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• W3136273607 abstract "The formation of UV-induced DNA damage and its repair are influenced by many factors that modulate lesion formation and the accessibility of repair machinery. However, it remains unknown which genomic sites are prioritized for immediate repair after UV damage induction, and whether these prioritized sites overlap with hotspots of UV damage. We identified the super hotspots subject to the earliest repair for (6-4) pyrimidine–pyrimidone photoproduct by using the eXcision Repair-sequencing (XR-seq) method. We further identified super coldspots for (6-4) pyrimidine–pyrimidone photoproduct repair and super hotspots for cyclobutane pyrimidine dimer repair by analyzing available XR-seq time-course data. By integrating datasets of XR-seq, Damage-seq, adductSeq, and cyclobutane pyrimidine dimer-seq, we show that neither repair super hotspots nor repair super coldspots overlap hotspots of UV damage. Furthermore, we demonstrate that repair super hotspots are significantly enriched in frequently interacting regions and superenhancers. Finally, we report our discovery of an enrichment of cytosine in repair super hotspots and super coldspots. These findings suggest that local DNA features together with large-scale chromatin features contribute to the orders of magnitude variability in the rates of UV damage repair. The formation of UV-induced DNA damage and its repair are influenced by many factors that modulate lesion formation and the accessibility of repair machinery. However, it remains unknown which genomic sites are prioritized for immediate repair after UV damage induction, and whether these prioritized sites overlap with hotspots of UV damage. We identified the super hotspots subject to the earliest repair for (6-4) pyrimidine–pyrimidone photoproduct by using the eXcision Repair-sequencing (XR-seq) method. We further identified super coldspots for (6-4) pyrimidine–pyrimidone photoproduct repair and super hotspots for cyclobutane pyrimidine dimer repair by analyzing available XR-seq time-course data. By integrating datasets of XR-seq, Damage-seq, adductSeq, and cyclobutane pyrimidine dimer-seq, we show that neither repair super hotspots nor repair super coldspots overlap hotspots of UV damage. Furthermore, we demonstrate that repair super hotspots are significantly enriched in frequently interacting regions and superenhancers. Finally, we report our discovery of an enrichment of cytosine in repair super hotspots and super coldspots. These findings suggest that local DNA features together with large-scale chromatin features contribute to the orders of magnitude variability in the rates of UV damage repair. Nucleotide excision repair is a versatile repair pathway that removes a variety of bulky and helix-distorting lesions caused by DNA-damaging agents, such as UV, cisplatin, and benzo(a)pyrene (1Wood R.D. Nucleotide excision repair in mammalian cells.J. Biol. Chem. 1997; 272: 23465-23468Abstract Full Text Full Text PDF PubMed Scopus (375) Google Scholar, 2Sancar A. Mechanisms of DNA repair by photolyase and excision nuclease (nobel lecture).Angew. Chem. Int. Ed. Engl. 2016; 55: 8502-8527Crossref PubMed Scopus (135) Google Scholar). It has two subpathways: global repair, which repairs DNA lesions throughout the whole genome, and transcription-coupled repair (TCR), which preferentially removes DNA lesions from the transcribed strand (TS) of transcriptionally active genes (3Mellon I. Spivak G. Hanawalt P.C. Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene.Cell. 1987; 51: 241-249Abstract Full Text PDF PubMed Scopus (1031) Google Scholar, 4Hanawalt P.C. Spivak G. Transcription-coupled DNA repair: Two decades of progress and surprises.Nat. Rev. 2008; 9: 958-970Crossref Scopus (755) Google Scholar). The two subpathways differ only in the damage recognition step and share the steps of dual incision bracketing the lesions, release of the excision products, repair synthesis, and ligation (5Reardon J.T. Sancar A. Nucleotide excision repair.Prog. Nucleic Acid Res. Mol. Biol. 2005; 79: 183-235Crossref PubMed Scopus (235) Google Scholar, 6Hu J. Selby C.P. Adar S. Adebali O. Sancar A. Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans.J. Biol. Chem. 2017; 292: 15588-15597Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar). UV-induced DNA damage, if not removed efficiently, will lead to mutations and possibly carcinogenesis in humans. UV in sunlight is a known mutagen and causative agent of skin cancer (7Hodis E. Watson I.R. Kryukov G.V. Arold S.T. Imielinski M. Theurillat J.P. Nickerson E. Auclair D. Li L. Place C. Dicara D. Ramos A.H. Lawrence M.S. Cibulskis K. Sivachenko A. et al.A landscape of driver mutations in melanoma.Cell. 2012; 150: 251-263Abstract Full Text Full Text PDF PubMed Scopus (1782) Google Scholar, 8Martincorena I. Roshan A. Gerstung M. Ellis P. Van Loo P. McLaren S. Wedge D.C. Fullam A. Alexandrov L.B. Tubio J.M. Stebbings L. Menzies A. Widaa S. Stratton M.R. Jones P.H. et al.Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.Science. 2015; 348: 880-886Crossref PubMed Scopus (932) Google Scholar), inducing DNA lesions, such as cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine–pyrimidone photoproducts [(6-4)PPs]. To better understand the molecular mechanisms of UV-induced mutagenesis and carcinogenesis, it is critical to identify the exact locations of DNA lesions and their repair efficiencies with single-nucleotide resolution on a genome-wide scale. With the advent of next-generation sequencing (NGS) technology, a number of NGS-based methods have been devised over the last 5 years to detect UV-induced DNA damage formation and repair across the whole genome (9Li W. Sancar A. Methodologies for detecting environmentally induced DNA damage and repair.Environ. Mol. Mutagen. 2020; https://doi.org/10.1002/em.22365Crossref Scopus (18) Google Scholar), including Excision-seq (10Bryan D.S. Ransom M. Adane B. York K. Hesselberth J.R. High resolution mapping of modified DNA nucleobases using excision repair enzymes.Genome Res. 2014; 24: 1534-1542Crossref PubMed Scopus (63) Google Scholar), eXcision Repair-sequencing (XR-seq) (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar), CPD-seq (12Mao P. Smerdon M.J. Roberts S.A. Wyrick J.J. Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: 9057-9062Crossref PubMed Scopus (82) Google Scholar), translesion XR-seq (13Li W. Hu J. Adebali O. Adar S. Yang Y. Chiou Y.Y. Sancar A. Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6752-6757Crossref PubMed Scopus (52) Google Scholar), high-sensitivity Damage-seq (14Hu J. Adebali O. Adar S. Sancar A. Dynamic maps of UV damage formation and repair for the human genome.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6758-6763Crossref PubMed Scopus (83) Google Scholar), and adductSeq (15Premi S. Han L. Mehta S. Knight J. Zhao D. Palmatier M.A. Kornacker K. Brash D.E. Genomic sites hypersensitive to ultraviolet radiation.Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 24196-24205Crossref PubMed Scopus (28) Google Scholar). Specifically, Damage-seq uses damage-specific immunoprecipitation and a high-fidelity DNA polymerase (which stops before the DNA damage during primer extension) to determine the exact positions of DNA damage (16Hu J. Lieb J.D. Sancar A. Adar S. Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: 11507-11512Crossref PubMed Scopus (97) Google Scholar); XR-seq directly measures the ongoing repair at a specific time point by isolating the excision products released during the repair for NGS (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar, 17Hu J. Li W. Adebali O. Yang Y. Oztas O. Selby C.P. Sancar A. Genome-wide mapping of nucleotide excision repair with XR-seq.Nat. Protoc. 2019; 14: 248-282Crossref PubMed Scopus (25) Google Scholar), and it has been successfully applied to generate genome-wide repair maps of UV damage with single-nucleotide resolution in humans (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar), Escherichia coli (18Adebali O. Chiou Y.Y. Hu J. Sancar A. Selby C.P. Genome-wide transcription-coupled repair in Escherichia coli is mediated by the Mfd translocase.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: E2116-E2125Crossref PubMed Scopus (50) Google Scholar), Saccharomyces cerevisiae (19Li W. Adebali O. Yang Y. Selby C.P. Sancar A. Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome.Proc. Natl. Acad. Sci. U. S. A. 2018; 115: E3408-E3415Crossref PubMed Scopus (21) Google Scholar), Arabidopsis thaliana (20Oztas O. Selby C.P. Sancar A. Adebali O. Genome-wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns.Nat. Commun. 