The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development

The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development | 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 The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development Carsten Daub, Isil Takan, Matthias Hörtenhuber, Noora Salokorpi, and 15 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9179233/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 The domestic dog is a powerful genetic model for complex traits, disease and behaviours relevant to human biology, yet the canine genome still lacks a systematic transcription-defined atlas of regulatory elements. Existing resources have improved annotation but largely infer regulatory activity from chromatin features rather than directly mapping transcription initiation at promoters and enhancers. Here, we address this gap using 114 CAGE-seq libraries spanning 56 tissues and developmental stages from 9 dogs. We identify 68,446 promoters and 46,661 active enhancers, and define their tissue-enriched activity across the canine body. Regulatory programmes are organized around shared transcription factor motif infrastructures, with prominent enrichment of KLF family motifs across tissues. The cerebellum emerges as a major regulatory hub, showing the highest density of enhancer-promoter interactions among brain regions. During embryogenesis, enhancer activity shifts from early neurodevelopmental patterning programmes, including OTX2 and ZIC1/4, towards regulators of functional maturation and synaptic organization, including AQP4 and NLGN3. Comparative analyses revealed 69 enhancers with highly similar regulatory structures linked to potential orthologous genes in dog and human. Together, these data establish a tissue-resolved transcription-based atlas of the canine regulatory genome that advances functional annotation and improves interpretation of non-coding variation in comparative and disease genomics. Biological sciences/Biological techniques/Experimental organisms/Model vertebrates/Dog Biological sciences/Molecular biology/Transcriptomics Biological sciences/Computational biology and bioinformatics/Gene regulatory networks Biological sciences/Genetics/Functional genomics/Gene expression profiling Biological sciences/Biological techniques/Bioinformatics Full Text Additional Declarations Yes there is potential Competing Interest. Hannes Lohi has previously consulted for Wisdom Panel Science & Diagnostics, Mars Petcare, a company that provides genetic testing services for dogs and partially funded this study. Supplementary Files SupplementaryFigures.pdf Supplementary Figures - The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development SupplementaryTables.xlsx Table S1, Table S2, Table S3, Table S4, Table S5, Table S6, Table S7, Table S8, Table S9 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-9179233","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":613487494,"identity":"d93e7c43-3117-4a88-ac68-1d70b229053b","order_by":0,"name":"Carsten 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Existing resources have improved annotation but largely infer regulatory activity from chromatin features rather than directly mapping transcription initiation at promoters and enhancers. Here, we address this gap using 114 CAGE-seq libraries spanning 56 tissues and developmental stages from 9 dogs. We identify 68,446 promoters and 46,661 active enhancers, and define their tissue-enriched activity across the canine body. Regulatory programmes are organized around shared transcription factor motif infrastructures, with prominent enrichment of KLF family motifs across tissues. The cerebellum emerges as a major regulatory hub, showing the highest density of enhancer-promoter interactions among brain regions. During embryogenesis, enhancer activity shifts from early neurodevelopmental patterning programmes, including OTX2 and ZIC1/4, towards regulators of functional maturation and synaptic organization, including AQP4 and NLGN3. 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