Integrative modelling of the genome structure and dynamics in fission yeast

Integrative modelling of the genome structure and dynamics in fission yeast | 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 Biological Sciences - Article Integrative modelling of the genome structure and dynamics in fission yeast Shin-ichi Tate, Soya Shinkai, Toshinori Namba, Takeshi Sugawara, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9062331/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Genome organization in the nucleus is highly structured and dynamic. Recent advances in genomic technology have enabled the measurement of genome-wide architecture and locus-specific motion, yielding contact maps and live-cell trajectories. However, these outcomes are derived from different modalities and are not directly comparable, with their quantitative integration being a key challenge. Here we establish a genome-wide live-cell imaging platform in fission yeast Schizosaccharomyces pombe, tracking 131 chromosomal loci, along with the spindle pole body (SPB) and nucleolus, to construct a quantitative map of locus dynamics. We integrate these dynamics with contact data through physics-based polymer modelling of Hi-C data. The resulting model reproduces genome-wide mobility patterns and known architectural features, including centromere and telomere clustering. The model also identifies distinct dynamical regimes: centromere- and telomere-proximal loci relax within ~150 s, whereas the remaining loci relax within ~70 s. SPB motion exhibits an oscillatory peak near 225 s and 1/f fluctuations. We use the model with SPB-directed forcing to show how these low-frequency components propagate through the genome to drive genome-wide chromatin displacements. Together, this predictive physics-based framework integrates genome structure and dynamics to reveal how nuclear mechanical driving forces shape chromosome motion, linking mechanically-driven chromatin responses to genome maintenance and regulation. Biological sciences/Biophysics/Biopolymers in vivo Biological sciences/Cell biology/Chromosomes Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryTable1.csv Insertion positions of lacO arrays in lacO/LacI-GFP. SupplementaryTable2.csv Genomic bin indices and annotations used for PHi-C analysis. SupplementaryVideo1.mp4 Live-cell imaging of the chromosomal locus and nuclear 959 landmarks in S. pombe. SupplementaryVideo2.mp4 PHi-C fitting of 2-point MSDs for all loci on chromosome I. SupplementaryVideo3.mp4 PHi-C fitting of 2-point MSDs for all loci on chromosome II. SupplementaryVideo4.mp4 PHi-C fitting of 2-point MSDs for all loci on chromosome III. SupplementaryVideo5.mp4 Dynamical behaviour of the PHi-C-inferred model. Cite Share Download PDF Status: Posted 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-9062331","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":603156934,"identity":"cb866542-228b-4ed5-8643-bb075846ef25","order_by":0,"name":"Shin-ichi 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