2018; 9: 1503Crossref PubMed Scopus (23) Google Scholar), mice (21Yang Y. Hu J. Selby C.P. Li W. Yimit A. Jiang Y. Sancar A. Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice.J. Biol. Chem. 2019; 294: 210-217Abstract Full Text Full Text PDF PubMed Scopus (11) Google Scholar), Drosophila melanogaster (22Deger N. Yang Y. Lindsey-Boltz L.A. Sancar A. Selby C.P. Drosophila, which lacks canonical transcription-coupled repair proteins, performs transcription-coupled repair.J. Biol. Chem. 2019; 294: 18092-18098Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar), Mycobacteria (23Selby C.P. Lindsey-Boltz L.A. Yang Y. Sancar A. Mycobacteria excise DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair.J. Biol. Chem. 2020; 295: 17374-17380Abstract Full Text Full Text PDF PubMed Scopus (4) Google Scholar), and Microcebus murinus (24Akkose U. Kaya V.O. Lindsey-Boltz L. Karagoz Z. Brown A.D. Larsen P.A. Yoder A.D. Sancar A. Adebali O. Comparative analyses of two primate species diverged by more than 60 million years show different rates but similar distribution of genome-wide UV repair events.bioRxiv. 2020; https://doi.org/10.1101/2020.04.06.027201Crossref Scopus (0) Google Scholar). Formation and repair of UV damage are influenced by multiple factors, including transcription (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar), transcription factor binding (14Hu J. Adebali O. Adar S. Sancar A. Dynamic maps of UV damage formation and repair for the human genome.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6758-6763Crossref PubMed Scopus (83) Google Scholar, 25Mao P. Brown A.J. Esaki S. Lockwood S. Poon G.M.K. Smerdon M.J. Roberts S.A. Wyrick J.J. ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma.Nat. Commun. 2018; 9: 2626Crossref PubMed Scopus (59) Google Scholar, 26Poulos R.C. Thoms J.A.I. Guan Y.F. Unnikrishnan A. Pimanda J.E. Wong J.W.H. Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the motif.Cell Rep. 2016; 17: 2865-2872Abstract Full Text Full Text PDF PubMed Scopus (34) Google Scholar, 27Sabarinathan R. Mularoni L. Deu-Pons J. Gonzalez-Perez A. Lopez-Bigas N. Nucleotide excision repair is impaired by binding of transcription factors to DNA.Nature. 2016; 532: 264-267Crossref PubMed Scopus (165) Google Scholar, 28Frigola J. Sabarinathan R. Gonzalez-Perez A. Lopez-Bigas N. Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites.Nucleic Acids Res. 2020; 49: 891-901Crossref Scopus (8) Google Scholar), post-transcriptional modification of histones (29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar), nucleosome positioning (12Mao P. Smerdon M.J. Roberts S.A. Wyrick J.J. Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: 9057-9062Crossref PubMed Scopus (82) Google Scholar), chromatin structure (29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar, 30Mao P. Wyrick J.J. Roberts S.A. Smerdon M.J. UV-induced DNA damage and mutagenesis in chromatin.Photochem. Photobiol. 2017; 93: 216-228Crossref PubMed Scopus (47) Google Scholar), and 3D genome architecture (31Garcia-Nieto P.E. Schwartz E.K. King D.A. Paulsen J. Collas P. Herrera R.E. Morrison A.J. Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis.EMBO J. 2017; 36: 2829-2843Crossref PubMed Scopus (44) Google Scholar). From the perspective of 3D genome organization, UV susceptibility generally is inversely correlated with chromatin accessibility (31Garcia-Nieto P.E. Schwartz E.K. King D.A. Paulsen J. Collas P. Herrera R.E. Morrison A.J. Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis.EMBO J. 2017; 36: 2829-2843Crossref PubMed Scopus (44) Google Scholar). At the nucleosome level, however, CPDs favor the outward-facing rotation setting in a nucleosome, and (6-4)PPs tend to form in nucleosome linker regions (12Mao P. Smerdon M.J. Roberts S.A. Wyrick J.J. Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: 9057-9062Crossref PubMed Scopus (82) Google Scholar, 30Mao P. Wyrick J.J. Roberts S.A. Smerdon M.J. UV-induced DNA damage and mutagenesis in chromatin.Photochem. Photobiol. 