High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution

High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution Raluca Gordan, Hana Wasserman, Bo Chi, Kaitlynne Bohm, Mingrui Duan, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8197218/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Genomic studies have revealed elevated damage and mutation rates in active transcription factor (TF) binding sites in UV-linked cancers. Previous investigations into the relationship between TF activity and UV DNA damage have primarily focused on select TFs or been done in aggregate across large cohorts of TFs at kilobase resolution. While collectively, there is evidence that TFs contribute to UV-induced mutagenesis by both enhancing initial damage formation and attenuating repair, there has yet to be a comprehensive characterization of these mechanisms on a per-TF basis. Using genome-wide maps of UV damage from human skin fibroblasts, we developed a scalable statistical framework to analyze TF-mediated mutagenic mechanisms across hundreds of TFs. We identify numerous previously unreported TFs that significantly enhance and / or inhibit damage formation in their binding sites. A systematic survey of TF-DNA complexes further revealed that positions of UV damage modulation coincide with TF-induced structural distortions that either protect or predispose DNA to photodimer formation. Additionally, we analyzed repair efficiency in TF binding sites with unprecedented resolution, identifying specific TFs and binding site positions likely to compete with repair factors. By comparing these results with skin cancer mutations, we distinguish mutation peaks driven by increased damage susceptibility versus attenuated repair, illustrating that TF-mediated mutagenesis is highly contextual and dependent on the TF, binding site position, and sequence context of the damaged locus. Our approach provides a robust statistical framework for elucidating mechanisms of mutagenic TF-binding and offers novel insights into the complex interplay between protein interactions, DNA damage, and repair. Biological sciences/Molecular biology/DNA damage and repair/DNA adducts Biological sciences/Molecular biology/Transcription/Transcriptional regulatory elements Biological sciences/Computational biology and bioinformatics/Computational models Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryTable1.xlsx Supplementary Dataset 1 SupplementaryTable6.xlsx Supplementary Dataset 6 SupplementaryTable2.xlsx Supplementary Dataset 2 SupplementaryTable5.xlsx Supplementary Dataset 5 SupplementaryTable4.xlsx Supplementary Dataset 4 SUPPLEMENTTFUVDamageManuscriptWasserman.pdf Supplementary Information nrreportingsummaryWasserman.pdf Reporting Summary SupplementaryTable3.xlsx Supplementary Dataset 3 ReportingsummaryNCOMMS2594127flatten.pdf Reporting Summary Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8197218","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":557643612,"identity":"af65bea2-b054-48cf-8be8-079b012bde34","order_by":0,"name":"Raluca 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Previous investigations into the relationship between TF activity and UV DNA damage have primarily focused on select TFs or been done in aggregate across large cohorts of TFs at kilobase resolution. While collectively, there is evidence that TFs contribute to UV-induced mutagenesis by both enhancing initial damage formation and attenuating repair, there has yet to be a comprehensive characterization of these mechanisms on a per-TF basis. Using genome-wide maps of UV damage from human skin fibroblasts, we developed a scalable statistical framework to analyze TF-mediated mutagenic mechanisms across hundreds of TFs. We identify numerous previously unreported\r\nTFs that significantly enhance and / or inhibit damage formation in their binding sites. A systematic survey of TF-DNA complexes further revealed that positions of UV damage modulation coincide with TF-induced structural distortions that either protect or predispose DNA to photodimer formation. Additionally, we analyzed repair efficiency in TF binding sites with unprecedented resolution, identifying specific TFs and binding site positions likely to compete with repair factors. By comparing these results with skin cancer mutations, we distinguish mutation peaks driven by increased damage susceptibility versus attenuated repair, illustrating that TF-mediated mutagenesis is highly contextual and dependent on the TF, binding site position, and sequence context of the damaged locus. Our approach provides a robust statistical framework for elucidating mechanisms of mutagenic TF-binding and offers novel insights into the complex interplay between protein interactions, DNA damage, and repair.","manuscriptTitle":"High-throughput characterization of transcription factors that modulate UV\ndamage formation and repair at single-nucleotide resolution","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-10 03:50:49","doi":"10.21203/rs.3.rs-8197218/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"2dcef414-bffc-4d46-b5af-98287d47e2d4","owner":[],"postedDate":"December 10th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":59351684,"name":"Biological sciences/Molecular biology/DNA damage and repair/DNA adducts"},{"id":59351685,"name":"Biological sciences/Molecular biology/Transcription/Transcriptional regulatory elements"},{"id":59351686,"name":"Biological sciences/Computational biology and bioinformatics/Computational models"}],"tags":[],"updatedAt":"2026-04-26T16:45:36+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-10 03:50:49","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8197218","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8197218","identity":"rs-8197218","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}