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| Status |
Public on Nov 21, 2023 |
| Title |
Whole-genome analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPD) photoproducts in the Caenorhabditis elegans (C. elegans) genome. We focus on the C. elegans ortholog of the human XPC-deficient strain (xpc-1) and its exclusive use of transcription-coupled repair. We provide evidence demonstrating the utility of xpc-1 XR-seq as a remarkable tool for detecting nascent transcription and identifying new transcripts. The integration of epigenetic markers, chromatin states, and non-coding RNA annotations supports the robust detection of intergenic nascent transcription by XR-seq. Overall, our results provide a comprehensive view of the transcription-coupled repair landscape in C. elegans, highlighting their potential contributions to our understanding of DNA repair mechanisms and non-coding RNA biology.
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| Overall design |
We employed XR-seq to evaluate genome-wide excision repair dynamics in xpc-1 C. elegans at distinct time points following UV exposure, specifically at 5 minutes, 1 hour, 8 hours, 16 hours, 24 hours, and 48 hours post-treatment. We also carried out poly(A) RNA-seq of wildtype and xpc-1 C. elegans.
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| Contributor(s) |
Kose C, Lindsey-Boltz LA, Sancar A, Jiang Y |
| Citation(s) |
37904932 |
| |
| Submission date |
Oct 12, 2023 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Yuchao Jiang |
| E-mail(s) |
yuchaojiang@tamu.edu
|
| Organization name |
Texas A&M University
|
| Street address |
3143 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platforms (2) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
| GPL32326 |
NextSeq 2000 (Caenorhabditis elegans) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA1027326 |
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