2017; 93: 216-228Crossref PubMed Scopus (47) Google Scholar). This is because the outward-facing rotation setting in a nucleosome has conformational flexibility to accommodate a CPD, and such flexibility does not alter the DNA structure dramatically. In contrast, (6-4)PP formation requires greater DNA structure distortion; the nucleosome structure has no conformational flexibility for a (6-4)PP, except in linker regions. Depending on the nature of the individual transcription factor and the DNA-damaging agent, binding of a transcription factor to DNA may stimulate, inhibit, or have no effect on DNA damage formation (14Hu J. Adebali O. Adar S. Sancar A. Dynamic maps of UV damage formation and repair for the human genome.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6758-6763Crossref PubMed Scopus (83) Google Scholar, 25Mao P. Brown A.J. Esaki S. Lockwood S. Poon G.M.K. Smerdon M.J. Roberts S.A. Wyrick J.J. ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma.Nat. Commun. 2018; 9: 2626Crossref PubMed Scopus (59) Google Scholar). For repair of UV damage, the accessibility of repair machinery plays an important role. Repair occurs earlier in open chromatin regions than in repressed regions (29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar), and late repair regions, such as heterochromatic regions and some transcription factor binding sites, are associated with higher mutation rates (27Sabarinathan R. Mularoni L. Deu-Pons J. Gonzalez-Perez A. Lopez-Bigas N. Nucleotide excision repair is impaired by binding of transcription factors to DNA.Nature. 2016; 532: 264-267Crossref PubMed Scopus (165) Google Scholar, 29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar, 32Roberts S.A. Brown A.J. Wyrick J.J. Recurrent noncoding mutations in skin cancers: UV damage susceptibility or repair inhibition as primary driver?.Bioessays. 2019; 41e1800152Crossref PubMed Scopus (5) Google Scholar, 33Perera D. Poulos R.C. Shah A. Beck D. Pimanda J.E. Wong J.W. Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes.Nature. 2016; 532: 259-263Crossref PubMed Scopus (118) Google Scholar). We compared UV damage maps with repair maps and found that UV-induced DNA damage, measured with low depth of coverage, is uniformly distributed at a large-scale level and that the overall repair in the human genome is heterogeneous (14Hu J. Adebali O. Adar S. Sancar A. Dynamic maps of UV damage formation and repair for the human genome.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6758-6763Crossref PubMed Scopus (83) Google Scholar, 29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar). A recent study reported CPD hyper hotspots located near genes in human melanocytes and fibroblasts and suggested that these hyper hotspots may drive direct physiological changes rather than cause rare mutations (15Premi S. Han L. Mehta S. Knight J. Zhao D. Palmatier M.A. Kornacker K. Brash D.E. Genomic sites hypersensitive to ultraviolet radiation.Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 24196-24205Crossref PubMed Scopus (28) Google Scholar). Despite recent progress in DNA damage formation and repair research, it is still unknown which genomic sites are prioritized for repair immediately after UV irradiation and whether those prioritized sites overlap hotspots of DNA damage. Furthermore, determining which genomic sites are subject to nucleotide excision repair at very late stages of damage removal will offer additional insight into the question. In this study, we sought to identify these genomic sites. We performed (6-4)PP XR-seq at 1 min and 2 min after UV treatment and integrated previously published data, which include (6-4)PP XR-seq ranging from 5 min to 4 h (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar, 29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar) and CPD XR-seq as early as 12 min (22Deger N. Yang Y. Lindsey-Boltz L.A. Sancar A. Selby C.P. Drosophila, which lacks canonical transcription-coupled repair proteins, performs transcription-coupled repair.J. Biol. Chem. 2019; 294: 18092-18098Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar) following UV irradiation. Using these methods, we identified repair super hotspots and super coldspots for (6-4)PPs and repair super hotspots for CPDs. By comparing these repair super hotspots and super coldspots with other high-throughput sequencing datasets that measure UV damage formation, we showed that neither repair super