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TCR is initiated when elongating RNA polymerase II encounters DNA damage, and thus analysis of genome-wide excision repair in XPC-mutants only repairing by TCR provides a unique opportunity to map transcription events missed by methods dependent on capturing RNA transcription products and thus limited by their stability and\/or modifications (5\u2019-capping or 3\u2019-polyadenylation). Here, we have performed eXcision Repair-sequencing (XR-seq) in the model organism <jats:italic>Caenorhabditis elegans<\/jats:italic> to generate genome-wide repair maps in a wild-type strain with normal excision repair, a strain lacking TCR (<jats:italic>csb-1<\/jats:italic>), and a strain that only repairs by TCR (<jats:italic>xpc-1<\/jats:italic>). Analysis of the intersections between the <jats:italic>xpc-1<\/jats:italic> XR-seq repair maps with RNA-mapping datasets (RNA-seq, long- and short-capped RNA-seq) reveal previously unrecognized sites of transcription and further enhance our understanding of the genome of this important model organism.<\/jats:p>","DOI":"10.1371\/journal.pgen.1011365","type":"journal-article","created":{"date-parts":[[2024,7,19]],"date-time":"2024-07-19T17:33:25Z","timestamp":1721410405000},"page":"e1011365","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegans"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2024-3566","authenticated-orcid":true,"given":"Cansu","family":"Kose","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6493-8194","authenticated-orcid":true,"given":"Laura A.","family":"Lindsey-Boltz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6469-4900","authenticated-orcid":true,"given":"Aziz","family":"Sancar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuchao","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,7,19]]},"reference":[{"issue":"1","key":"pgen.1011365.ref001","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.cell.2014.03.008","article-title":"The noncoding RNA revolution-trashing old rules to forge new ones","volume":"157","author":"TR Cech","year":"2014","journal-title":"Cell"},{"issue":"8","key":"pgen.1011365.ref002","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1038\/s41576-018-0013-2","article-title":"Controlling nuclear RNA levels","volume":"19","author":"M Schmid","year":"2018","journal-title":"Nat Rev Genet"},{"issue":"6","key":"pgen.1011365.ref003","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","article-title":"Long non-coding RNAs: definitions, functions, challenges and recommendations","volume":"24","author":"JS Mattick","year":"2023","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"1","key":"pgen.1011365.ref004","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Z Wang","year":"2009","journal-title":"Nat Rev Genet"},{"key":"pgen.1011365.ref005","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.37344","article-title":"Chromatin accessibility dynamics across C. elegans development and ageing","volume":"7","author":"J Janes","year":"2018","journal-title":"Elife"},{"issue":"8","key":"pgen.1011365.ref006","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1101\/gr.153668.112","article-title":"The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures","volume":"23","author":"RA Chen","year":"2013","journal-title":"Genome Res"},{"issue":"1","key":"pgen.1011365.ref007","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/s41596-018-0093-7","article-title":"Genome-wide mapping of nucleotide excision repair with XR-seq","volume":"14","author":"J Hu","year":"2019","journal-title":"Nat Protoc"},{"key":"pgen.1011365.ref008","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0079-6603(04)79004-2","article-title":"Nucleotide excision repair","volume":"79","author":"JT Reardon","year":"2005","journal-title":"Prog Nucleic Acid Res Mol Biol"},{"issue":"8","key":"pgen.1011365.ref009","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1073\/pnas.89.8.3664","article-title":"Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5\u2019 and the 6th phosphodiester bond 3\u2019 to the photodimer","volume":"89","author":"JC Huang","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"30","key":"pgen.1011365.ref010","doi-asserted-by":"crossref","first-page":"8502","DOI":"10.1002\/anie.201601524","article-title":"Mechanisms of DNA Repair by Photolyase and Excision Nuclease (Nobel Lecture)","volume":"55","author":"A. 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