Pervasive co-regulation of alternative splicing with transcription initiation and termination.

Pervasive co-regulation of alternative splicing with transcription initiation and termination. | 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 Pervasive co-regulation of alternative splicing with transcription initiation and termination. Wu Wei, Xiaodong Song, Huiying Yan, Yanhong Hong, Jiaming Huang, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7727550/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 Nascent RNA processing requires coordination of transcription and splicing to yield accurate gene products. However, the basis of this co-regulation remains enigmatic. Here, we develop longPASS, a system that accurately identifies and quantitates transcription start site (TSS) and polyadenylation site (PAS) usage in long-read RNA sequencing data. longPASS systematically reveals thousands of TSS/PAS-associated alternative splicing events (TASE) in human cells, uncovering pervasive, consistent TASEs across genetic perturbations, human tissues, and individuals. Co-occurring pairs of TASE-exons and TASE-TSS/PASs are proximal and show increased RNA-RNA spatial interactions. Large-scale screening reveals that the RBMX protein specifically binds PAS-TASE pairs. Indeed, RBMX knockdown, but not canonical splicing factors, disrupts the co-regulation of splicing and PAS usage in TASEs. Manipulating RNA polymerase II elongation also affects PAS-TASE co-regulation, with slower elongation rates leading to increased co-occurrence. Overall, our analysis reveals pervasive co-regulation between alternative splicing and TSS/PAS usage is mediated by RBMX interaction, Pol II elongation rates, and linked to ageing. Biological sciences/Computational biology and bioinformatics Biological sciences/Molecular biology/RNA metabolism/RNA splicing Biological sciences/Molecular biology/Transcription Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Supplementarytables.zip Table S1. longPASS-defined TSS/PAS clusters in long-read RNA sequencing data of RNA sequins, related to Figure 1. Table S2. longPASS-defined TSS/PAS clusters in long-read RNA sequencing data of human K562 cells, related to Figure 1. Table S3. Identified TASE pairs in K562 cells in this study, related to Figure 2. Table S4. RNA binding protein public assays used in this study, related to Figure 4. Table S5. Validation of the elongation rates of pol II mutants, related to Figure 5. SuppFigsspilit.pdf Supplementary Figs S1-6 TASSmanuscriptlinks.docx links 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. 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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-7727550","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":528610662,"identity":"6c2d714a-2faa-46c5-a280-fb18d3ccb76f","order_by":0,"name":"Wu 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