hotspots nor super coldspots overlap hotspots of UV damage. Moreover, we demonstrated that repair super hotspots are significantly enriched in both frequently interacting regions (FIREs) and superenhancers. We also found an enrichment of cytosine in both repair super hotspots and super coldspots. Our findings suggest that both local chromatin structures (e.g., transcription factor binding and previously assembled repair machinery members in the proximity of super hotspots) and large-scale chromatin features make it feasible for DNA damage to be rapidly removed in repair super hotspots. This effective integrity maintenance at repair super hotspots may confer a selective advantage. To identify which genomic sites are prioritized for nucleotide excision repair immediately after UV irradiation and which sites are subject to repair only at the latest stage of DNA damage removal, we designed an experimental and analytical framework to systematically investigate excision repair kinetics and UV damage formation over a time course. Removal of (6-4)PP occurs mainly through global repair and is completed within 4 h after UV irradiation (29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar, 34Hu J. Choi J.H. Gaddameedhi S. Kemp M.G. Reardon J.T. Sancar A. Nucleotide excision repair in human cells: Fate of the excised oligonucleotide carrying DNA damage in vivo.J. Biol. Chem. 2013; 288: 20918-20926Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar, 35Li W. Liu W. Kakoki A. Wang R. Adebali O. Jiang Y. Sancar A. Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells.J. Biol. Chem. 2019; 294: 5914-5922Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar). However, the removal of CPD requires both global repair and TCR, and the entire process takes days to complete (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar, 29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar, 35Li W. Liu W. Kakoki A. Wang R. Adebali O. Jiang Y. Sancar A. Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells.J. Biol. Chem. 2019; 294: 5914-5922Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar). We have shown that global repair dominates CPD removal in the first 12 min after UV irradiation in normal human skin fibroblast 1 (NHF1) cells, and then at later time points, TCR also facilitates CPD removal (22Deger N. Yang Y. Lindsey-Boltz L.A. Sancar A. Selby C.P. Drosophila, which lacks canonical transcription-coupled repair proteins, performs transcription-coupled repair.J. Biol. Chem. 2019; 294: 18092-18098Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar). To avoid the confounding effects of transcription levels and TCR, we chose to focus on global repair of CPD and thus identified prioritized genomic sites for CPD repair in the first 12 min after UV irradiation. Figure 1A shows an outline of the experimental design we used to measure excision repair kinetics and UV damage formation. Specifically, we performed (6-4)PP XR-seq at 1 and 2 min after 20 J/m2 UV treatment in NHF1 and adopted previous NHF1 XR-seq data for (6-4)PP repair at 5 min, 20 min, 1 h, 2 h, and 4 h (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar, 29Adar S. Hu J. Lieb J.D. Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2124-2133Crossref PubMed Scopus (103) Google Scholar) and CPD repair at 12 min (22Deger N. Yang Y. Lindsey-Boltz L.A. Sancar A. Selby C.P. Drosophila, which lacks canonical transcription-coupled repair proteins, performs transcription-coupled repair.J. Biol. Chem. 2019; 294: 18092-18098Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar). Refer to Table S1 for detailed XR-seq sample information. Damage-seq for both (6-4)PPs and CPDs at 0 min in NHF1 cells (14Hu J. Adebali O. Adar S. Sancar A. Dynamic maps of UV damage formation and repair for the human genome.