{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T21:50:09Z","timestamp":1789681809312,"version":"4.0.1"},"reference-count":91,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"Ministry of Education","doi-asserted-by":"publisher","award":["RS-2023-00250327"],"award-info":[{"award-number":["RS-2023-00250327"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"Ministry of Education","doi-asserted-by":"publisher","award":["RS-2025-25440216"],"award-info":[{"award-number":["RS-2025-25440216"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Education and the BUSAN","award":["2026-ANCHOR-02-003"],"award-info":[{"award-number":["2026-ANCHOR-02-003"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Transcription-coupled nucleotide excision repair (TC-NER) removes transcription-blocking lesions from active genes, but how lesion-stalled RNA polymerase II (RNAPII) is converted into a repair-accessible substrate remains incompletely understood. Active chromatin is dynamic but not topology-free. RNAPII elongation generates torsional stress that is buffered by nucleosome dynamics, chromatin remodelers, topoisomerases, and gene-body organization. Upon lesion-induced RNAPII arrest, this buffering system may fail locally, creating a topologically and architecturally constrained repair substrate. Here, we integrate established mechanisms of CSB-dependent RNAPII remodeling and recently defined ubiquitin-dependent clearance pathways with a testable model in which local torsional stress and topoisomerase-mediated relaxation influence repair permissiveness. In this framework, CSB remodels and organizes lesion-stalled RNAPII complexes, whereas topoisomerase may contribute to relaxation of transcription-generated supercoiling, thereby promoting a repair-permissive chromatin state. Recent evidence further indicates that CRL4CSA-dependent RNAPII ubiquitylation initiates a hierarchical clearance program in which TFIIH\/XPD drives rapid RNAPII displacement and VCP\/p97 provides a backup extraction pathway. Together, these findings support a model in which TC-NER is possibly licensed not only by repair-factor recruitment but also by coordinated remodeling of RNAPII architecture, chromatin topology, and polymerase fate.<\/jats:p>","DOI":"10.3390\/ijms27167244","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T09:04:01Z","timestamp":1786698241000},"page":"7244","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Topology Resetting During Transcription-Coupled Nucleotide Excision Repair"],"prefix":"10.3390","volume":"27","author":[{"given":"Tae-Hee","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Radiation Oncology and Molecular Radiation Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-6209-5695","authenticated-orcid":false,"given":"Jeseok","family":"Jeon","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4367-5305","authenticated-orcid":false,"given":"Seo-Gyeong","family":"Jo","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6013-900X","authenticated-orcid":false,"given":"Tae-Hong","family":"Kang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nrm3822","article-title":"Understanding nucleotide excision repair and its roles in cancer and ageing","volume":"15","author":"Marteijn","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/s41580-019-0169-4","article-title":"The DNA damage response to transcription stress","volume":"20","author":"Lans","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Jeon, J., and Kang, T.H. (2025). Transcription-Coupled Repair and R-Loop Crosstalk in Genome Stability. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26083744"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/cr.2008.6","article-title":"Transcription-coupled nucleotide excision repair in mammalian cells: Molecular mechanisms and biological effects","volume":"18","author":"Fousteri","year":"2008","journal-title":"Cell Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2104","DOI":"10.1038\/s41467-020-15903-8","article-title":"The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II","volume":"11","author":"Mevissen","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1038\/s41467-026-68413-4","article-title":"Hierarchical mechanisms control the clearance of DNA lesion-stalled RNA polymerase II","volume":"17","author":"Yakoub","year":"2026","journal-title":"Nat. Commun."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2138","DOI":"10.1021\/acs.biochem.5c00114","article-title":"Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes","volume":"64","author":"Govers","year":"2025","journal-title":"Biochemistry"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.dnarep.2018.08.006","article-title":"Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair","volume":"71","author":"Wang","year":"2018","journal-title":"DNA Repair"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1016\/j.jmb.2019.12.034","article-title":"TADs or no TADS: Lessons from Single-cell Imaging of Chromosome Architecture","volume":"432","author":"Cattoni","year":"2020","journal-title":"J. Mol. