to designing cancer-specific promoters starts with identifying the key response elements that bind the TFs. These TFs were identified by a multi-omics approach that utilizes transcriptomics, proteomics and phospho-proteomics to identify TFs that are highly upregulated in cancer cells or tissues, compared to normal cells or tissues. TFs identified using the multi-omics approach in non-small cell lung cancer (NSCLC) were categorized by major driver mutations and signaling pathways (FIG. 21B). TFs identified are downstream of major NSCLC driver mutations (e.g., EGFR, KRAS, TP53, etc.) and signaling pathways. Combining specific elements across multiple pathways can ensure broad cancer coverage of cancer specific expression of a reporter gene or a gene of interest. For example, based on the above analysis, a synthetic promoter can be designed to include elements to ensure coverage of LUAD and LUSC dysregulated pathways by combining elements and probing various signaling pathways.
To build a synthetic promoter, one can use the known DNA binding site (TFBS) as a sequence element to “sense” that TF's presence, and if present, that TF upon binding to the promoter, will recruit additional transcriptional machinery and co-factors such as RNA polymerase. There are also additional signal-based elements that are not cancer-specific, but generally can attract more transcriptional machinery to a promoter that has been activated.
The transcription start site (TSS) is the driving component of the core promoter. Two approaches have been used to design the core: (1) using a minimal basal promoter, which is frequently used to create response elements and (2) using the core region of a cancer-specific promoter, which adds additional specificity to the construct. The three components—cancer-activated response elements, signal elements, and cancer-specific cores—are each modular and highly engineerable.
Synthetic Construct Design and Cloning
Core Promoters
A minimal cancer-specific core promoter can comprise a short DNA sequence within the promoter region of a gene that is specifically activated or repressed in cancer cells compared to normal cells. The core promoter region is a critical regulatory element that controls the initiation of transcription by RNA polymerase II. The coreBIRC5 element comprises a 74 bp element from the 3′ end of the promoter consisting of a TP53 half-site, and 33 bp after the transcriptional start site (TSS).
Equivalent types of core promoter sequences were also created for endogenous promoters AGR2, CST1, and FAM111B by evaluating candidate sequences in the UCSC Genome Browser and limiting assessment from −300 bp to +100 bp relative to the predicted TSS of the endogenous promoter. Boundaries of the core sequences were further trimmed based on a combination of the following: presence of ChIP-Seq peaks (including general TFs and indicators of active promoter regions such as RNA Pol II, DNAse I, H3K4me1, H3K4me3 peaks), TFs that may indicate cancer specificity by presence in cancer cell lines and absence in non-cancerous cell lines, abundance of predicted TFBS via JASPAR or HOMER motif analysis, and/or retaining regions of high species conservation.
The TATA-TSS minimal core (37 bp) comprises a canonical TATA site with a 23 bp GC-rich spacer 5′ end to or upstream of the TSS, which can mediate high expression.
Tiled Transcription Factor Binding Sites
JASPAR (open-access database of curated and non-redundant transcription factor (TF) binding profiles from six different taxonomic groups) consensus sequences were used as the DNA binding domain and tiled consecutively or with a 3 bp spacer between the DNA binding domains to fill a size of 125 bp. Ultramers were ordered from Integrated DNA Technologies (IDT) with a common sequence at the 3′ end. Single-stranded ultramers were PCR-amplified using a common reverse primer to add appropriate restriction enzyme digestion sites as described below. Ultramer sequences are listed in Table 2.







TABLE 2







Ultramer sequences










SEQ ID NO.
Reference
Sequence Name
Sequence





344
312398676
TTF-1_1_no space
AAT AGG TAC CAC TAG TGG TTT TGT GGG





GTT TTG TGG GGT TTT GTG GGG TTT TGT





GGG GTT TTG TGG GGT TTT GTG GGG TTT





TGT GGG GTT TTG TGG GGT TTT GTG GGG





TTT TGT GGT GCG CTC CCG ACA TGC CCC





GC


 


345
312398677
MAX MYC_no
AAT AGG TAC CAC TAG TAG TTC AAC ACG




space
TGG TCT GGG AGT TCA ACA CGT GGT CTG





GGA GTT CAA CAC GTG GTC TGG GAG TTC





AAC ACG TGG TCT GGG AGT TCA ACA CGT





GGT CTG GGT GCG CTC CCG ACA TGC CCC





GC


 


346
312398678
TTF-1_1_3bp space
AAT AGG TAC CAC TAG TGG TTT TGT GGA





GAG GTT TTG TGG TCG GGT TTT GTG GGA





CGG TTT TGT GGC TAG GTT TTG TGG ACT





GGT TTT GTG GTG CGG TTT TGT GGG TAG





GTT TTG TGG TGC GCT CCC GAC ATG CCC





CGC


 


347
312398679
MAX_MYC_3bp
AAT AGG TAC CAC TAG TAG TTC AAC ACG




space
TGG TCT GGG AGA AGT TCA ACA CGT GGT





CTG GGT CGA GTT CAA CAC GTG GTC TGG





GGA CAG TTC AAC ACG TGG TCT GGG CTA





AGT TCA ACA CGT GGT CTG GGT GCG CTC





CCG ACA TGC CCC GC


 


348
312398680
TTF-1_2_no space
AAT AGG TAC CAC TAG TAG CCA CTT GAA





ATT AGC CAC TTG AAA TTA GCC ACT TGA





AAT TAG CCA CTT GAA ATT AGC CAC TTG





AAA TTA GCC ACT TGA AAT TAG CCA CTT





GAA ATT TGC GCT CCC GAC ATG CCC CGC


 


349
312398681
GATA6_no space
AAT AGG TAC CAC TAG TGA CAG ATA AGA





AAG ACA GAT AAG AAA GAC AGA TAA GAA





AGA CAG ATA AGA AAG ACA GAT AAG AAA





GAC AGA TAA GAA AGA CAG ATA AGA AAG





ACA GAT AAG AAA TGC GCT CCC GAC ATG





CCC CGC


 


350
312398682
TTF-1_2_3bp space
AAT AGG TAC CAC TAG TAG CCA CTT GAA





ATT AGA AGC CAC TTG AAA TTT CGA GCC





ACT TGA AAT TGA CAG CCA CTT GAA ATT





CTA AGC CAC TTG AAA TTA CTA GCC ACT





TGA AAT TTG CGC TCC CGA CAT GCC CCG C


 


351
312398683
GATA6_3bp space
AAT AGG TAC CAC TAG TGA CAG ATA AGA





AAA GAG ACA GAT AAG AAA TCG GAC AGA





TAA GAA AGA CGA CAG ATA AGA AAC TAG





ACA GAT AAG AAA ACT GAC AGA TAA GAA





ATG CGA CAG ATA AGA AAT GCG CTC CCG





ACA TGC CCC GC


 


352
312398684
TTF-1_3_no space
AAT AGG TAC CAC TAG TCT GGG AAC AAG





TGC TGG GAA CAA GTG CTG GGA ACA AGT





GCT GGG AAC AAG TGC TGG GAA CAA GTG





CTG GGA ACA AGT GCT GGG AAC AAG TGC





TGG GAA CAA GTG TGC GCT CCC GAC ATG





CCC CGC


 


353
312398685
GATAI_no space
AAT AGG TAC CAC TAG TTT CTA ATC TAT





TTC TAA TCT ATT TCT AAT CTA TTT CTA





ATC TAT TTC TAA TCT ATT TCT AAT CTA





TTT CTA ATC TAT TTC TAA TCT ATT TCT





AAT CTA TTG CGC TCC CGA CAT GCC CCG C


 


354
312398686
TTF-1_3_3bp space
AAT AGG TAC CAC TAG TCT GGG AAC AAG





TGA GAC TGG GAA CAA GTG TCG CTG GGA





ACA AGT GGA CCT GGG AAC AAG TGC TAC





TGG GAA CAA GTG ACT CTG GGA ACA AGT





GTG CCT GGG AAC AAG TGT GCG CTC CCG





ACA TGC CCC GC


 


355
312398687
GATA1_3bp space
AAT AGG TAC CAC TAG TTT CTA ATC TAT





AGA TTC TAA TCT ATT CGT TCT AAT CTA





TGA CTT CTA ATC TAT CTA TTC TAA TCT





ATA CTT TCT AAT CTA TTG CTT CTA ATC





TAT TGC GCT CCC GAC ATG CCC CGC


 


356
312398688
TTF-1_4_no space
AAT AGG TAC CAC TAG TGA CTC CTC AAG





GGG ACT CCT CAA GGG GAC TCC TCA AGG





GGA CTC CTC AAG GGG ACT CCT CAA GGG





GAC TCC TCA AGG GGA CTC CTC AAG GGG





ACT CCT CAA GGG TGC GCT CCC GAC ATG





CCC CGC


 


357
312398689
FOSL1_no space
AAT AGG TAC CAC TAG TGG TGA CTC ATG





GGT GAC TCA TGG GTG ACT CAT GGG TGA





CTC ATG GGT GAC TCA TGG GTG ACT CAT





GGG TGA CTC ATG GGT GAC TCA TGG GTG





ACT CAT GTG CGC TCC CGA CAT GCC CCG C


 


358
312398690
TTF-1_4_3bp space
AAT AGG TAC CAC TAG TGA CTC CTC AAG





GGA GAG ACT CCT CAA GGG TCG GAC TCC





TCA AGG GGA CGA CTC CTC AAG GGC TAG





ACT CCT CAA GGG ACT GAC TCC TCA AGG





GTG CGA CTC CTC AAG GGT GCG CTC CCG





ACA TGC CCC GC


 


