Cold-dependent ELF6 accumulation drives H3K27me3 demethylation to regulate flowering time response to low ambient temperature

Cold-dependent ELF6 accumulation drives H3K27me3 demethylation to regulate flowering time response to low ambient temperature | 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 Research Article Cold-dependent ELF6 accumulation drives H3K27me3 demethylation to regulate flowering time response to low ambient temperature Ana Luna, Laura Poza-Viejo, Iván del Olmo, Burcu Arikan, Sara González-Bodí, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5893753/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Flowering time is an important crop trait, as premature or delayed flowering can significantly reduce yields. Plants flower in response to a defined set of endogenous and environmental cues. While the effects of ambient temperature on flowering time are well-studied, the role of epigenetic modifiers in the floral thermosensory pathway remains largely unexplored. Here, we show that the histone demethylases EARLY FLOWERING 6 (ELF6) and JUMONJI 13 (JMJ13) act redundantly to fine-tune temperature-dependent flowering. We found that the elf6-3 jmj13-1 double mutant is hyposensitive to the flowering delay induced by low ambient temperature. Genetic analyses indicated that this response requires FLOWERING LOCUS M ( FLM ) and, to a lesser extent, its homolog FLOWERING LOCUS C ( FLC ). Consistent with these genetic requirements, transcript and chromatin immunoprecipitation (ChIP) analyses revealed that ELF6 and JMJ13 modulate FLM and FLC expression. ChIP assays showed that both proteins associate with FLM and FLC , but with distinct dynamics: JMJ13 exhibited low-level, constitutive occupancy, whereas ELF6 recruitment was temperature and development dependent. Remarkably, ELF6 binding was detected earlier in development under low ambient temperature, coincident with increased ELF6 protein accumulation in germinating seedlings. Together, our data support a model in which low ambient temperature promotes early ELF6 recruitment to limit repressive histone H3 lysine 27 trimethylation (H3K27me3) accumulation at thermoresponsive floral repressors, thereby enabling appropriate gene expression and flowering-time control. These findings identify H3K27me3 demethylases as key components of the floral thermosensory pathway and highlight epigenetic mechanisms linking ambient temperature to flowering. Biological sciences/Plant sciences/Plant development Biological sciences/Genetics/Epigenetics Flowering temperature demethylase H3K27me3 FLM FLC ELF6 JMJ13 Full Text Additional Declarations The authors declare no competing interests. Supplementary Files FigSup.pdf Supplemental Figures TableS1.docx Table S1 TableS2.docx Table S2 SupplementaryDataS1.xlsx Dataset 2 SupplementaryDataS2.xlsx Dataset 2 Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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-5893753","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":411331478,"identity":"cd87ccae-7f1e-4e68-b946-4fa83354b773","order_by":0,"name":"Ana Luna","email":"","orcid":"https://orcid.org/0009-0005-9254-2820","institution":"Universidad Politécnica de Madrid","correspondingAuthor":false,"prefix":"","firstName":"Ana","middleName":"","lastName":"Luna","suffix":""},{"id":411331477,"identity":"56e0a62b-9d0c-40b5-9459-ed9873b47d9e","order_by":1,"name":"Laura Poza-Viejo","email":"","orcid":"https://orcid.org/0000-0001-6252-3964","institution":"Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC","correspondingAuthor":false,"prefix":"","firstName":"Laura","middleName":"","lastName":"Poza-Viejo","suffix":""},{"id":411331479,"identity":"3a6c41a1-fcc7-46d9-bedd-4b4653504461","order_by":2,"name":"Iván del Olmo","email":"","orcid":"https://orcid.org/0000-0002-5169-4335","institution":"Centro de Biología Molecular Severo Ochoa (CSIC-UAM)","correspondingAuthor":false,"prefix":"","firstName":"Iván","middleName":"del","lastName":"Olmo","suffix":""},{"id":411331480,"identity":"84fa1384-8f02-4850-b086-8fa2f4e76b9a","order_by":3,"name":"Burcu Arikan","email":"","orcid":"https://orcid.org/0000-0002-8973-0813","institution":"Istanbul University","correspondingAuthor":false,"prefix":"","firstName":"Burcu","middleName":"","lastName":"Arikan","suffix":""},{"id":411331481,"identity":"4095653c-bc18-4e5e-a0fa-35328027c030","order_by":4,"name":"Sara González-Bodí","email":"","orcid":"https://orcid.org/0000-0003-3178-2976","institution":"Universidad Politécnica de Madrid","correspondingAuthor":false,"prefix":"","firstName":"Sara","middleName":"","lastName":"González-Bodí","suffix":""},{"id":411331482,"identity":"af7b6ec9-826e-42d8-a4c7-0b2f87138dbb","order_by":5,"name":"Wenhao Yan","email":"","orcid":"https://orcid.org/0000-0001-8165-7335","institution":"Huazhong Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Wenhao","middleName":"","lastName":"Yan","suffix":""},{"id":411331483,"identity":"cd838b0c-7273-4182-a9a0-d505764c451d","order_by":6,"name":"Kerstin Kaufmann","email":"","orcid":"https://orcid.org/0000-0001-7960-6256","institution":"[email