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6758-6763Crossref PubMed Scopus (83) Google Scholar) was also included to determine the distribution of initial UV damage formation. Because release and degradation of excision products occur simultaneously and XR-seq does not measure the absolute number of excision products over time intervals (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar, 34Hu J. Choi J.H. Gaddameedhi S. Kemp M.G. Reardon J.T. Sancar A. Nucleotide excision repair in human cells: Fate of the excised oligonucleotide carrying DNA damage in vivo.J. Biol. Chem. 2013; 288: 20918-20926Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar), it is necessary to perform XR-seq as early as possible to identify genomic sites that are subject to excision repair immediately after UV treatment. To determine the earliest time point and the optimal number of cells suitable for (6-4)PP XR-seq, we first performed in vivo excision assay at 0 and 2 min in NHF1 cells (Fig. 1B). As shown in Figure 1B, the primary excision products, ranging from 23 to 30 nt, can be seen at 2 min, but there are no degradation products at this time point and no signal at 0 min after UV treatment. Based on this excision assay, we performed the (6-4)PP XR-seq at 1 and 2 min to identify genomic sites subject to immediate repair after UV treatment. Analyses of the two biological replicates for (6-4)PP XR-seq show high reproducibility (Fig. S1). As expected, length distribution and nucleotide frequency for reads from (6-4)PP XR-seq (1 and 2 min) and CPD XR-seq (12 min) are in agreement with previously reported data (Fig. S2) (11Hu J. Adar S. Selby C.P. Lieb J.D. Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.Genes Dev. 2015; 29: 948-960Crossref PubMed Scopus (146) Google Scholar). Moreover, the TS/(TS + nontranscribed strand [NTS]) repair ratios in (6-4)PP XR-seq (1 min and 4 h) are on par with that in CPD XR-seq (12 min), indicating that the vast majority of DNA damage is removed by global repair by these time benchmarks (Fig. S3) (14Hu J. Adebali O. Adar S. Sancar A. Dynamic maps of UV damage formation and repair for the human genome.Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 6758-6763Crossref PubMed Scopus (83) Google Scholar, 22Deger N. Yang Y. Lindsey-Boltz L.A. Sancar A. Selby C.P. Drosophila, which lacks canonical transcription-coupled repair proteins, performs transcription-coupled repair.J. Biol. Chem. 2019; 294: 18092-18098Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar). Using genome-wide repair data from XR-seq, we performed principal component (PC) analysis (36Jolliffe I.T. Cadima J. Principal component analysis: A review and recent developments.Philos. Trans. A Math. Phys. Eng. Sci. 2016; 374: 20150202Crossref PubMed Scopus (2493) Google Scholar) on the top 2000 highly variable genes to generate a low-dimensional representation of the data (Fig. 1C). PC analysis is a dimension reduction technique that extracts underlying structure of the data. It finds a sequence of linear combinations of the features/genes, as PCs, which have maximal variance. The first and second PCs (shown as PC1 and PC2 in Fig. 1C) are uncorrelated so that they can be uniquely estimated. Since TCR does not significantly contribute to the repair of the majority of (6-4)PPs in NHF1 cells, the first and second PCs do not differ between the TS and NTS repair. Importantly, a reconstructed repair trajectory lines up well with the time points, suggesting that repair pattern differs over the time course (Fig. 1C). We developed a computational framework to identify the early repair and late repair genomic sites by using time-course XR-seq data. Briefly, we first segmented the genome into consecutive bins of 50 bp long, then identified bins containing a significantly higher number of reads at early and late time points using a thresholding approach on the downsampled reads (Fig. S4). Figure 1D shows the distributions of read counts per genomic bin across all samples; we note enrichment of both early repair at 1 min and late repair at 4 h. In total, we identified 331 early repair genomic sites for (6-4)PP repair and 192 early repair genomic sites for CPD repair; we identified 105 late repair genomic sites for (6-4)PP repair (Tables S2–S4). These identified genomic sites are clusters of excision products, and we define the earliest-repair sites as repair super hotspots and the latest-repair sites as super coldspots. While this method was effective in identifying the top few hundred repair hotspots and coldspots, we also normalized and tested repair enrichment with a more rigorous Poisson log linear model (37Witten D.M. Classification and clustering of sequencing data using a Poisson model.Ann. Appl. Stat. 2011;" @default.