359
312398691
FOSL1_3bp space
AAT AGG TAC CAC TAG TGG TGA CTC ATG





AGA GGT GAC TCA TGT CGG GTG ACT CAT





GGA CGG TGA CTC ATG CTA GGT GAC TCA





TGA CTG GTG ACT CAT GTG CGG TGA CTC





ATG TGC GCT CCC GAC ATG CCC CGC


 


360
312398692
TCF7_no space
AAT AGG TAC CAC TAG TCG GGC TTT GAT





CTT TCG GGC TTT GAT CTT TCG GGC TTT





GAT CTT TCG GGC TTT GAT CTT TCG GGC





TTT GAT CTT TCG GGC TTT GAT CTT TCG





GGC TTT GAT CTT TTG CGC TCC CGA CAT





GCC CCG C


 


361
312398693
STAT3_no space
AAT AGG TAC CAC TAG TCT TCT GGG AAA





CTT CTG GGA AAC TTC TGG GAA ACT TCT





GGG AAA CTT CTG GGA AAC TTC TGG GAA





ACT TCT GGG AAA CTT CTG GGA AAC TTC





TGG GAA ATG CGC TCC CGA CAT GCC CCG C


 


362
312398694
TCF7_3bp space
AAT AGG TAC CAC TAG TCG GGC TTT GAT





CTT TAG ACG GGC TTT GAT CTT TTC GCG





GGC TTT GAT CTT TGA CCG GGC TTT GAT





CTT TCT ACG GGC TTT GAT CTT TAC TCG





GGC TTT GAT CTT TTG CGC TCC CGA CAT





GCC CCG C


 


363
312398695
STAT3_3bp space
AAT AGG TAC CAC TAG TCT TCT GGG AAA





AGA CTT CTG GGA AAT CGC TTC TGG GAA





AGA CCT TCT GGG AAA CTA CTT CTG GGA





AAA CTC TTC TGG GAA ATG CCT TCT GGG





AAA TGC GCT CCC GAC ATG CCC CGC


 


364
312398696
TCF7:L2_no space
AAT AGG TAC CAC TAG TGC GCT TTG ATG





TGC GGG GCG GCC CTT TGA AGT TGG CGC





TTT GAT GTG CGG GGC GGC CCT TTG AAG





TTG GCG CTT TGA TGT GCG GGG CGG CCC





TTT GAA GTT GTG CGC TCC CGA CAT GCC





CCG C


 


365
312398697
STAT:STAT no
AAT AGG TAC CAC TAG TAA TTC TTA GAA




space
ATA AAT TCT TAG AAA TAA ATT CTT AGA





AAT AAA TTC TTA GAA ATA AAT TCT TAG





AAA TAA ATT CTT AGA AAT AAA TTC TTA





GAA ATA TGC GCT CCC GAC ATG CCC CGC


 


366
312398698
TCF7:L2_3bp space
AAT AGG TAC CAC TAG TGC GCT TTG ATG





TGC GGG GCG GCC CTT TGA AGT TGA GAG





CGC TTT GAT GTG CGG GGC GGC CCT TTG





AAG TTG TCG GCG CTT TGA TGT GCG GGG





CGG CCC TTT GAA GTT GTG CGC TCC CGA





CAT GCC CCG C


 


367
312398699
STAT:STAT_3bp
AAT AGG TAC CAC TAG TAA TTC TTA GAA




space
ATA AGA AAT TCT TAG AAA TAT CGA ATT





CTT AGA AAT AGA CAA TTC TTA GAA ATA





CTA AAT TCT TAG AAA TAA CTA ATT CTT





AGA AAT ATG CGC TCC CGA CAT GCC CCG C


 


368
312398700
MSC_no space
AAT AGG TAC CAC TAG TAA CAG CTG TTA





ACA GCT GTT AAC AGC TGT TAA CAG CTG





TTA ACA GCT GTT AAC AGC TGT TAA CAG





CTG TTA ACA GCT GTT AAC AGC TGT TTG





CGC TCC CGA CAT GCC CCG C


 


369
312398701
SOX9_no space
AAT AGG TAC CAC TAG TAA AAC AAA GGA





TCC TTT GTT TTA AAA CAA AGG ATC CTT





TGT TTT AAA ACA AAG GAT CCT TTG TTT





TAA AAC AAA GGA TCC TTT GTT TTA AAA





CAA AGG ATC CTT TGT TTT TGC GCT CCC





GAC ATG CCC CGC


 


370
312398702
MSC_3bp space
AAT AGG TAC CAC TAG TAA CAG CTG TTA





GAA ACA GCT GTT TCG AAC AGC TGT TGA





CAA CAG CTG TTC TAA ACA GCT GTT ACT





AAC AGC TGT TTG CAA CAG CTG TTG TAA





ACA GCT GTT TGC GCT CCC GAC ATG CCC





CGC


 


371
312398703
SOX9_3bp space
AAT AGG TAC CAC TAG TAA AAC AAA GGA





TCC TTT GTT TTA GAA AAA CAA AGG ATC





CTT TGT TTT TCG AAA ACA AAG GAT CCT





TTG TTT TGA CAA AAC AAA GGA TCC TTT





GTT TTT GCG CTC CCG ACA TGC CCC GC


 


372
312398704
ZEB1_no space
AAT AGG TAC CAC TAG TCA CCT GCA CCT





GCA CCT GCA CCT GCA CCT GCA CCT GCA





CCT GCA CCT GCA CCT GCA CCT GCA CCT





GCA CCT GTG CGC TCC CGA CAT GCC CCG C


 


373
312398705
HNF4_no space
AAT AGG TAC CAC TAG TAA AGT CCA AGT





CCA AAA GTC CAA GTC CAA AAG TCC AAG





TCC AAA AGT CCA AGT CCA AAA GTC CAA





GTC CAA AAG TCC AAG TCC AAA AGT CCA





AGT CCA TGC GCT CCC GAC ATG CCC CGC


 


374
312398706
ZEB1_3bp space
AAT AGG TAC CAC TAG TCA CCT GAG ACA





CCT GTC GCA CCT GGA CCA CCT GCT ACA





CCT GAC TCA CCT GTG CCA CCT GAG ACA





CCT GTC GCA CCT GGA CCA CCT GTG CGC





TCC CGA CAT GCC CCG C


 


375
312398707
HNF4_3bp space
AAT AGG TAC CAC TAG TAA AGT CCA AGT





CCA AGA AAA GTC CAA GTC CAT CGA AAG





TCC AAG TCC AGA CAA AGT CCA AGT CCA





CTA AAA GTC CAA GTC CAA CTA AAG TCC





AAG TCC ATG CGC TCC CGA CAT GCC CCG C


 


