High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo

High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo | 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-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo Julia Zeitlinger, Sergio García-Moreno Alcántara, Simon Bourdareau, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8428476/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 TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex interacts with and functions at different promoter types in vivo is still lacking. Here, we employed ChIP-nexus to capture high resolution binding footprints of all Drosophila TFIID subunits across the genome. These footprints reveal TFIID sub-modules whose DNA contacts suggest new structural details. At different promoter types, the footprints of the TAFs are very similar, suggesting the presence of engaged TFIID across all promoters. In contrast, the binding profile of TBP is promoter-specific, enabling us to identify TATA, DPR, and TCT/housekeeping promoters de novo, along with their underlying core promoter elements. Notably, our data point to NC2 being specific for TBP binding at the TATA box and suggest that TATA promoters show both TAF-dependent and TAF-independent initiation in vivo. These data suggest a model for the increased burst size observed at TATA promoters and provide a comprehensive resource for linking structural and biochemical results to in vivo data. Biological sciences/Genetics/Genomics Biological sciences/Structural biology TFIID TBP NC2 ChIP-nexus promoter selection Drosophila kc167cells transcriptional bursting Full Text Additional Declarations Yes there is potential Competing Interest. J.Z. owns a patent on ChIP-nexus (US-10287628). All other authors declare no competing interests. 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-8428476","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":572297948,"identity":"1b13a854-3b7b-4804-b4d9-8a240c11fde4","order_by":0,"name":"Julia Zeitlinger","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAt0lEQVRIiWNgGAWjYBACxhkMjA9I1sJswJBAkh4JBjYJ0rQwz25/Vvnzh01iv/TxBwwf99QS4bA5B9Ju8ySkJc7syzFgnPHsOBFaZiQcu82QcDh3wxkeBmaeA8eI0ZLYVvgDqGX/GfYHxGpJZmPgAdnCw2AA1FJDjF+OMUvzpKXVzzjDY3BwxoEDhLUYzm5/+PGHjY0xfw/7wwcfDtQRoaUBiQO04jBhLfJofCJsGQWjYBSMghEHAJK3PLtbzYN5AAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-5172-3335","institution":"Stowers Institute for Medical Research","correspondingAuthor":true,"prefix":"","firstName":"Julia","middleName":"","lastName":"Zeitlinger","suffix":""},{"id":572297949,"identity":"614e25df-ac73-48dd-bc8d-51ed559fc063","order_by":1,"name":"Sergio García-Moreno Alcántara","email":"","orcid":"https://orcid.org/0000-0003-3695-4677","institution":"Stowers Institute for Medical Research","correspondingAuthor":false,"prefix":"","firstName":"Sergio","middleName":"García-Moreno","lastName":"Alcántara","suffix":""},{"id":572297950,"identity":"3af6f2b9-d6a6-42bf-b40c-ccbe78fa7596","order_by":2,"name":"Simon Bourdareau","email":"","orcid":"","institution":"Stowers Institute for Medical Research","correspondingAuthor":false,"prefix":"","firstName":"Simon","middleName":"","lastName":"Bourdareau","suffix":""},{"id":572297951,"identity":"53c77edd-d6ff-4d90-93d5-f5be6a3b0d1e","order_by":3,"name":"Melanie Weilert","email":"","orcid":"https://orcid.org/0000-0001-8683-4580","institution":"Stowers Institute for Medical Research","correspondingAuthor":false,"prefix":"","firstName":"Melanie","middleName":"","lastName":"Weilert","suffix":""}],"badges":[],"createdAt":"2025-12-22 21:50:41","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8428476/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8428476/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":101752092,"identity":"ef3494b3-9ead-484a-9854-995f5031a51e","added_by":"auto","created_at":"2026-02-03 10:25:18","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3924005,"visible":true,"origin":"","legend":"Article File","description":"","filename":"TFIIDformattedforjournal.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8428476/v1_covered_934f9d70-f7bc-416f-95e6-492fb908a6b7.pdf"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nJ.Z. owns a patent on ChIP-nexus (US-10287628). 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Here, we employed ChIP-nexus to capture high\r\nresolution binding footprints of all Drosophila TFIID subunits across the genome. These \r\nfootprints reveal TFIID sub-modules whose DNA contacts suggest new structural details. \r\nAt different promoter types, the footprints of the TAFs are very similar, suggesting the \r\npresence of engaged TFIID across all promoters. In contrast, the binding profile of TBP is \r\npromoter-specific, enabling us to identify TATA, DPR, and TCT/housekeeping promoters \r\nde novo, along with their underlying core promoter elements. Notably, our data point to NC2 \r\nbeing specific for TBP binding at the TATA box and suggest that TATA promoters show both \r\nTAF-dependent and TAF-independent initiation in vivo. These data suggest a model for the \r\nincreased burst size observed at TATA promoters and provide a comprehensive resource for \r\nlinking structural and biochemical results to in vivo data.","manuscriptTitle":"High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-30 06:26:55","doi":"10.21203/rs.3.rs-8428476/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":"329a100d-ffb9-46e6-ad62-1edf287236c9","owner":[],"postedDate":"January 30th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":60904306,"name":"Biological sciences/Genetics/Genomics"},{"id":60904307,"name":"Biological sciences/Structural biology"}],"tags":[],"updatedAt":"2026-01-30T06:26:56+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-30 06:26:55","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8428476","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8428476","identity":"rs-8428476","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}