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| Status |
Public on Nov 03, 2020 |
| Title |
Heritable Pattern of Oxidized DNA Base Repair Coincides with Pre-Targeting of Repair Complexes to Open Chromatin |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and coimmunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its nonacetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting reduced mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily-conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ~500 million years ago during the buildup of free atmospheric oxygen.
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| Overall design |
Mapping acetylated NEIL1 in HCT116 cells
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| Contributor(s) |
Bacolla A, Sengupta S, Ye Z, Yang C, Mitra J, De-Paula RB, Hegde ML, Ahmed Z, Mort M, Cooper DN, Mitra S, Tainer JA |
| Citation(s) |
33300026 |
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| Submission date |
Dec 19, 2019 |
| Last update date |
Feb 25, 2022 |
| Contact name |
Sankar Mitra |
| E-mail(s) |
sankarmtr326@gmail.com, smitra2@houstonmethodist.org
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| Phone |
(832) 298-7550
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| Organization name |
Houston Methodist Resrarch Institute
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| Department |
Houston Methodist Cancer Center
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| Street address |
6445 Main Street
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA596647 |
| SRA |
SRP238204 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142324_RAW.tar |
3.8 Gb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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