376
312398708
BIRC5_core REV
CCA TGG TGG CTT TAC CAA CAG TAC CGG





ATT GCC AAG CTT GGC CGC CGA GGC CAG





ATC TTG ATA TCC TCG AGG CTA GCC CAC





CTC TGC CAA CGG GTC CCG CGA CTC AAA





TCT GGC GGT TAA TGG CGC GCC GCG GGG





CAT GTC GGG AGC GCA GGT ACC G









Cloning into Firefly Reporter Vector

To generate a reporter construct for use in measuring promoter activity, DNA fragments of interest were cloned into a standard Firefly Luciferase (FLUC) reporter vector from Promega (pGL4.10[luc2] Promega E6651). Two cloning methods were used: restriction enzyme cloning and Gibson assembly.
For restriction enzyme cloning, DNA fragments containing promoter sequences were amplified by PCR using primers designed to incorporate KpnI and NheI restriction enzyme recognition sites in the PCR products. The PCR products were then digested with the appropriate restriction enzymes, purified using gel extraction kits (Zymo Cat #D4001), and ligated into the FLUC vector that had been digested with the same enzymes using NEB Quick Ligation™ Kit (Cat #M2200), a standard DNA ligation kit. The ligation mixture was transformed into E. coli Stable cells (C3040H), and clones were screened by restriction enzyme digestion and DNA sequencing to confirm the correct insert.
For Gibson assembly, Gibson Assembly® Master Mix (NEB E2611), a standard PCR master mix, was used. Briefly, PCR products containing the promoter of interest and the FLUC vector were generated using primers designed to create overlapping regions between the two fragments. The PCR products were then mixed with Gibson Assembly® Master Mix and incubated at 50° C. for 1 hour. The resulting mixture was then transformed into E. coli Stable cells, and clones were screened by DNA sequencing to confirm the correct assembly.
DNA was scaled up and purified using QIAGEN® Plasmid Plus Midi (Cat #12945), a standard plasmid purification kit, or equivalent. Briefly, larger cultures were prepared from bacterial glycerol stocks containing the plasmid DNA. A 2 mL culture was started in the morning and larger cultures inoculated for overnight growth at 37° C. Purified DNA was used for subsequent in vitro and in vivo transfections.
Cell Lines
Cells were maintained according to standard protocols with recommended media described below and incubated at 37° C. and 5% CO2. H1299 (human non-small cell lung carcinoma cell line derived from the lymph node), H520 (squamous cell carcinoma), and LK-2 (squamous cell carcinoma) cells were cultured in standard RPMI1640 medium supplemented with 10% (v/v) fetal bovine serum. IMR90 (normal lung fibroblast cell line) cells were cultured in standard EMEM supplemented with 10% (v/v) fetal bovine serum. A549 (pulmonary adenocarcinoma) cells were cultured in standard F-12K medium supplemented with 10% (v/v) fetal bovine serum.
Patient-derived xenograft (PDX) cell lines licensed from Charles River Laboratories (CRL) were cultured in standard RPMI1640 medium with 25 mM HEPES and L-glutamine (#FG1385, Biochrom, Berlin, Germany), supplemented with 10% (v/v) fetal calf serum (Sigma, Tauflkirchen, Germany) and 0.1 mg/ml Gentamycin (Life Technologies, Karlsruhe, Germany).
Lonza primary-like cell line SAEC-1 were cultured using the Lonza SAGM™ Small Airway Epithelial Cell Growth Medium BulletKit® (CC-3118). Lonza Normal Human Bronchial Epithelial (NHBE) and Chronic Obstructive Pulmonary Disease (COPD) primary-like cell lines were cultured using Lonza Bronchial Epithelial Cell Growth Medium BulletKit® (CC-3170).
Approximately 24 hours prior to conducting experimentations, cells were plated to achieve a confluence of 70-80/on the day of transfection.
Transfections
For transient transfections, Lipofectamine™ 3000 (Thermo Fisher), a transfection agent comprising DOSPA (2,3-dioleoyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propaniminium trifluoroacetate) and DOPE (dioleoyl phosphatidylethanolamine), was used according to the manufacturer's instructions. Briefly, for each well, 100 ng of plasmid DNA was mixed with 0.2 μL of P3000™ reagent, a neutral/helper co-lipid, and 0.2 μL of Lipofectamine™ 3000 and 2 ng of control DNA in 100 μL Opti-MEM™ medium, a serum-reduced minimal essential medium, and the mixture was incubated at room temperature for 20 minutes. The transfection mixture was then added to the cells in a 96-well plate and the cells were incubated for 24 hours.
Luciferase Assays and Analysis
Approximately 24 hours after the transfection, firefly luciferase and Renilla luciferase levels were measured from each well using the Promega Dual-Glo® Luciferase System (E2940) with a working volume of 50 μL.
Data are presented as raw output of Firefly Luciferase Relative Light Units (FLUC RLUs) relative to constitutively active promoters, % of EF1A or % of CMV or relative to another strong, constitutive promoter. A plasmid encoding for Renilla luciferase was added into transfection mixtures at a low ratio to control for variance in transfection efficiency between parallel wells of cells. Normalization for transfection and well-to-well variability was performed by dividing the FLUC RLU output by the Renilla luciferase (RLUC) RLU output from the CMV-RLUC co-transfection control. Normalized FLUC/RLUC may also be presented as % of expression relative to EF1A.
Chromatin Immunoprecipitation (ChIP)—Quantitative PCR (qPCR)
24 hours after transfection, cells (10-cm dish) were fixed with 1% formaldehyde for 10 minutes at room temperature. Cells were then washed twice with ice-cold PBS. Then, cells were harvested using cell scraper in 2 ml of ice-cold PBS with protease inhibitors and centrifuged at 2000 rpm at 4° C. for 5 minutes. The cell pellets were lysed in 200 μL (per 100 μL cell pellet) of 1% SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1) with protease inhibitors, and the extracts were sonicated using a Misonix Sonicator® 3000 instrument and a microtip probe (use 1 second on, 0.5 second pulse for 15 seconds at power setting of 2; put on ice for 15 seconds to chill the tube; 6-9 cycles were performed). Samples were then centrifuged at 12,000×g at 4° C. for 10 minutes, and supernatant was collected. Samples were diluted to 2 ml in ChIP dilution buffer (1% Triton™ X-100, a non-ionic surfactant, 2 mM EDTA, 20 mM Tris-HCl, pH 8, 150 mM NaCl) with protease inhibitors. 40 μL of the diluted sample was kept aside as the input fraction before preclearing with non-blocked 75 μL ProteinA Agarose/Salmon Sperm DNA (50% Slurry) for 30 minutes at 4° C. with agitation. Agarose was pelleted by centrifugation (10,000×g-15,000×g) and the supernatant fraction was collected. 60 μL blocked agarose beads were added to the supernatant fraction per reaction with control rabbit IgG, anti-c-Jun, or anti-FRA2 rabbit antibodies (purchased from CellSignaling) and incubated at 4° C. overnight with rotation. Immune complexes were washed once with low salt wash buffer, once with high salt wash buffer, once with LiCl wash buffer with 0.1% SDS, and two times with Tris-EDTA buffer. DNA-protein complex was eluted in ChIP elution buffer (1% SDS, 0.1M NaHCO3). Cross-links were reversed at 65° C. for 2 hours. DNA was purified by QIAquick® Spin Miniprep Kit following the manufacturer's protocol (Qiagen). For all quantitative PCR (qPCR) analyses, Taqman primer/probe assay for target gene promoter binding was performed using QuantStudio 6 Flex machine.
RNA-Seq and Principal Component Analysis
Briefly, raw sequencing data was aligned to GRCh38/hg38 using Spliced Transcripts Alignment to a Reference (STAR). The resulting Binary Alignment Map (BAM) files were analyzed using feature counts against a transcriptomic reference based on Gencode 36 (gencodegenes.org/human/release_36). The resulting gene-level counts for protein-coding genes were upper-quartile normalized, transformed into Fragments Per Kilobase of transcript per Million mapped reads (FPKM-UQ), and log 2 transformed. Clinical Proteomic Tumor Analysis Consortium (CPTAC) RNA-seq data in FPKM-UQ unit was directly downloaded from linkedOmics data portal.
PCA (R package PCAtools version 2.6.0), a dimensionality reduction method, was used to cluster the samples using the RNA-seq profiles. PCA was either performed on all genes, expression-quantified as FPKM-UQ, or on genes restricted to the relevant gene sets downloaded from MSigDB (gsea-msigdb.org/gsea/msigdb/).
Results
Synthetic Promoters Dependent on Dysregulated FOS and a Core-Cancer Specific Promoter are Highly Active
The use of synthetic promoters composed of tiled transcription factor binding sites (TFBSs) and a minimal core promoter to improve gene expression in cancer cells was investigated. The expression of a reporter gene expressed from a panel of synthetic promoter constructs was tested and the expression levels were compared to the expression levels of the reporter expressed from the endogenous BIRC5 (Survivin) promoter, a combination of three endogenous cancer-activated promoters, or constitutive controls such as EF1a and CMV promoters.
FIG. 30A demonstrates that the synthetic constructs generated (FOS-coreBIRC5) outperformed the individual or multiplexed endogenous promoters in terms of both strength and sensitivity across PDX cell lines, having up to 10-fold more signal than the endogenous BIRC5 (Survivin) promoter and equivalent or better signal than the multiplexed endogenous promoters. The FOS-coreBIRC5 promoter also showed sensitivity capturing patient LXFL1121, which was missed by all other multiplexed endogenous promoters. The FOS-coreBIRC5 promoter had similar expression level as the endogenous BIRC5 promoter in normal lung fibroblast, bronchial epithelial (NHBE), and small airway epithelial cells (SAEC) (FIG. 30B).
While the FOS binding site used is the DNA binding motif for a variety of bZIP-like transcription factors, including Jun and FOS family (FOS, FOSB, FOSL1, and FOSL2), cancer-activated upregulation of FOSL2 is expected and is primarily driving the differential expression of this promoter, as FOSL2 was identified as one of the top candidates in the multi-omics analysis performed as a part of Multi-Omics Factor Analysis (MOFA) for NSCLC specific transcription factor identification (FIGS. 31-32). This MOFA utilized an unsupervised integration of different -omics data available from CPTAC's LUAD and lung squamous cell carcinoma (LUSQ) tumor and patient matched Normal Adjacent Tissues (NAT) samples and restricted gene analysis to TFs and phosphorylation sites of those TFs. The initial analysis of NSCLC patients consistently showed FOSL2 as one of the top activated transcription factors in NSCLC, especially by protein abundance and phosphorylation abundance (FIGS. 31-32). However, based on the literature evidence, other various FOS family members can be also used, as high FOSL1 expression has been shown in KRAS driven lung and pancreatic cancers, and gross upregulation of c-Fos and its binding partner c-Jun has been shown in NSCLC.
To prove the hypothesis that FOS-coreBIRC5 activity is directly responsive to varying levels of FOSL2, a chromatin immunoprecipitation (ChIP) assay was performed to determine whether the FOSL2 protein binds directly to the FOS-coreBIRC5 in cell lines where the FOS-coreBIRC5 promoter is active. The results showed that the FOS-coreBIRC5 sequence is 14 times more enriched in the FOSL2 pulldown versus the non-specific pulldown of the same construct (FIG. 33). The coreBIRC5 promoter alone construct that does not contain the putative FOSL2 binding sequences serves as a negative control, demonstrating that there is no enrichment of the DNA sequence upon a pulldown of the FOSL2 or c-Jun proteins. This mechanistically proves that the response element binds directly the FOSL2 transcription factor as well as its dimerization partner, c-Jun.
Additional TF Response Element Promoters Using coreBIRC5
In addition to the FOS response element, more than 20-30 working response elements to transcription factors dysregulated in NSCLC were engineered. A high-throughput screening approach was implemented to test and design thousands of unique response elements at a time. FIG. 34 shows a small subset of these transcription factors (FOSL2, ETV4, TWIST1) across a panel of eight different lung cancer PDX cell lines, as well as NSCLC cell line H1299 and control normal fibroblast cell line IMR-90, demonstrating that several of these chimeric promoters can drive fairly high expression in a variety of cancer cell lines, especially compared to the initial endogenous (1000 bp) BIRC5 promoter, while still maintaining high specificity.
Predictability of Synthetic Promoters: B-Cat/Wnt Pathway Synthetic Promoter
While many of the synthetic TFBS constructs tested had increased sensitivity and specificity relative to endogenous promoters, it was also found that synthetic promoters containing binding sites for the TCF/LEF family of transcription factors showed significant activity in only one of the primary models (PDX430, FIG. 35), while maintaining high specificity as evidenced by a lack of signal in normal cell lines such as IMR-90 fibroblasts. As TCF7 is a well-studied acting transcription factor in the B-catenin/Wnt signaling pathway, it was postulated that this cell line uniquely represented a Wnt-dependent tumor.
A principal component analysis (PCA) was performed on the transcriptome data from Charles River on all NSCLC PDX tumors, as well as CCLE, the Cancer Cell Line Encyclopedia. The primary differentiator (PC1) was driven by inherent transcriptomic differences between the PDX cell lines (blue) and the immortalized traditional cell lines (red), likely due to similar genetic drift in the immortalized cell lines due to many generations of adjustment to plastic. However, by PC2, PDX430 was uniquely situated in PC2, and within the CCLE cell lines, NCI-H520 and LK2 plot similarly by PC2. This is driven by nearly identical profiles in key Wnt pathway genes Wnt7B, CCND1, FZD3, AXIN2, and NKD1.
These similarly profiled cell lines were purchased and transfected with a panel of synthetic constructs including the TCF7 and TCF7L1 variants, and as shown in FIG. 17, H520 and LK-2 predictably activated the TCF7 promoter, while KRAS-driven cell lines H1299 and A549 did not show any activation of the Wnt-pathway promoter, especially as compared to the FOS driven promoter.
