Single-nucleus and spatial transcriptome identify brain landscape of gene regulatory networks associated with behavioral maturation in honeybees

Single-nucleus and spatial transcriptome identify brain landscape of gene regulatory networks associated with behavioral maturation in honeybees | 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 Single-nucleus and spatial transcriptome identify brain landscape of gene regulatory networks associated with behavioral maturation in honeybees Hao Zheng, Xiaohuan Mu, Qun Liu, Jie Ma, Yating Qin, Zijing Zhang, and 27 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-2527530/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 08 Apr, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Animal behavior is associated with the gene regulatory network (GRN) coordinating gene expression levels in the brain. The eusocial honeybees with natural behavioral plasticity provide an ideal model for studying the relationship between brain activity and behaviors. Here, using single-nucleus RNA sequencing and spatial transcriptomics, we profile the expression changes of 121,247 brain cells associated with the behavioral maturation of honeybees from nursing to foraging outside. We identified 24 subpopulations of brain cells, including Kenyon, glia, optic lobes, and olfactory projection neurons. Compared to non-social insects, Drosophila, the Keyon cells display a high diversity in the mushroom body of honeybees. Integrating spatial and cellular profiles finds that the mushroom body and optic lobes show specifically high activities of the regulons led by different transcription factors. The stripe regulon is activated explicitly in the foragers’ small- and middle-type Keyon cells implicated in spatial learning and navigation behavior. These suggest that the activity of individual brain cells is coordinated by specific GRNs during the behavioral transition of honeybees. Our results provide a deeper understanding of the behavior-associated brain heterogeneity in GRN, which may be a key driver for the division of labor in social life. Biological sciences/Zoology/Entomology Biological sciences/Neuroscience/Social behaviour Apis mellifera gene regulatory network single-nucleus RNA sequencing spatial transcriptome social behavior Full Text Additional Declarations There is NO Competing Interest. Cite Share Download PDF Status: Published Journal Publication published 08 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. 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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-2527530","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":352985968,"identity":"5dc45bdc-3d4c-4fcd-8a31-001098f067a2","order_by":0,"name":"Hao 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with behavioral maturation in honeybees","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Apis mellifera, gene regulatory network, single-nucleus RNA sequencing, spatial transcriptome, social behavior","lastPublishedDoi":"10.21203/rs.3.rs-2527530/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-2527530/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Animal behavior is associated with the gene regulatory network (GRN) coordinating gene expression levels in the brain. The eusocial honeybees with natural behavioral plasticity provide an ideal model for studying the relationship between brain activity and behaviors. Here, using single-nucleus RNA sequencing and spatial transcriptomics, we profile the expression changes of 121,247 brain cells associated with the behavioral maturation of honeybees from nursing to foraging outside. We identified 24 subpopulations of brain cells, including Kenyon, glia, optic lobes, and olfactory projection neurons. Compared to non-social insects, Drosophila, the Keyon cells display a high diversity in the mushroom body of honeybees. Integrating spatial and cellular profiles finds that the mushroom body and optic lobes show specifically high activities of the regulons led by different transcription factors. The stripe regulon is activated explicitly in the foragers’ small- and middle-type Keyon cells implicated in spatial learning and navigation behavior. These suggest that the activity of individual brain cells is coordinated by specific GRNs during the behavioral transition of honeybees. Our results provide a deeper understanding of the behavior-associated brain heterogeneity in GRN, which may be a key driver for the division of labor in social life.","manuscriptTitle":"Single-nucleus and spatial transcriptome identify brain landscape of gene regulatory networks associated with behavioral maturation in honeybees","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-09-13 03:08:27","doi":"10.21203/rs.3.rs-2527530/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":"10f3daad-0028-4b7c-bca8-a2d2ee779c54","owner":[],"postedDate":"September 13th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":37494632,"name":"Biological sciences/Zoology/Entomology"},{"id":37494633,"name":"Biological sciences/Neuroscience/Social behaviour"}],"tags":[],"updatedAt":"2025-04-09T07:07:14+00:00","versionOfRecord":{"articleIdentity":"rs-2527530","link":"https://doi.org/10.1038/s41467-025-58614-8","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2025-04-08 04:00:00","publishedOnDateReadable":"April 8th, 2025"},"versionCreatedAt":"2024-09-13 03:08:27","video":"","vorDoi":"10.1038/s41467-025-58614-8","vorDoiUrl":"https://doi.org/10.1038/s41467-025-58614-8","workflowStages":[]},"version":"v1","identity":"rs-2527530","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-2527530","identity":"rs-2527530","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}