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"166701","DOI":"10.1016\/j.jmb.2020.11.001","article-title":"Nucleosome Clutches are Regulated by Chromatin Internal Parameters","volume":"433","author":"Tsao","year":"2021","journal-title":"J. Mol. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"102211","DOI":"10.1016\/j.ceb.2023.102211","article-title":"Technological advances in probing 4D genome organization","volume":"84","author":"Soroczynski","year":"2023","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"eadu0577","DOI":"10.1126\/sciadv.adu0577","article-title":"Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome","volume":"11","author":"Naganuma","year":"2025","journal-title":"Sci. Adv."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/s41588-023-01603-8","article-title":"The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes","volume":"56","author":"Brahma","year":"2024","journal-title":"Nat. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"102690","DOI":"10.1016\/j.sbi.2023.102690","article-title":"Nucleosomes unwrapped: Structural perspectives on transcription through chromatin","volume":"82","author":"Farnung","year":"2023","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"12161","DOI":"10.1093\/nar\/gkad1066","article-title":"Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery","volume":"51","author":"Vega","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"dev182766","DOI":"10.1242\/dev.182766","article-title":"Chromatin topology, condensates and gene regulation: Shifting paradigms or just a phase?","volume":"146","author":"Mir","year":"2019","journal-title":"Development"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nsmb.2723","article-title":"Transcription-generated torsional stress destabilizes nucleosomes","volume":"21","author":"Teves","year":"2014","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/nar\/gkab1252","article-title":"DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases","volume":"50","author":"Tripathi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1093\/nar\/gkad1181","article-title":"Single-molecule visualization of twin-supercoiled domains generated during transcription","volume":"52","author":"Janissen","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1038\/s41594-024-01377-5","article-title":"Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression","volume":"32","author":"Yao","year":"2025","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"eadv0134","DOI":"10.1126\/science.adv0134","article-title":"Chromatin buffers torsional stress during transcription","volume":"391","author":"Qian","year":"2026","journal-title":"Science"},{"key":"ref_22","first-page":"E2538","article-title":"Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II","volume":"115","author":"Wang","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2418","DOI":"10.1093\/nar\/gkab085","article-title":"Current and emerging roles of Cockayne syndrome group B (CSB) protein","volume":"49","author":"Tiwari","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/s41467-021-27686-7","article-title":"Topoisomerase I (TOP1) dynamics: Conformational transition from open to closed states","volume":"13","author":"Takahashi","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/nrm.2016.111","article-title":"Roles of eukaryotic topoisomerases in transcription, replication and genomic stability","volume":"17","author":"Pommier","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/S1097-2765(00)80132-X","article-title":"Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair","volume":"2","author":"Sugasawa","year":"1998","journal-title":"Mol. Cell"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.dnarep.2005.01.001","article-title":"The UV-damaged DNA binding protein mediates efficient targeting of the nucleotide excision repair complex to UV-induced photo lesions","volume":"4","author":"Moser","year":"2005","journal-title":"DNA Repair"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"a012625","DOI":"10.1101\/cshperspect.a012625","article-title":"Mammalian transcription-coupled excision repair","volume":"5","author":"Vermeulen","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"103126","DOI":"10.1016\/j.dnarep.2021.103126","article-title":"Transcription-coupled nucleotide excision repair: New insights revealed by genomic approaches","volume":"103","author":"Duan","year":"2021","journal-title":"DNA Repair"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3018","DOI":"10.1093\/nar\/gkac174","article-title":"RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: From molecular basis to functional