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| Status |
Public on Apr 19, 2015 |
| Title |
Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We developed a method for genome-wide mapping of DNA excision repair named XR-seq (eXcision Repair-seq). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating a ~30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells, cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts ((6-4)PPs). In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern, and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bi-directional eRNA production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.
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| Overall design |
We have performed XR-seq for two types of UV-induced damages (CPD and (6-4)PP) in three different cell lines: NHF1, XP-C (XP4PA-SV-EB, GM15983)), and CS-B (CS1ANps3g2, GM16095). Two biological replicates were performed for each experiment, in which independent cell populations were UV treated and subjected to XR-seq.
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| Contributor(s) |
Hu J, Adar S, Selby CP, Lieb JD, Sancar A |
| Citation(s) |
25934506, 37844222 |
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| Submission date |
Apr 15, 2015 |
| Last update date |
Nov 16, 2023 |
| Contact name |
Sheera Adar |
| Organization name |
Hebrew University of Jerusalem
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| Department |
Department of Microbiology and Molecular Genetics
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| Lab |
Sheera Adar
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| Street address |
Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem
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| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
91120 |
| Country |
Israel |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA281260 |
| SRA |
SRP057214 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67941_CPD1h_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw |
73.5 Mb |
(ftp)(http) |
BW |
| GSE67941_CPD1h_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw |
85.9 Mb |
(ftp)(http) |
BW |
| GSE67941_CSB64_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw |
130.6 Mb |
(ftp)(http) |
BW |
| GSE67941_CSB64_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw |
135.1 Mb |
(ftp)(http) |
BW |
| GSE67941_CSBCPD_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw |
111.9 Mb |
(ftp)(http) |
BW |
| GSE67941_CSBCPD_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw |
111.7 Mb |
(ftp)(http) |
BW |
| GSE67941_PP641h_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw |
149.1 Mb |
(ftp)(http) |
BW |
| GSE67941_PP641h_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw |
148.8 Mb |
(ftp)(http) |
BW |
| GSE67941_XPC64_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw |
68.7 Mb |
(ftp)(http) |
BW |
| GSE67941_XPC64_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw |
67.6 Mb |
(ftp)(http) |
BW |
| GSE67941_XPCCPD_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw |
68.5 Mb |
(ftp)(http) |
BW |
| GSE67941_XPCCPD_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw |
67.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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