Cell lineage-resolved embryonic morphological map reveals novel signaling regulating cell fate and size asymmetry

Cell lineage-resolved embryonic morphological map reveals novel signaling regulating cell fate and size asymmetry | 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 Cell lineage-resolved embryonic morphological map reveals novel signaling regulating cell fate and size asymmetry Zhongying Zhao, Guoye Guan, Zelin Li, Yiming Ma, Pohao Ye, Jianfeng Cao, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4664717/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 18 Apr, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Understanding the dynamic evolutions of cellular morphology throughout development is crucial for elucidating the mechanisms of morphogenesis and organogenesis. However, a systematic and detailed characterization of these processes poses a significant challenge. In this study, we introduce a comprehensive real-time morphological map covering over 95% of the cells produced during Caenorhabditis elegans embryogenesis, constituted by nearly 400,000 3D cell regions. Our map integrates information about identity, lineage, fate, shape, volume, surface area, and contact area for each individual cell, together with lineage-specific gene expression profiles, all of which are accessible through our custom-designed software and website. This morphological map enables vivid and precise characterization of key morphogenetic events, such as dorsal intercalation, intestinal morphogenesis, and body-wall muscle assembly. Furthermore, we reveal that the Notch and Wnt signaling pathways, in concert with mechanical forces from cell-cell interactions, orchestrate the asymmetry of both cell fate and cell size. Additionally, our analysis of cell-cell contact maps and lineage-specific gene expression profiles uncovers a cascade of Notch signaling events that drive the cell size asymmetries critical for kidney development. This resource lays the foundation for in-depth studies of the regulatory networks that determine cell fate, size, and cell cycle length throughout C. elegans embryogenesis. Biological sciences/Cell biology/Cellular imaging Biological sciences/Developmental biology/Embryogenesis/Cell lineage Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryTable.zip Supplementary Table SupplementaryMovie.zip Supplementary Movie Cite Share Download PDF Status: Published Journal Publication published 18 Apr, 2025 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. 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-4664717","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":346754649,"identity":"bc4118ca-faf2-4aa7-95d1-2c30b2a89557","order_by":0,"name":"Zhongying 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