Core Promoter Signal Elements
In addition to cancer-specific response elements, synthetic promoters can also be engineered with general activating elements comprising transcriptional factor binding sites and elements, GC-Box, antioxidant response elements (ARE). These can be combined with minimal core promoters or with synthetic promoter constructs containing TFBS such as FOSL-core BIRC5.
The “Low,” “Medium,” and “High” expressing elements were added to core promoters. Addition of activating elements resulted in increased signal strength of the promoters.
New Cancer-Specific Core Promoters
In addition to modifying proximal promoter regions, alternative core promoters from endogenous promoters beyond BIRC5 can be combined with synthetic enhancer sequences to increase signal strength while maintaining specificity. Based on the analysis of coreBIRC5 element, it was hypothesized that other “core” regions of endogenous cancer-dysregulated promoters could also serve as the core element in the synthetically engineered promoters and it was sought to understand whether they also maintain the specificity driven by coreBIRC5 while increasing sensitivity or signal strength.
Based on the previous positive results with the FAM111B, AGR2 and CST1 promoters, the use of the core elements isolated from these were first explored. Increasingly short variants of the core were tested and the 165 bp (FAM111B), 360 bp (AGR2), and 191 bp (CST1) version of these cores were further chosen. As shown in FIG. 36, new chimeric promoters FOS-coreFAM111B, FOS-coreAGR2, FOS-coreCST1 led to dramatic improvements in signal strength (up to 20-fold) as compared to FOS-coreBIRC5. As previously suggested, these constructs had improvements over the full-length version of the respective endogenous promoters as well. The new cores also maintained high specificity compared to the completely permissive core TATA-TSS (gray) in normal lung models of human small airway epithelial cells (SAEC-6, SAEC-7) and normal human lung fibroblasts (NHLF-2), although core-FAM111B may not maintain as much specificity in fibroblasts.
Additional experiments have similarly shown that alternative core promoters coreAGR2 and coreCST1 can partner well with TFs besides FOS to drive higher signal while maintaining cancer specificity (FIGS. 24-26). FIG. 24 shows that response elements for TCF7 and TP53 which are particularly active in cell lines PDX430 and PDX586, respectively, gained additional strength without loss in specificity by using alternate core promoters AGR2, CST1 and FAM111B. Furthermore, addition of TCF tiles to FOS-coreAGR2 improved expression of the reporter gene in various cell lines tested, including cancer cell lines, CRL PDX cell lines, and primary normal lung cells (FIG. 26).
Conclusion
By creating synthetic response elements that are bound by the presence of transcription factors whose expression is dysregulated in cancer, chimeric promoters with high sensitivity and specificity have been engineered to drive cancer specific expression of a reporter gene or a gene of interest. Engineered synthetic promoters can drive substantially higher expression of a reporter gene or a gene of interest than the endogenous promoter of the BIRC5 gene. Furthermore, synthetic promoters can maintain cancer specificity when comparing lung cancer models to normal small airway epithelial cells or lung fibroblasts. Most importantly, the activation of synthetic promoters as opposed to endogenous promoters is highly predictable, as demonstrated by the analysis of the TCF7 chimeric promoter.
Example 3: Detection of Hepatocellular Carcinoma in an Orthotopic Mouse Model
Synthetic promoters designed for highly specific cancer-activated expression of a gene in tumors is applicable to malignancies beyond the non-small cell lung cancer (NSCLC). In this example, the utility of a rational-based sequence engineered approach of a highly specific and strong liver cancer promoter is demonstrated. For example, a known alpha-fetoprotein (AFP) promoter drove the expression of a gene up to 200-fold higher in liver cancer cell lines without any increase in basal activity in non-liver and normal cell lines. The promoter-mediated strong cancer-activated expression, when combined with the reporter and delivery aspects of the platform, was demonstrated by blood-based biomarkers and imaging markers (assayed by staining) in an in vivo model of liver cancer.
Hepatocellular carcinoma can greatly benefit from additional technologies in the early detection and diagnostic space. Risk of HCC is highly elevated in patients with chronic liver disease, including those with chronic Hepatitis B (HBV) or with cirrhosis from other severe liver diseases such as HBV, HCV, or NASH. At-risk patients are closely monitored for disease progression into a malignancy, but the tools currently available are highly limited. Semi-annual abdominal ultrasounds and the AFP blood marker test are the only two surveillance tests in clinical guidelines and with broad adoption, but their performance has been quite poor in detecting early-stage malignancies, which are much more likely to be cured & treated effectively than later stage cancers.
Both abdominal ultrasound and AFP blood tests have less than optimal sensitivities, with the AFP test shown to detect HCC with only 63% sensitivity. In particular, ultrasound effectiveness is highly variable based on operator, and is markedly difficult in obese patients and patients with NASH. A novel diagnostic modality described herein could bridge the gap between these screens and diagnosis, either bypassing physical biopsies or further reducing the population that is subjected to them. These patients include those for whom ultrasounds can be inconclusive due to high levels of cirrhosis or indeterminate liver nodules that simply don't have the hallmark radiological features of HCC. Additionally, for patients with small liver nodules (<2 cm), it is difficult to distinguish HCC from benign dysplastic nodules or intrahepatic cholangiocarcinoma (bile duct cancer).
From a scientific perspective, lipid nanoparticles (LNPs) have traditionally been known for their ability to mediate highly effective delivery in the liver, which can be a benefit to liver cancer diagnostics platform, provided that the reporter expression post-delivery is still highly cancer-specific to avoid noise from normal liver. This example provides a strong example of a rational engineering approach applied to endogenous promoters to create a unique liver cancer promoter (named AFP-3) and show that when coupled with a LNP formulation, the platform can provide strong cancer-activated synthetic biomarker expression in primary liver tumors.
The goal is to assess the signal-to-noise response of a liver-tropic formulation using an engineered promoter specific to liver cancer in the Hep3B orthotopic liver tumor model in mice.
Engineering & Testing of the AFP-3 Promoter
Cloning
To generate a reporter construct for use in measuring promoter activity, DNA fragments of interest were cloned into a standard Firefly Luciferase (FLuc) reporter vector from Promega (pGL4.10[luc2] Promega E6651) using the KpnI and NheI restriction enzymes.
The promoter region of interest was amplified using PCR primers with flanking restriction enzyme sites, and the PCR product was purified and digested with the appropriate restriction enzymes. BIRC5 promoter was amplified from approximately −1000 bp to +33 bp relative to the predicted transcriptional start site (TSS) of the endogenous promoter. The AFP promoter was amplified from approximately −250 bp to +28 bp relative to the TSS. AFP-3 was subcloned from AFP using mutagenic primers containing the desired point mutations. Ligated vectors were transformed into E. coli Stable cells, and clones were screened by DNA sequencing to confirm the correct assembly.
DNA was scaled up and purified using QIAGEN® Plasmid Plus Midi (Cat #12945)-), a standard plasmid purification kit, or equivalent. Purified DNA was used for subsequent in vitro and in vivo transfections. Promoters were transferred into Nanoplasmid vectors utilizing restriction enzyme cloning with restriction enzymes flanking the promoter region.
Cell Culture & Transfections
Cells were maintained according to standard protocols with recommended media listed below and incubated at 37° C. and 5% CO2.
SNU-449, H1299 cells were cultured in standard RPMI1640 medium supplemented with 10% (v/v) fetal bovine serum. HepG2 (human hepatocellular carcinoma), Hep3B (human hepatocellular adenocarcinoma), PLC/PRF/5 (human hepatocellular carcinoma), C3A (clonal derivative of HepG2), MRC-9 (fibroblast) and IMR-90 (control normal fibroblast cell line) cells were cultured in standard EMEM supplemented with 10% (v/v) fetal bovine serum. MeWo (human melanoma cell line) cells were cultured in standard DMEM supplemented with 10% (v/v) fetal bovine serum.
Approximately 24 hours prior to transfections, cells were plated to achieve a confluence of 70-80% on the day of transfections. For transient transfections, Lipofectamine™ 3000, a transfection agent comprising DOSPA (2,3-dioleoyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propaniminium trifluoroacetate) and DOPE (dioleoyl phosphatidylethanolamine), was used according to the manufacturer's instructions. Briefly, for each well, 100 ng of plasmid DNA was mixed with 0.2 μL of P3000™ reagent, a neutral/helper co-lipid, and 0.2 μL of Lipofectamine™ 3000 and 2 ng of control DNA in 100 μL Opti-MEM™ medium, a serum-reduced minimal essential medium, and the mixture was incubated at room temperature for 20 minutes. The transfection mixture was added to the cells in a 96-well plate and incubated for 24 hours.
Luciferase Readouts
Approximately 24 hours after transfection, firefly luciferase and renilla luciferase levels were measured from each well using the Promega Dual-Glo® Luciferase System (E2940) with a working volume of 50 μL.
Hep3B Murine Experiment
Cell Culture
The Hep3B-luc tumor cells (ATCC, Manassas, VA, cat #HB-8064) were maintained in vitro as a monolayer culture in EMEM medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, at 37° C. in an atmosphere of 5% CO2 in air. The tumor cells were routinely sub-cultured twice weekly by trypsin-EDTA treatment. The cells growing in an exponential growth phase were harvested and counted for tumor inoculation.
Orthotopic Tumor Implantation
The female BALB/c nude mice were anesthetized with 20 μL/g Avertin (2,2,2-tribromoethanol). For pain relief, the animals were dosed with 10 mg/kg of Carprofen 30 minutes before surgery and 6 hours post-surgery.
Each of the anesthetized mice was properly positioned. The abdomen skin was sterilized with 70% ethanol and the surgical site was prepared in a sterile condition. A small incision was across the abdominal wall. The left lobe of the liver was identified and exposed. Approximately 3×106 Hep3B-luc cells with BD Matrigel®, a standard mix of extracellular matrix proteins, in 20 μL (PBS: Matrigel®=1:1) were injected into the left lobe of the liver. The injection site was monitored for leakage of cells and after confirmation of no leakage of cells, the left lobe of the liver was placed back to the abdominal cavity. The abdominal wall was then closed, and the skin was closed with surgical suture. These mice were continuously monitored for their complete recovery from anesthesia.
Bioluminescence Measurements
The surgically inoculated mice were weighted and intraperitoneally injected luciferin at 150 mg/kg. After 10 minutes of the luciferin administration, the animals were pre-anesthetized with the mixture gas of oxygen and isoflurane. When the animals were in a complete anesthetic state, they were moved into the imaging chamber for bioluminescence measurements with IVIS (Lumina III). The bioluminescence of the whole animal body, including primary and metastatic tumors, was measured and images were recorded.
Assignment to Groups
Bioluminescence from the Hep3B-luc tumor cells were measured on all tumor bearing mice at Day 7, Day 14, and Day 20 post implantation. Randomization of animals for tumor bearing mice was based on the imaging at Day 20 post implantation, and randomization of non-tumor bearing mice was based on the body weight taken at Day 20 post implantation. Mice were selected at Day 21 post implantation, and mice bearing established tumors were assigned to 9 groups (1, 4, or 5 mice/group) using an Excel-based randomization procedure performing stratified randomization based upon the intensity of bioluminescence. Normal mice (no tumors) were also assigned to 5 groups (2 or 5 mice/group) using the same method. Administration of test article was started at Day 21 post implantation.
Observations
All the procedures related to animal handling, care and the treatment in the study were performed according to the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of WuXi AppTec following the guidance of the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). At the time of routine monitoring, the animals were daily checked for any effects of tumor growth and treatments on normal behavior such as mobility, food and water consumption (by looking only), body weight gain/loss (body weights were measured twice a week and at Day 20 post implantation as well as every occurrence prior to bleed), eye/hair matting and any other abnormal effect as stated in the protocol. Death and observed clinical signs were recorded on the basis of the numbers of animals within each subset.
Sample Collection and Endpoints
Serum Collection:
For Groups 1, 2, 9, 13 and 14: Bleed 1 day before testing of test article, and at 48 hours after dosing (terminal).
Tissue Collection:
For all non-tumored mice Groups 3-14: collect left lobe and right lobe separately and snap frozen at 48 hours after dosing.
For all tumored-mice Groups 3-13: collect tumor, left lobe and right lobe separately, bisect each of them and snap frozen half, then the other half into FFPE at 48 hours after dosing.
Animals & Housing Conditions


