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Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C\u2013containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C\u2013&amp;gt;T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.<\/jats:p>","DOI":"10.1093\/nar\/gkae517","type":"journal-article","created":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T11:04:15Z","timestamp":1718622255000},"page":"8254-8270","source":"Crossref","is-referenced-by-count":3,"title":["ASH1L guards <i>cis<\/i>-regulatory elements against cyclobutane pyrimidine dimer induction"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9895-5301","authenticated-orcid":false,"given":"Michelle\u00a0N","family":"Yancoskie","sequence":"first","affiliation":[{"name":"Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , Zurich 8057,\u00a0 Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reihaneh","family":"Khaleghi","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , Zurich 8057,\u00a0 Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anirvinya","family":"Gururajan","sequence":"additional","affiliation":[{"name":"Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032,\u00a0 India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aadarsh","family":"Raghunathan","sequence":"additional","affiliation":[{"name":"Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032,\u00a0 India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aryan","family":"Gupta","sequence":"additional","affiliation":[{"name":"Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032,\u00a0 India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Diethelm","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , Zurich 8057,\u00a0 Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corina","family":"Maritz","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , Zurich 8057,\u00a0 Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6808-5950","authenticated-orcid":false,"given":"Shana\u00a0J","family":"Sturla","sequence":"additional","affiliation":[{"name":"Department of Health Sciences and Technology, ETH Zurich , Zurich 8092,\u00a0 Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2549-919X","authenticated-orcid":false,"given":"Marimuthu","family":"Krishnan","sequence":"additional","affiliation":[{"name":"Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032,\u00a0 India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanspeter","family":"Naegeli","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , Zurich 8057,\u00a0 Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,6,17]]},"reference":[{"key":"2024081123573727900_B1","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/nar\/20.2.225","article-title":"Sequence specificity of cyclobutane pyrimidine dimers in DNA treated with solar (ultraviolet B) radiation","volume":"20","author":"Mitchell","year":"1992","journal-title":"Nucleic Acids Res."},{"key":"2024081123573727900_B2","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/s42764-020-00009-8","article-title":"Mechanisms of UV-induced mutations and skin cancer","volume":"1","author":"Pfeifer","year":"2020","journal-title":"Genome Instab. 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B"},{"key":"2024081123573727900_B69","doi-asserted-by":"crossref","first-page":"3590","DOI":"10.1529\/biophysj.107.118612","article-title":"Predicting thymine dimerization yields from molecular dynamics simulations","volume":"94","author":"Law","year":"2008","journal-title":"Biophys. 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Rep."},{"key":"2024081123573727900_B90","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1111\/j.1751-1097.2007.00226.x","article-title":"The protective role of melanin against UV damage in human skin","volume":"84","author":"Brenner","year":"2008","journal-title":"Photochem. Photobiol."},{"key":"2024081123573727900_B91","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1111\/php.12433","article-title":"Human hair as a natural sun protection agent: a quantitative study","volume":"91","author":"de\u00a0G\u00e1lvez","year":"2015","journal-title":"Photochem. Photobiol."},{"key":"2024081123573727900_B92","doi-asserted-by":"crossref","first-page":"9057","DOI":"10.1073\/pnas.1606667113","article-title":"Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution","volume":"113","author":"Mao","year":"2016","journal-title":"Proc. Natl. Acad. Sci. 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Chem."},{"key":"2024081123573727900_B96","doi-asserted-by":"crossref","first-page":"6644","DOI":"10.1073\/pnas.84.19.6644","article-title":"UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases","volume":"84","author":"Gale","year":"1987","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2024081123573727900_B97","doi-asserted-by":"crossref","first-page":"e1007823","DOI":"10.1371\/journal.pgen.1007823","article-title":"Nucleosome positions establish an extended mutation signature in melanoma","volume":"14","author":"Brown","year":"2018","journal-title":"PLoS Genet."},{"key":"2024081123573727900_B98","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1006\/jmbi.1995.0331","article-title":"UV light as a footprinting agent: modulation of UV-induced DNA damage by transcription factors bound at the promoters of three human genes","volume":"249","author":"Tornaletti","year":"1995","journal-title":"J. Mol. 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