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| Status |
Public on Mar 15, 2016 |
| Title |
Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We recently developed a high-resolution genome wide assay for mapping DNA excision repair named eXcision Repair-sequencing (XR-seq) (GEO accession: GSE67941) We have now used this assay to assay the effect of chromatin state on DNA repair. Here we report the results of a time-course of the repair of the UV induced damages cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs] in normal human skin fibroblasts. Comparison of this data to histone modification and DNA-seq maps (ENCODE) revealed initial repair of both damages is enriched in open and active chromatin states, whereas repair in heterochromatic and repressed chromatin states is relatively low and persists to later time points.
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| Overall design |
We performed XR-seq for two types of UV induced damages (CPD and (6-4)PP) at multiple time points after UV irradiation, in normal NHF1, and CS-B (CS1ANps3g2, GM16095) fibroblast cell lines. Two biological replicates were performed for each experiment in which independent independent cell populations were UV treated and subjected to XR-seq. For assaying CPD repair, cells were irradiated with 10J/m2 and for assaying (6-4)PP cells were irradiated with 20J/m2. Raw data for the 1h time points of (6-4)PP repair are the same as in GEO accession GSE67941).
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| Contributor(s) |
Adar S, Hu J, Lieb JD, Sancar A |
| Citation(s) |
27036006 |
| |
| Submission date |
Dec 29, 2015 |
| Last update date |
Oct 15, 2019 |
| Contact name |
Sheera Adar |
| Organization name |
Hebrew University of Jerusalem
|
| Department |
Department of Microbiology and Molecular Genetics
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| Lab |
Sheera Adar
|
| Street address |
Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem
|
| 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 (30)
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| Relations |
| BioProject |
PRJNA307178 |
| SRA |
SRP067879 |
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