Whole-genome analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans
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. 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.