    
    
        Species: Mus musculus 
        Strain: BALB/c nude
        Age: 6-8 weeks
        Sex: female
        Body weight: 18-22 g
        Number of animals: 56 mice plus spare
        Animal supplier: Beijing Vital River Laboratory Animal Co. LTD
        Animal quality certificate number: 20221208Abzz0619000836, 20221208Abzz0619000874, 20221212Abzz0619000183

Housing Condition

    
    


The mice were kept in individual ventilation cages at constant temperature (20-26° C.) and humidity (40-70%). Cages were made of polycarbonate with a size of 375 mm×215 mm×180 mm. The bedding material was corn cob, which was changed twice per week. Animals had free access to irradiation sterilized dry granule food during the entire study period. Animals had free access to sterile drinking water.
Results
Design and Validation of AFP-3 Promoter for Activation in Liver Cancer
The alpha-fetoprotein (AFP) promoter has been extensively studied and shown to confer selective expression of transgenes in hepatocellular carcinoma (HCC) in vitro and in vivo. The AFP transcript is normally expressed in normal fetal livers but not adult livers, and then is known to be re-activated in about 70% of liver cancers. Thus, circulating AFP protein is a well-known marker for liver cancer, but the promoter is also well studied to drive specific expression in liver cancer models proportional to the level of AFP expression in the HCC studied.
However, as with most endogenous promoters, the level of expression from the AFP promoter is remarkably low, gating its effectiveness in previous applications of liver activated expression. In an effort to create a stronger and more robust activating promoter, a bioinformatic analysis was performed and it was found that there were suboptimal binding sequences for TFs. To boost transcription level, the promoter was rationally engineered by strengthening the dimerized binding sites for HNF-1A, TF binding sites within the AFP promoter, to be closer to the known consensus site for HNF-1A from other promoters (FIG. 38A). Modification of these sequences to have a greater consensus with the ideal binding site can create a more durable and longer interaction of the HNF1A with the AFP promoter, allowing this TF to drive more expression from the TSS in the promoter. These small, rational edits to the base pairs in the promoter led to the reporter construct expressing firefly luciferase to increase expression between 20 to 200-fold in liver cancer cell lines HepG2, Hep3B, PLC, CA3 and SNU-449 (FIG. 38B) while continuing to maintain highly specific liver expression, as shown by continued lack of activity in lung normal cell lines IMR-90, MRC-9, as well as lung cancer H1299 and melanoma MeWo cell lines.
In Vivo Experimental Design and Groups
In orthotopic models of HCC, cancer cells are directly inoculated into the liver parenchyma, which allows the tumor to be studied within the correct target organ. In this study, the Hep3B human HCC cell line was orthotopically implanted into the left lobe of the liver for tumor-bearing mice. The cell line used includes a luciferase-based marker to track tumor growth over time and allow for fair assignment of groups based on tumor size. Luciferase and body weight data are shown in Tables 3 & 4 and FIG. 42, demonstrating appropriate tumor growth over 20 days before the mice were randomized and assigned experimental groups in Table 5.







