SFPQ Directs Histone H3.3 Deposition to R-Loops in DNA Repeats to Protect Genome Stability

SFPQ Directs Histone H3.3 Deposition to R-Loops in DNA Repeats to Protect Genome Stability | 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 SFPQ Directs Histone H3.3 Deposition to R-Loops in DNA Repeats to Protect Genome Stability Stefan Schoeftner, Alessandro Ferrando, Alice Gambelli, Pamela Veneziano Broccia, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5721144/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 24 Feb, 2026 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract R-loops are three-stranded nucleic acid structures that contain an RNA:DNA hybrid duplex and an unpaired single stranded DNA loop. Unscheduled or persistent R-loops drive genome instability by creating conflicts with transcription and replication. Up to 75% of the human genome comprises repetitive DNA elements that can engage in R-loop formation. We demonstrate that the RNA binding protein SFPQ suppresses R-loop mediated replication stress and DNA damage at repeat elements such as telomeres, (peri)-centromeres, LINE-1 and SINE elements. SFPQ shows in-vitro R-loop binding activity, binds to chromatin containing R-loops and recruits the histone H3.3 specific chaperon DAXX to maintain a correct nucleosome template that antagonizes R-loop formation. Loss of SFPQ results in DAXX delocalization from repeat elements, reduction of histone H3.3 incorporation, replication stress mediated genome instability and the formation of cytoplasmatic DNA species, which activate innate immunity pathways via the cGAS/STING pathway resulting improved sarcoma patient survival. Biological sciences/Molecular biology/Chromatin Biological sciences/Cell biology/Chromosomes R-loop SFPQ DAXX H3.3 DNA repeats genome stability innate immunity Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Supplementarytable7.xlsx Supplementary table 7 Movie.avi Supplementary Video Cite Share Download PDF Status: Published Journal Publication published 24 Feb, 2026 Read the published version in Nature Communications → 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-5721144","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":406648427,"identity":"8d7b4b04-9b98-4367-85bf-e34b78440839","order_by":0,"name":"Stefan Schoeftner","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA3klEQVRIiWNgGAWjYHACNiCWAzEYHzAwSIDoBmK0GIOUMhsAtQAZjI2E9MC1sIEIwtbI9x9+9uBDhUGdOXvvs2reHRZ18g3M7Q/waTG4kWZuOOOMgYRlz3Gz27xnJCQMDhBwmIEED5s0b9sfCaBettu8bUAthPwi338GqOWfgYTB/WdsxSAt8g2EvH8gB6ilAajlBhsbM0gLA0GH3Ugzk5xxzEByw5k0Zsm5bRKSGw4zNs7A77DDzyQ+1BjwGxw/xvjhbVsdv3x7+4MPeB2GCZhJVD8KRsEoGAWjABMAAGqEQV3GSPkWAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-8918-6627","institution":"Università degli Studi di Trieste","correspondingAuthor":true,"prefix":"","firstName":"Stefan","middleName":"","lastName":"Schoeftner","suffix":""},{"id":406648428,"identity":"26b54206-61ff-4ac4-a553-1b108d0e2978","order_by":1,"name":"Alessandro Ferrando","email":"","orcid":"","institution":"Università degli Studi di Trieste","correspondingAuthor":false,"prefix":"","firstName":"Alessandro","middleName":"","lastName":"Ferrando","suffix":""},{"id":406648429,"identity":"0cb9db5f-e3d9-4ae8-aaff-c0dd1c260dca","order_by":2,"name":"Alice Gambelli","email":"","orcid":"","institution":"University of Trieste","correspondingAuthor":false,"prefix":"","firstName":"Alice","middleName":"","lastName":"Gambelli","suffix":""},{"id":406648430,"identity":"ca87bb6e-d34c-407b-ac3e-ba711d9c7aa6","order_by":3,"name":"Pamela Veneziano Broccia","email":"","orcid":"","institution":"Università degli Studi di Trieste","correspondingAuthor":false,"prefix":"","firstName":"Pamela","middleName":"Veneziano","lastName":"Broccia","suffix":""},{"id":406648431,"identity":"a37b3282-93df-4e6c-9453-94c97de06368","order_by":4,"name":"Annie Zappone","email":"","orcid":"","institution":"Università degli Studi di Trieste","correspondingAuthor":false,"prefix":"","firstName":"Annie","middleName":"","lastName":"Zappone","suffix":""},{"id":406648432,"identity":"97cf0381-3c74-4912-b3e1-f933d955b2bc","order_by":5,"name":"Luisa Napolitano","email":"","orcid":"","institution":"Consiglio Nazionale delle Ricerche","correspondingAuthor":false,"prefix":"","firstName":"Luisa","middleName":"","lastName":"Napolitano","suffix":""},{"id":406648433,"identity":"6047074c-ba45-4032-8dab-afffb8a05bb9","order_by":6,"name":"Giulia Canarutto","email":"","orcid":"https://orcid.org/0000-0001-5010-7269","institution":"International Centre for Genetic Engineering \u0026 Biotechnology","correspondingAuthor":false,"prefix":"","firstName":"Giulia","middleName":"","lastName":"Canarutto","suffix":""},{"id":406648434,"identity":"a1b72e44-b987-4b43-9ea9-e4c3679f1632","order_by":7,"name":"Michele Giaquinto","email":"","orcid":"","institution":"Università degli Studi di Trieste","correspondingAuthor":false,"prefix":"","firstName":"Michele","middleName":"","lastName":"Giaquinto","suffix":""},{"id":406648435,"identity":"e570d6b1-aeaa-487a-9d03-01e65420193a","order_by":8,"name":"Eleonora Petti","email":"","orcid":"https://orcid.org/0000-0001-8189-1906","institution":"IRCCS - 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