• W3136273607 created "2021-03-29" @default.
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• W3136273607 date "2021-01-01" @default.
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• W3136273607 title "Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome" @default.
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• W3136273607 cites W1970279120 @default.
• W3136273607 cites W1973062929 @default.
• W3136273607 cites W2018363492 @default.
• W3136273607 cites W2022545349 @default.
• W3136273607 cites W2036897871 @default.
• W3136273607 cites W2038531677 @default.
• W3136273607 cites W2046082575 @default.
• W3136273607 cites W2059901912 @default.
• W3136273607 cites W2065006553 @default.
• W3136273607 cites W2070021921 @default.
• W3136273607 cites W2076154138 @default.
• W3136273607 cites W2078753112 @default.
• W3136273607 cites W2090037139 @default.
• W3136273607 cites W2093267013 @default.
• W3136273607 cites W2098279314 @default.
• W3136273607 cites W2103441770 @default.
• W3136273607 cites W2108234281 @default.
• W3136273607 cites W2115655831 @default.
• W3136273607 cites W2116298638 @default.
• W3136273607 cites W2128388251 @default.
• W3136273607 cites W2133676450 @default.
• W3136273607 cites W2134471382 @default.
• W3136273607 cites W2136229065 @default.
• W3136273607 cites W2142270559 @default.
• W3136273607 cites W2142644202 @default.
• W3136273607 cites W2153087859 @default.
• W3136273607 cites W2157009395 @default.
• W3136273607 cites W2169964199 @default.
• W3136273607 cites W2179302559 @default.
• W3136273607 cites W2259938310 @default.
• W3136273607 cites W2261190630 @default.
• W3136273607 cites W2313953393 @default.
• W3136273607 cites W2339240569 @default.
• W3136273607 cites W2341025815 @default.
• W3136273607 cites W2416744721 @default.
• W3136273607 cites W2465729593 @default.
• W3136273607 cites W2505939414 @default.
• W3136273607 cites W2526788217 @default.
• W3136273607 cites W2527599664 @default.
• W3136273607 cites W2557097554 @default.
• W3136273607 cites W2563038222 @default.
• W3136273607 cites W2587545536 @default.
• W3136273607 cites W2620040559 @default.
• W3136273607 cites W2625172670 @default.
• W3136273607 cites W2625176645 @default.
• W3136273607 cites W2744259285 @default.
• W3136273607 cites W2747348737 @default.
• W3136273607 cites W2778217919 @default.
• W3136273607 cites W2784832113 @default.
• W3136273607 cites W2793725693 @default.
• W3136273607 cites W2802201353 @default.
• W3136273607 cites W2809093940 @default.
• W3136273607 cites W2810981777 @default.
• W3136273607 cites W2899863167 @default.
• W3136273607 cites W2904628210 @default.
• W3136273607 cites W2909202541 @default.
• W3136273607 cites W2917027509 @default.
• W3136273607 cites W2917258609 @default.
• W3136273607 cites W2922308786 @default.
• W3136273607 cites W2924903871 @default.
• W3136273607 cites W2949384760 @default.
• W3136273607 cites W2951694241 @default.
• W3136273607 cites W2952664869 @default.
• W3136273607 cites W2980663740 @default.
• W3136273607 cites W2983095819 @default.
• W3136273607 cites W3002964216 @default.
• W3136273607 cites W3008922053 @default.
• W3136273607 cites W3093648603 @default.
• W3136273607 cites W3103302162 @default.
• W3136273607 cites W3106938813 @default.
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• W3136273607 doi "https://doi.org/10.1016/j.jbc.2021.100581" @default.
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