TABLE 3







Raw Data of Body Weight Measurements











BW
Tumor
Animal No.
0a
2














Group 1
N
5797
23.36
21.05


MC3-Form-1

5798
23.66
20.96


1.4 mg/kg

5800
21.02
19.67


10 μL/g

5801
22.90
20.54


IV, Single dose

5806
24.14
22.89




Mean
23.02
21.02




SEM
0.54
0.53


Group 2
Y
5708
23.41
20.87


MC3-Form-1

5729
20.85
18.99


1.4 mg/kg

5744
23.32
21.01


10 μL/g

5764
20.32
17.89


IV, Single dose

5775
20.62
18.03




Mean
21.70
19.36




SEM
0.68
0.67


Group 3
N
5795
23.02
21.48


NP357 and JetPEI

5805
23.02
21.48


0.7 mg/kg






5 μL/g






IV, Single dose








Mean
23.02
21.48




SEM
0.00
0.00


Group 4
Y
5733
20.97
20.76


NP357 and JetPEI

5736
22.32
20.81


0.7 mg/kg

5739
20.13
17.84


5 μL/g

5747
24.00
21.31


IV, Single dose

5749
21.53
19.84




Mean
21.79
20.11




SEM
0.66
0.62


Group 5
N
5799
23.39
21.09


MC3-Form-2

5804
22.26
20.55


2.8 mg/kg






10 μL/g






IV, Single dose








Mean
22.83
20.82




SEM
0.57
0.27


Group 6
Y
5718
21.20
17.81


MC3-Form-2

5731
23.74
19.57


2.8 mg/kg

5745
23.42
18.67


10 μL/g

5763
22.43
16.96


IV, Single dose

5771
23.17
18.88




Mean
22.79
18.38




SEM
0.45
0.45


Group 7
Y
5720
24.82
22.41


MC3-Form-3

5751
22.02
19.09


1.4 mg/kg

5762
22.42
20.10


10 μL/g

5785
22.04
19.55


IV, Single dose

5787
22.59
20.40




Mean
22.78
20.31




SEM
0.52
0.57


Group 8
Y
5709
22.56
19.84


MC3-Form-4

5754
22.20
20.64


0.7 mg/kg

5756
22.45
20.25


10 μL/g

5761
22.28
20.39


IV, Single dose

5772
23.92
20.73




Mean
22.68
20.37




SEM
0.32
0.16


Group 9
Y
5704
23.30
20.68


MC3-Form-5 diluted 1:2

5721
22.65
20.57


0.7 mg/kg

5724
24.74
22.36


10 μL/g

5782
21.96
19.42


IV, Single dose

5788
20.09
18.21




Mean
22.55
20.25




SEM
0.77
0.69


Group 10
Y
5702
21.86
18.23


MC3-Form-6

5726
23.15
19.10


1.4 mg/kg

5769
22.05
17.21


10 μL/g

5774
20.91
17.19


IV, Single dose

5781
22.84
18.99




Mean
22.16
18.14




SEM
0.39
0.41


Group 11
N
5794
23.76
21.79


MC3-Form-7

5802
22.40
19.66


2.8 mg/kg






10 μL/g






IV, Single dose








Mean
23.08
20.73




SEM
0.68
1.07


Group 12
Y
5703
25.38
22.75


MC3-Form-7

5711
22.00
20.73


2.8 mg/kg

5730
21.71
19.26


10 μL/g

5789
20.93
18.48


IV, Single dose








Mean
22.51
20.31




SEM
0.98
0.94


Group 13
Y
5719
22.11
21.66


PBS






10 μL/g






IV, Single dose








Mean
22.11
21.66




SEM
—
—


Group 14
N
5791
27.22
25.08


MC3-Form-5 diluted 1:2

5792
21.17
19.75


0.7 mg/kg

5793
21.84
19.94


10 μL/g

5796
23.19
21.27


IV, Single dose

5803
21.79
20.53




Mean
23.04
21.31




SEM
1.10
0.98





Note:


adays after the start of treatment.













TABLE 4







Bioluminescence










TV
Tumor
Animal No.
0a





Group 2
Y
5708
3.367E+09


MC3-Form-1

5729
7.370E+09


1.4 mg/kg

5744
8.847E+09


10 μL/g

5764
7.500E+09


IV, Single dose

5775
4.111E+09




Mean
6.239E+09




SEM
1.059E+09


Group 4
Y
5733
4.683E+09


NP357 and JetPEI

5736
9.999E+09


0.7 mg/kg

5739
8.016E+09


5 μL/g

5747
2.125E+09


IV, Single dose

5749
6.586E+09




Mean
6.282E+09




SEM
1.356E+09


Group 6
Y
5718
7.971E+09


MC3-Form-2

5731
4.694E+09


2.8 mg/kg

5745
6.386E+09


10 μL/g

5763
2.822E+09


IV, Single dose

5771
9.288E+09




Mean
6.232E+09




SEM
1.148E+09


Group 7
Y
5720
3.778E+09


MC3-Form-3

5751
8.746E+09


1.4 mg/kg

5762
6.683E+09


10 μL/g

5785
9.662E+09


IV, Single dose

5787
2.267E+09




Mean
6.227E+09




SEM
1.415E+09


Group 8
Y
5709
9.165E+09


MC3-Form-4

5754
2.435E+09


0.7 mg/kg

5756
4.592E+09


10 μL/g

5761
7.135E+09


IV, Single dose

5772
7.896E+09




Mean
6.245E+09




SEM
1.210E+09


Group 9
Y
5704
8.262E+09


MC3-Form-5 diluted 1:2

5721
3.337E+09


0.7 mg/kg

5724
8.483E+09


10 μL/g

5782
7.793E+09


IV, Single dose

5788
3.307E+09




Mean
6.236E+09




SEM
1.195E+09


Group 10
Y
5702
3.083E+09


MC3-Form-6

5726
6.548E+09


1.4 mg/kg

5769
8.508E+09


10 μL/g

5774
7.457E+09


IV, Single dose

5781
5.539E+09




Mean
6.227E+09




SEM
9.267E+08


Group 12
Y
5703
2.731E+09


MC3-Form-7

5711
4.297E+09


2.8 mg/kg

5730
8.090E+09


10 μL/g

5789
9.780E+09


IV, Single dose







Mean
6.225E+09




SEM
1.634E+09


Group 13
Y
5719
6.283E+09


PBS





10 μL/g





IV, Single dose







Mean
6.283E+09




SEM
—





Note:


adays after the start of treatment.






This study was designed to assess the cancer-activated gene expression using different delivery formulations, with an LNP shown to be highly effective at delivery in the liver. One cohort (Table 5, Groups 1, 2, 9, and 14) used a secreted embryonic alkaline phosphatase (SEAP) reporter protein to study the activation of the AFP-3 promoter versus the Survivin (BIRC5) promoter. The other groups contained a lead imaging reporter, HSV-sr39tk with a 9-amino acid epitope tag (hemagglutinin) fused to the terminus, a modification that is commonly used to study the expression levels of proteins. The hemagglutinin (HA) tag allows for the use of high affinity anti-HA antibodies to study the protein expression of sr39tk through immunohistochemistry (IHC).







TABLE 5







Experimental Groups in Hep3B Orthotopic Liver Tumor Study






















Dosing








Dose
Dosing
Volume



Group
N
Tumor
Treatment
Delivery
(mg/kg)
Route
(mL/kg)
Schedule


















1
5
N
NP003
LNP
1.4
IV
10
single dose





(BIRC5-SEAP)







2
5
Y
NP003
LNP
1.4
IV
10
single dose





(BIRC5-SEAP)







3
2
N
NP357
LNP
0.7
IV
5
single dose





(AFP-3-sr39tk)







4
5
Y
NP357
LNP
0.7
IV
5
single dose


5
2
N
NP357
LNP
2.8
IV
10
single dose


6
5
Y
NP357
LNP
2.8
IV
10
single dose


7
5
Y
NP357
LNP
1.4
IV
10
single dose


8
5
Y
NP357
LNP
0.7
IV
10
single dose


9
5
Y
NP041
LNP
1.4
IV
10
single dose





(AFP-3-SEAP)







10
5
Y
NP355
LNP
1.4
IV
10
single dose





(CAG-sr39tk)







11
2
N
NP357
LNP
2.8
IV
10
single dose


12
4
Y
NP357
LNP
2.8
IV
10
single dose


13
1
Y
NA
LNP
NA
IV
10
single dose


14
5
N
NP041
LNP
1.4
IV
10
single dose





(AFP-3-SEAP)