consequences","volume":"50","author":"Agapov","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/ng.2230","article-title":"UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair","volume":"44","author":"Schwertman","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2341","DOI":"10.1038\/s41467-025-57593-0","article-title":"Molecular model of TFIIH recruitment to the transcription-coupled repair machinery","volume":"16","author":"Paul","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3490","DOI":"10.1038\/s41467-024-47935-9","article-title":"Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure","volume":"15","author":"Thijssen","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Park, J.M., and Kang, T.H. (2016). Transcriptional and Posttranslational Regulation of Nucleotide Excision Repair: The Guardian of the Genome against Ultraviolet Radiation. Int. J. Mol. Sci., 17.","DOI":"10.3390\/ijms17111840"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41594-023-01207-0","article-title":"Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair","volume":"31","author":"Kokic","year":"2024","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"7089","DOI":"10.1038\/s41467-024-51463-x","article-title":"Coordination of transcription-coupled repair and repair-independent release of lesion-stalled RNA polymerase II","volume":"15","author":"Zhu","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.dnarep.2015.09.003","article-title":"Nucleotide excision repair in humans","volume":"36","author":"Spivak","year":"2015","journal-title":"DNA Repair"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.dnarep.2015.09.013","article-title":"Histone modification and chromatin remodeling during NER","volume":"36","author":"Waters","year":"2015","journal-title":"DNA Repair"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"203","DOI":"10.4161\/nucl.29085","article-title":"Gearing up chromatin: A role for chromatin remodeling during the transcriptional restart upon DNA damage","volume":"5","author":"Mandemaker","year":"2014","journal-title":"Nucleus"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"7001","DOI":"10.1038\/s41467-021-27295-4","article-title":"Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair","volume":"12","author":"Yan","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1016\/j.cell.2020.02.010","article-title":"Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair","volume":"180","author":"Nakazawa","year":"2020","journal-title":"Cell"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"7024","DOI":"10.1073\/pnas.84.20.7024","article-title":"Supercoiling of the DNA template during transcription","volume":"84","author":"Liu","year":"1987","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1016\/j.cell.2008.02.022","article-title":"Dynamic regulation of nucleosome positioning in the human genome","volume":"132","author":"Schones","year":"2008","journal-title":"Cell"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature11232","article-title":"The accessible chromatin landscape of the human genome","volume":"489","author":"Thurman","year":"2012","journal-title":"Nature"},{"key":"ref_45","first-page":"625210","article-title":"Histone Chaperones Spt6 and FACT: Similarities and Differences in Modes of Action at Transcribed Genes","volume":"2011","author":"Duina","year":"2011","journal-title":"Genet. Res. Int."},{"key":"ref_46","first-page":"116","article-title":"Transcription through chromatin by RNA polymerase II: Histone displacement and exchange","volume":"618","author":"Kulaeva","year":"2007","journal-title":"Mutat. Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.tig.2012.02.005","article-title":"Overcoming the nucleosome barrier during transcript elongation","volume":"28","author":"Petesch","year":"2012","journal-title":"Trends Genet."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.bbagrm.2012.08.015","article-title":"Mechanism of transcription through a nucleosome by RNA polymerase II","volume":"1829","author":"Kulaeva","year":"2013","journal-title":"Biochim. ET Biophys. Acta"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Kujirai, T., Ehara, H., Sekine, S.I., and Kurumizaka, H. (2023). Structural Transition of the Nucleosome during Transcription Elongation. Cells, 12.","DOI":"10.3390\/cells12101388"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"194659","DOI":"10.1016\/j.bbagrm.2020.194659","article-title":"Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation","volume":"1864","author":"Oh","year":"2021","journal-title":"Biochim. ET Biophys. Acta Gene Regul. Mech."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.molcel.2012.04.009","article-title":"R loops: From transcription byproducts to threats to genome stability","volume":"46","author":"Aguilera","year":"2012","journal-title":"Mol. Cell"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/S0021-9258(17)49903-0","article-title":"The balancing act of R-loop biology: The good, the bad, and the ugly","volume":"295","author":"Hegazy","year":"2020","journal-title":"J. Biol. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"7471","DOI":"10.1093\/nar\/gky660","article-title":"Mechanistic insights into the regulation of transcription and transcription-coupled DNA repair by Cockayne syndrome protein B","volume":"46","author":"Boetefuer","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Cho, I., Tsai, P.F., Lake, R.J., Basheer, A., and Fan, H.Y. (2013). ATP-dependent chromatin remodeling by Cockayne syndrome protein B and NAP1-like histone chaperones is required for efficient transcription-coupled DNA repair. PLoS Genet., 9.","DOI":"10.1371\/journal.pgen.1003407"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.cell.2016.02.036","article-title":"RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription","volume":"165","author":"Baranello","year":"2016","journal-title":"Cell"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1146\/annurev.biochem.70.1.369","article-title":"DNA topoisomerases: Structure, function, and mechanism","volume":"70","author":"Champoux","year":"2001","journal-title":"Annu. Rev. Biochem."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1126\/science.279.5356.1534","article-title":"A model for the mechanism of human topoisomerase I","volume":"279","author":"Stewart","year":"1998","journal-title":"Science"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/j.cell.2014.05.038","article-title":"Mechanism of transcriptional bursting in bacteria","volume":"158","author":"Chong","year":"2014","journal-title":"Cell"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1111\/j.1365-2958.2005.05006.x","article-title":"Growth inhibition mediated by excess negative supercoiling: The interplay between transcription elongation, R-loop formation and DNA topology","volume":"59","author":"Drolet","year":"2006","journal-title":"Mol. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"4684","DOI":"10.1074\/jbc.REV119.006364","article-title":"Emerging roles for R-loop structures in the management of topological stress","volume":"295","author":"Chedin","year":"2020","journal-title":"J. Biol. Chem."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"e2210480120","DOI":"10.1073\/pnas.2210480120","article-title":"Transcription shapes 3D chromatin organization by interacting with loop extrusion","volume":"120","author":"Banigan","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"102920","DOI":"10.1016\/j.sbi.2024.102920","article-title":"Transcriptional machinery as an architect of genome structure","volume":"89","author":"Fursova","year":"2024","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"eadd4920","DOI":"10.1126\/sciadv.add4920","article-title":"Untangling the roles of TOP2A and TOP2B in transcription and cancer","volume":"8","author":"Wilson","year":"2022","journal-title":"Sci. Adv."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/s41580-022-00452-3","article-title":"Human topoisomerases and their roles in genome stability and organization","volume":"23","author":"Pommier","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"7643","DOI":"10.1128\/MCB.20.20.7643-7653.2000","article-title":"ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor","volume":"20","author":"Citterio","year":"2000","journal-title":"Mol. Cell Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1016\/0092-8674(92)90390-X","article-title":"ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne\u2019s syndrome and preferential repair of active genes","volume":"71","author":"Troelstra","year":"1992","journal-title":"Cell"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/gim.2015.110","article-title":"The Cockayne Syndrome Natural History (CoSyNH) study: Clinical findings in 102 individuals and recommendations for care","volume":"18","author":"Wilson","year":"2016","journal-title":"Genet. Med."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/s41586-021-03906-4","article-title":"Structural basis of human transcription-DNA repair coupling","volume":"598","author":"Kokic","year":"2021","journal-title":"Nature"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"25486","DOI":"10.1073\/pnas.2013379117","article-title":"Cockayne syndrome B protein acts as an ATP-dependent processivity factor that helps RNA polymerase II overcome nucleosome barriers","volume":"117","author":"Xu","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"6374","DOI":"10.1038\/s41467-024-50584-7","article-title":"The small CRL4(CSA) ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics","volume":"15","author":"Lee","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/s41556-021-00692-z","article-title":"Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability","volume":"23","author":"Geijer","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"4740","DOI":"10.1016\/j.molcel.2024.10.030","article-title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","volume":"84","author":"Ramadhin","year":"2024","journal-title":"Mol. Cell"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"7107","DOI":"10.1016\/j.cell.2024.10.018","article-title":"STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair","volume":"187","author":"Park","year":"2024","journal-title":"Cell"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"12767","DOI":"10.1093\/nar\/gkae787","article-title":"STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading","volume":"52","author":"Tan","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"gkaf1303","DOI":"10.1093\/nar\/gkaf1303","article-title":"PARP1 and PARylation facilitate transcription-coupled DNA repair by stabilizing the CSB-RNAPII complex","volume":"53","author":"Robu","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1074\/jbc.M115.694992","article-title":"Poly(ADP-ribosyl)ation-dependent Transient Chromatin Decondensation and Histone Displacement following Laser Microirradiation","volume":"291","author":"Strickfaden","year":"2016","journal-title":"J. Biol. Chem."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.cell.2019.08.055","article-title":"R Loops: From Physiological to Pathological Roles","volume":"179","author":"Aguilera","year":"2019","journal-title":"Cell"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"6260","DOI":"10.1073\/pnas.1819476116","article-title":"Interplay between DNA sequence and negative superhelicity drives R-loop structures","volume":"116","author":"Stolz","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Brochu, J., Breton, E.V., and Drolet, M. (2020). Supercoiling, R-loops, Replication and the Functions of Bacterial Type 1A Topoisomerases. Genes, 11.","DOI":"10.3390\/genes11030249"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"105307","DOI":"10.1016\/j.jbc.2023.105307","article-title":"Helicases in R-loop Formation and Resolution","volume":"299","author":"Yang","year":"2023","journal-title":"J. Biol. Chem."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1101\/gad.573310","article-title":"Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis","volume":"24","author":"French","year":"2010","journal-title":"Genes Dev."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"6031","DOI":"10.1038\/s41467-024-50298-w","article-title":"Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation","volume":"15","author":"Zhang","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.cell.2017.07.043","article-title":"Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses","volume":"170","author":"Hamperl","year":"2017","journal-title":"Cell"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.neuron.2014.06.034","article-title":"DNA damage and its links to neurodegeneration","volume":"83","author":"Madabhushi","year":"2014","journal-title":"Neuron"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"8511","DOI":"10.1038\/s41467-024-52860-y","article-title":"Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair","volume":"15","author":"Yu","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"7091","DOI":"10.1016\/j.cell.2024.10.020","article-title":"STK19 positions TFIIH for cell-free transcription-coupled DNA repair","volume":"187","author":"Mevissen","year":"2024","journal-title":"Cell"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1002\/em.22568","article-title":"The role of Transcription Factor IIH complex in nucleotide excision repair","volume":"65","author":"Hoag","year":"2024","journal-title":"Environ. Mol. Mutagen."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2004","DOI":"10.1093\/emboj\/20.8.2004","article-title":"ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes","volume":"20","author":"Ura","year":"2001","journal-title":"EMBO J."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"3372","DOI":"10.15252\/embj.201695742","article-title":"Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair","volume":"36","author":"Ruthemann","year":"2017","journal-title":"EMBO J."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1101\/gad.307702.117","article-title":"Chromatin and nucleosome dynamics in DNA damage and repair","volume":"31","author":"Hauer","year":"2017","journal-title":"Genes Dev."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1146\/annurev-biochem-052621-091205","article-title":"Transcription-Coupled Nucleotide Excision Repair and the Transcriptional Response to UV-Induced DNA Damage","volume":"92","author":"Olthof","year":"2023","journal-title":"Annu. Rev. Biochem."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/16\/7244\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T09:04:51Z","timestamp":1786698291000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/16\/7244"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,14]]},"references-count":91,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ijms27167244"],"URL":"https:\/\/doi.org\/10.3390\/ijms27167244","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,14]]}}}