SEAP Results

Mice were IV-dosed with EM-40 formulated reporter constructs containing the SEAP reporter, as described in the previous section. Two different DNA nanoplasmids were used; one was comprised with the Survivin (BIRC5) cancer-activated promoter driving SEAP expression and one with the AFP-3 promoter to drive liver cancer activated expression. Once expressed in cancer cells, SEAP is secreted into the blood and a simple blood draw can be collected to reveal the presence of cancer. As expected, SEAP is secreted into the serum by the construct. Control blood draws from all animals before dosing (Day 0 in FIG. 39) showed undetectable background/basal activity in serum from tumor-bearing and normal mice (below the assay's LLOQ of 0.4 pg/12.5 μL serum). At the day 3 bleed, there was a significant difference in the SEAP biomarker availability in serum between non-tumor and tumor mice dosed with the same formulation. For mice dosed with Survivin, the non-tumor animals still showed undetectable background levels of SEAP, and a 7-fold increase over background expression in tumor-bearing mice. While there was a small amount of the reporter SEAP in the non-tumor mice dosed with AFP-3-SEAP, the fold-activation in tumor-bearing mice was higher, at nearly 100-fold the average SEAP expression in the non-tumor background.
IHC Results
Additional experiments were performed to determine which cells from a target organ contributed to the strong SEAP signal driven from the modified AFP3 promoter in the DNA nanoplasmids. The sequences encoding for SEAP were removed from the DNA nanoplasmid and replaced with sequences encoding for a version of the sr39TK PET Reporter Gene that had been modified with a HA (hemagglutinin) tag—a 9 bp epitope tag. Using antibodies against HA, IHC was performed on formalin fixed paraffin embedded (FFPE) liver tissues using a commonly available anti-HA antibody.
Mice were implanted with liver orthotopic tumors of Hep3B as previously described. EM-040 formulated DNA nanoplasmids that are comprised of the modified AFP-3 promoter to drive the expression of the HA-tagged sr39Tk PET Reporter Gene were injected systemically into the mice. Following 3 days of expression, the mice were sacrificed, their livers were harvested and then processed for IHC staining using the anti-HA antibody. H&E staining which can help distinguish different tissue structures and cell types within a sample, and correlate with expression by IHC to structural location and cell type was also performed. Control-stained sections of tumors and normal left & right lobes of the liver from mice dosed with a non-HA tag expressing construct (in this case BIRC5-SEAP) showed no non-specific staining, demonstrating that the method used specifically and accurately detected only the sr39tk-HA reporter from the construct.
Tumor sections from AFP-3-sr39tk dosed mice (FIGS. 40A-40C) showed strong expression of the construct in a significant portion of cells within the tumor, at both the 2.8 and 1.4 mg/kg dose levels, with no detected expression in left lobe cells bordering the tumor, or the non-tumor right lobe of the liver within the same mice.
The mice dosed with CAG-sr39tk was similarly studied. Because CAG is a very strong and constitutive promoter, it should accurately exhibit where delivery and expression is possible. While IHC is not quantitative by nature, the qualitative assessment of the tumors (as shown in FIGS. 41A-41F) showed that the CAG-driven construct exhibited equivalent levels of expression in tumors to the AFP-3 promoter, which was remarkable given that that CAG is considered one of the strongest constitutive promoters available in gene therapy. CAG expression was also preferentially localized to the tumor tissue as opposed to normal hepatocytes in the left or right lobe of the liver (possibly indicating that the nature of the highly vascularized tissue helps distribute the vector preferentially to the tumor tissues versus normal), but did show strong expression in disperse single cells in representative left and right lobe sections which were not observed with the more specific AFP-3 (FIGS. 41C and 41D).
Conclusion
These series of experiments demonstrate the utility of the cancer-specific gene expression in an orthotopic liver tumor model, demonstrating delivery to primary liver tumors as well as activation in the context of a human liver cancer cell. The LNP formulation demonstrates highly effective delivery to tumor cells upon IV dosing.
The AFP-3 promoter showed a nearly 100-fold higher activation in the blood marker SEAP than the BIRC5 promoter in the Hep3B-model, and IHC analysis also showed highly specific and strong expression in tumor cells and not in normal liver cells. The highly qualitative IHC data demonstrated strong levels of activation of the AFP-3 promoter and the ability of the combined components to deliver and express in a cancer-specific manner.
Example 4: Benign Versus Malignant, Inflammation and Specificity
Multi-omics (RNA-seq, proteomics, and ATAC-seq) methodology was used to analyze benign tissue/cell samples. FIG. 43A shows number of different benign tissue/cell samples used for multi-omics analysis. Details of multi-omics methodology was described in Examples 1 and 2. Analysis of 160 Epithelial-Mesenchymal Transition (EMT) genes defined by the Molecular Signatures Database (MsigDB; see Liberzon A., et al. The Molecular Signatures Database hallmark gene set collection. Cell Syst. 2015 Dec. 23; 1(6):417-425) using multi-omics and principal component analysis (PCA) demonstrated a transcriptomic difference between malignant human lung cancer (Clinical Proteomic Tumor Analysis Consortium (CPTAC) lung tumor) and benign lesions (NAT), and internal benign) (FIGS. 43B-43D).
Next, using CBA/J mice model infected with Mycobacterium tuberculosis (M. tb; S. Major, J. Turner, and G. Beamer. Tuberculosis in CBA/J Mice. Veterinary Pathology 2013 50:6, 1016-1021), reporter gene expression driven by FOS-core-BIRC5 synthetic promoter was analyzed. There was no expression of reporter gene in granulomatous lesions caused by M.tb infection in CBA/J mice despite high disease burden (FIG. 44), suggesting there is no cancer-activated expression in granulomas, which is a model of benign tissue lesions.
The examples and embodiments described herein are for illustrative purposes only and various modifications or changes suggested to persons skilled in the art are to be included within the spirit and purview of this application and scope of the appended claims.
EMBODIMENTS
The following embodiments are not intended to be limiting in any way.
Embodiment 1: A recombinant polynucleotide comprising:

    
    
        (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and
        (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells.
    
    


Embodiment 2: A recombinant polynucleotide comprising:

    
    
        (a) a core promoter comprising a transcription start site (TSS) and two or more promoter elements derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and
        (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells.
    
    


Embodiment 3: The recombinant polynucleotide of Embodiment 1 or 2, further comprising a plurality of enhancers.
Embodiment 4: A recombinant polynucleotide comprising:

    
    
        (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF) and
        (b) a plurality of enhancers.
    
    


Embodiment 5: A recombinant polynucleotide comprising:

    
    
        (a) a core promoter comprising a transcription start site (TSS), wherein the core promoter is derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF),
        (b) a plurality of binding sites for one or more transcription factors (TFs), wherein said one or more TFs are expressed at higher levels or more active in cancer cells compared to non-cancer cells, and
        (c) a plurality of enhancers.
    
    


Embodiment 6: The recombinant polynucleotide of any one of embodiments 3-5, wherein said plurality of enhancers are derived from one or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells.
Embodiment 7: The recombinant polynucleotide of any one of embodiments 3-6, wherein the plurality of enhancers are derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells, wherein one of said plurality of enhancers comprises:

    
    
        (i) a transcription regulatory element with at least 90% sequence homology to an enhancer consensus sequence of two or more homologous cancer-responsive genes, and/or
        (ii) a sequence capable of binding a transcription associated protein as determined by chromatin immunoprecipitation (ChIP) or an in vitro transfection reporter assay.
    
    


Embodiment 8: The recombinant polynucleotide of any one of embodiments 1-7, wherein said core promoter further comprises two or more promoter elements derived from two or more cancer-responsive genes that are either expressed at a higher level or are more active in cancer cells compared to non-cancer cells and operably linked to an open reading frame (ORF).
Embodiment 9: The recombinant polynucleotide of any one of embodiments 1-8, wherein said one or more cancer-responsive genes are derived from a human subject.
Embodiment 10: The recombinant polynucleotide of any one of embodiments 6-9, wherein: (a) said core promoter, and (b) said plurality of binding sites for one or more TFs or said plurality of enhancers derived from one or more cancer-responsive genes are not derived from a same cancer-responsive gene.
Embodiment 11: The recombinant polynucleotide of any one of embodiments 7-10, wherein said enhancer consensus sequence of two or more homologous cancer-responsive genes is a consensus sequence of an enhancer sequence derived from two or more cancer-responsive genes that has at least 90% sequence identity between two or more human cancer-responsive genes.
Embodiment 12: The recombinant polynucleotide of any one of embodiments 3-11, wherein at least one of the plurality of enhancers comprises a CpG island.
Embodiment 13: The recombinant polynucleotide of any one of embodiments 3-11, wherein at least one of the plurality of enhancers does not comprise a CpG island.
Embodiment 14: The recombinant polynucleotide of any one of embodiments 1-13, wherein said higher levels of TF expression in cancer cells compared to non-cancer cells is determined by chromatin immunoprecipitation (ChIP).
Embodiment 15: The recombinant polynucleotide of any one of embodiments 1-14, further comprising an open reading frame (ORF), wherein said core promoter is operably linked to said ORF.
Embodiment 16: The recombinant polynucleotide of any one of embodiments 1-15, wherein said plurality of binding sites for one or more TFs are 5′ to said core promoter.
Embodiment 17: The recombinant polynucleotide of any one of embodiments 3-16, wherein said plurality of enhancers are 5′ to said core promoter and 3′ to said plurality of binding sites for one or more TFs, if present.
Embodiment 18: The recombinant polynucleotide of any one of embodiments 1-17, wherein said plurality of binding sites for one or more TFs comprises two or more binding sites for one TF, wherein each of the plurality of binding sites for one or more TFs is sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide.
Embodiment 19: The recombinant polynucleotide of any one of embodiments 1-17, wherein said plurality of binding sites for one or more TFs comprises two or more binding sites for two or more TFs, wherein each of the plurality of binding sites for one or more TFs is non-sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide.
Embodiment 20: The recombinant polynucleotide of any one of embodiments 1-19, wherein said plurality of binding sites for one or more TFs comprise a plurality of TRPS1, MNX1, TWIST1, ETV4, FOSL2, NFIC, EN2, TFDP1, PITX2, TCF7L1, VENTX, HOXB9, DLX1, MYCN, SIX4, TP63, SOX11, E2F8, TFDP1, SURV, TOXE, EN1, ZBTB7B, SP3, SIX2, XBP1, HIF-1A, CREB3L1, HSF-1, MTF1, NFE2L2, USF2, TP73, USF2, POU2F2, HOXA1, FOXO1, TFAP4, BACH1, E2F4, HOXC10, KLF11, FOXM1, E2F2, RUNX1, SOX4, RREB1, ETV4, HES6, ASCL1, TWIST1, FOXA3, PITX2, HOXB2, EN2, DLX4, GRHL1, FOXA, HIF, E2F6, FOSL1, NF-1, RFX6, EL4, or NFκB TF binding sites.
Embodiment 21: The recombinant polynucleotide of any one of embodiments 1-20, further comprising a spacer element comprising 1-10 nucleotides between each of plurality of binding sites for one or more TFs.
Embodiment 22: The recombinant polynucleotide of any one of embodiments 1-21, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise TCF7, MNX1, HOXC10, TP53, CEACAM5, CEP55, FAM111B, CST1, BIRC5, FOS, TWIST1, E2F2, KIF20A, or ETV4.
Embodiment 23: The recombinant polynucleotide of any one of embodiments 1-22, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise two or more of TCF7, MNX1, HOXC10, TPS3, CEACAM5, CEP55, FAM111B, CST1, BIRC5, FOS, TWIST1, E2F2, KIF20A, or ETV4.
Embodiment 24: The recombinant polynucleotide of any one of embodiments 1-22, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise TCF7 and HOXC10.
Embodiment 25: The recombinant polynucleotide of any one of embodiments 1-22, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise TP53 and CEP55.
Embodiment 26: The recombinant polynucleotide of any one of embodiments 1-22, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise FAM111B and KIF20A.
Embodiment 27: The recombinant polynucleotide of any one of embodiments 1-22, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise BIRC5 and E2F2.
Embodiment 28: The recombinant polynucleotide of any one of embodiments 1-22, wherein said one or more cancer-responsive genes from which said core promoter is derived comprise CEACAM5 and TWIST1.
Embodiment 29: The recombinant polynucleotide of any one of embodiments 1-28, wherein said core promoter comprises a region from about −300 bp to +100 bp relative to said TSS.
Embodiment 30: The recombinant polynucleotide of any one of embodiments 3-29, wherein said plurality of enhancers comprises at least two enhancer sequences, wherein each of said at least two enhancer sequences comprises (i) the same enhancer sequences, (ii) different enhancer sequences, or (iii) a combination thereof.
Embodiment 31: The recombinant polynucleotide of embodiment 30, wherein each of said at least two enhancer sequences is sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide.
Embodiment 32: The recombinant polynucleotide of embodiment 30, wherein each of said at least two enhancer sequences is sequentially arranged at 5′ to said core promoter and at 3′ to said plurality of binding sites of one or more TFs, if present, in the recombinant polynucleotide.
Embodiment 33: The recombinant polynucleotide of embodiment 30, wherein each of said at least two enhancer sequences comprises (ii), wherein each of said plurality of enhancers comprising different enhancer sequences is non-sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide.
Embodiment 34: The recombinant polynucleotide of embodiment 30, wherein each of said at least two enhancer sequences comprises (ii), wherein each of said plurality of enhancers is non-sequentially arranged at 5′ to said core promoter and at 3′ to said plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide.
Embodiment 35: The recombinant polynucleotide of embodiment 30, wherein each of said at least two enhancer sequences comprises (iii), wherein each of said plurality of enhancers comprising a combination of the same and different enhancer sequences is non-sequentially arranged at 5′ to said core promoter in the recombinant polynucleotide.
Embodiment 36: The recombinant polynucleotide of embodiment 30, wherein each of said at least two enhancer sequences comprises (iii), wherein each of said plurality of enhancers comprising a combination of the same and different enhancer sequences is non-sequentially arranged at 5′ to said core promoter and at 3′ to said plurality of binding sites for one or more TFs, if present, in the recombinant polynucleotide.
Embodiment 37: The recombinant polynucleotide of any one of embodiments 3-36, wherein said plurality of enhancers comprises at least two EBS, C/EBP, ARE, DRE, NFκB, GC-box, UN5CL, BOP1, RTN4RL2, ARNTL2, AGR2, LHX2, TRNP1, MU5AC, or DOK4 enhancer sequences.
Embodiment 38: The recombinant polynucleotide of any one of embodiments 1-37, wherein expression of said ORF is increased when said recombinant polynucleotide is introduced to cancer cells compared to non-cancer cells.
Embodiment 39: The recombinant polynucleotide of any one of embodiments 1-37, wherein expression of said ORF is increased in a first plurality of cancer cells when said recombinant polynucleotide is introduced to said first plurality of cancer cells compared to a second plurality of cancer cells, wherein said first plurality of cancer cells and said second plurality of cancer cells are different types of cancer cells.
Embodiment 40: The recombinant polynucleotide of embodiment 38 or 39, wherein said cancer cells comprise malignant cancer cells.
Embodiment 41: The recombinant polynucleotide of any one of embodiments 38-40, wherein said cancer cells comprise lung cancer cells, colorectal cancer cells, breast cancer cells, or hepatocellular carcinoma cells.
Embodiment 42: The recombinant polynucleotide of any one of embodiments 38-40, wherein said cancer cells comprise cells associated with colorectal cancer, hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
Embodiment 43: The recombinant polynucleotide of embodiment 42, wherein said cancer cells comprise cells associated with two or more cancers comprising colorectal cancer, hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
Embodiment 44: The recombinant polynucleotide of any one of embodiments 3-43, wherein said core promoter, said plurality of binding sites for one or more transcription factors (TFs), said plurality of enhancers, or said recombinant polynucleotide comprises a sequence from Table 1A, Table 1B, or Table 1C.
Embodiment 45: A recombinant polynucleotide comprising any of the sequences from Table 1A, Table 1B, or Table 1C.
Embodiment 46: A recombinant polynucleotide comprising a human alpha-fetoprotein (AFP) promoter sequence comprising a plurality of HNF-1A TF binding sites, wherein each HNF-1A binding site comprises the sequence 5′-GTTAATTATTAAC-3′ (SEQ ID NO: 128).
Embodiment 47: A vector comprising the recombinant polynucleotide of any one of embodiments 1-46.
Embodiment 48: A pharmaceutical composition comprising the recombinant polynucleotide of any one of embodiments 1-46 or the vector of embodiment 47 and a pharmaceutically acceptable excipient, carrier, or diluents.
Embodiment 49: A lipid nanoparticle (LNP) comprising the recombinant polynucleotide of any one of embodiments 1-46, the vector of embodiment 47, or the pharmaceutical composition of embodiment 48.
Embodiment 50: A cell comprising the recombinant polynucleotide of any one of embodiments 1-46, the vector of embodiment 47, the pharmaceutical composition of embodiment 48, or the LNP of embodiment 49.
Embodiment 51: A method of selectively expressing a reporter protein in a cancer or tumor cell, comprising contacting said tumor cell the recombinant polynucleotide according to any one of embodiments 1-46, the vector of embodiment 47, the pharmaceutical composition of embodiment 48, or the LNP of embodiment 49, wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding said reporter protein, wherein said ORF is operatively linked to said synthetic promoter.
Embodiment 52: A method comprising:

    
    
        (a) administering to a subject the pharmaceutical composition of embodiment 48; or a composition comprising the recombinant polynucleotide of any one of embodiments 1-46, the vector of embodiment 47, or the LNP of embodiment 49; wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and
        (b) detecting said reporter protein,
        wherein said pharmaceutical composition or said composition induces expression of said reporter protein preferentially in diseased cells in said subject compared to in non-disease cells, and wherein a relative ratio of said reporter protein expressed in said diseased cells over said non-diseased cells is greater than 1.0.
    
    


Embodiment 53: The method of embodiment 52, wherein said relative ratio of said reporter protein expressed in said diseased cells over said non-diseased cells is greater than 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 13.5, 14.0, 14.5, or about 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0, 85.0, 90.0, 95.0, or about 100.0.
Embodiment 54: A method for treating a subject having or suspected of having a disease, comprising administering to said subject the pharmaceutical composition of embodiment 48; or a composition comprising the recombinant polynucleotide of any one of embodiments 1-46, the vector of embodiment 47, or the LNP of embodiment 49;

    
    
        wherein the recombinant polynucleotide further comprises an open reading frame (ORF) encoding a therapeutic protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, wherein said pharmaceutical composition or said composition induces expression of said therapeutic protein preferentially in diseased cells in said subject compared to in non-disease cells, and wherein a relative ratio of said therapeutic protein expressed in said diseased cells over said non-diseased cells is greater than 1.0.
    
    


Embodiment 55: The method of any one of embodiments 52-54, wherein said diseased cells comprise a cancer or tumor cell.
Embodiment 56: The method of embodiment 51 or 55, wherein said cancer or tumor cell is associated with colorectal cancer (CRC), hepatocellular carcinoma, lung cancer, liver cancer, breast cancer, prostate cancer, cervix cancer, uterus cancer, pancreas cancer, kidney cancer, stomach cancer, bladder cancer, ovary cancer, brain cancer, head and neck cancer, eye cancer, mouth cancer, throat cancer, esophagus cancer, chest cancer, bone cancer, rectum or other gastrointestinal tract organ cancer, spleen cancer, skeletal muscle cancer, subcutaneous tissue cancer, testicles or other reproductive organ cancer, skin cancer, thyroid cancer, blood cancer, or lymph nodes cancer.
Embodiment 57: A method comprising:

    
    
        (a) administering to a subject the pharmaceutical composition of embodiment 48; or a composition comprising the recombinant polynucleotide of any one of embodiments 1-46, the vector of embodiment 47, or the LNP of embodiment 49; wherein said recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and
        (b) localizing a tumor or an absence thereof in a body of said subject via expression of said reporter protein using an imaging technique performed on said body of said subject.
    
    


Embodiment 58: A method comprising:

    
    
        (a) introducing to a subject suspected of having a cancer via intravenous administration the pharmaceutical composition of embodiment 48; or a composition comprising the recombinant polynucleotide of any one of embodiments 1-46, the vector of embodiment 47, or the LNP of embodiment 49; wherein said recombinant polynucleotide further comprises an open reading frame (ORF) encoding a reporter protein, wherein said ORF is operatively linked to a synthetic promoter in said recombinant polynucleotide, and
        (b) detecting said reporter protein from said subject.
    
    


Embodiment 59: A method comprising:

    
    
        (a) introducing to a subject suspected of having a cancer via intravenous administration a plurality of recombinant polynucleotides, wherein: said plurality of recombinant polynucleotides comprises a plurality of different promoters of genes overexpressed in a tumor cell versus a normal tissue or functional fragments thereof operably linked to genes encoding reporter proteins, wherein said plurality of different promoters of genes overexpressed in said tumor cell versus said normal tissue drive expression of said corresponding reporter proteins in a cell affected by said cancer, wherein said DNA molecules are selected from the group consisting of nanoplasmids and linear double-stranded DNA molecules; and
        (b) detecting said reporter proteins from said subject.