protected]","correspondingAuthor":false,"prefix":"","firstName":"Kerstin","middleName":"","lastName":"Kaufmann","suffix":""},{"id":411331484,"identity":"6c521948-c1da-408b-a173-9dd065a17dee","order_by":7,"name":"Franziska Turck","email":"","orcid":"https://orcid.org/0000-0002-4982-5949","institution":"Max Planck Institute for Plant Breeding Research","correspondingAuthor":false,"prefix":"","firstName":"Franziska","middleName":"","lastName":"Turck","suffix":""},{"id":411331476,"identity":"94c8e760-0c0a-46c7-925e-8038e85f4586","order_by":8,"name":"Pedro Crevillén","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0003-1276-9792","institution":"Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC","correspondingAuthor":true,"prefix":"","firstName":"Pedro","middleName":"","lastName":"Crevillén","suffix":""}],"badges":[],"createdAt":"2025-01-24 08:20:50","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-5893753/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-5893753/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":106963449,"identity":"8d7de641-2569-4709-b00d-934535ae7883","added_by":"auto","created_at":"2026-04-15 09:44:26","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1551217,"visible":true,"origin":"","legend":"","description":"","filename":"Luna2026.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5893753/v2_covered_4d961a78-1062-47c4-b41f-f2bf0a5881f2.pdf"},{"id":106914108,"identity":"c667d300-5ee2-4b47-87be-c3306a39b898","added_by":"auto","created_at":"2026-04-14 17:31:19","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1220938,"visible":true,"origin":"","legend":"\u003cp\u003eSupplemental Figures\u003c/p\u003e","description":"","filename":"FigSup.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5893753/v2/39111435adbccc5460799e52.pdf"},{"id":106914110,"identity":"3b23afd5-911c-4cf2-8a85-330981eb4132","added_by":"auto","created_at":"2026-04-14 17:31:19","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":14786,"visible":true,"origin":"","legend":"\u003cp\u003eTable S1\u003c/p\u003e","description":"","filename":"TableS1.docx","url":"https://assets-eu.researchsquare.com/files/rs-5893753/v2/b4807d8b4de45edeb4804eff.docx"},{"id":106914109,"identity":"d3cfc1ed-4706-47b8-9b06-dc062f98b2e3","added_by":"auto","created_at":"2026-04-14 17:31:19","extension":"docx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":13638,"visible":true,"origin":"","legend":"\u003cp\u003eTable S2\u003c/p\u003e","description":"","filename":"TableS2.docx","url":"https://assets-eu.researchsquare.com/files/rs-5893753/v2/d5d96bc801392e6037a97cb0.docx"},{"id":106914112,"identity":"31637926-f1a8-43b5-a143-58f666012a26","added_by":"auto","created_at":"2026-04-14 17:31:19","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":44984778,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 2\u003c/p\u003e","description":"","filename":"SupplementaryDataS1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5893753/v2/772b117e91690edfdfce2364.xlsx"},{"id":106961491,"identity":"007db4f3-1074-441c-9f5a-25ba7d39d0f3","added_by":"auto","created_at":"2026-04-15 09:25:46","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":11211,"visible":true,"origin":"","legend":"\u003cp\u003eDataset 2\u003c/p\u003e","description":"","filename":"SupplementaryDataS2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5893753/v2/3889f339d5830a326ea01249.xlsx"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003e\u003cstrong\u003eCold-dependent ELF6 accumulation drives H3K27me3 demethylation to regulate flowering time response to low ambient temperature\u003c/strong\u003e\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Flowering, temperature, demethylase, H3K27me3, FLM, FLC, ELF6, JMJ13 ","lastPublishedDoi":"10.21203/rs.3.rs-5893753/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5893753/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eFlowering time is an important crop trait, as premature or delayed flowering can significantly reduce yields. Plants flower in response to a defined set of endogenous and environmental cues. While the effects of ambient temperature on flowering time are well-studied, the role of epigenetic modifiers in the floral thermosensory pathway remains largely unexplored. Here, we show that the histone demethylases EARLY FLOWERING 6 (ELF6) and JUMONJI 13 (JMJ13) act redundantly to fine-tune temperature-dependent flowering. We found that the \u003cem\u003eelf6-3 jmj13-1\u003c/em\u003e double mutant is hyposensitive to the flowering delay induced by low ambient temperature. Genetic analyses indicated that this response requires \u003cem\u003eFLOWERING LOCUS M\u003c/em\u003e (\u003cem\u003eFLM\u003c/em\u003e) and, to a lesser extent, its homolog \u003cem\u003eFLOWERING LOCUS C\u003c/em\u003e (\u003cem\u003eFLC\u003c/em\u003e). Consistent with these genetic requirements, transcript and chromatin immunoprecipitation (ChIP) analyses revealed that ELF6 and JMJ13 modulate \u003cem\u003eFLM\u003c/em\u003e and \u003cem\u003eFLC\u003c/em\u003e expression. ChIP assays showed that both proteins associate with \u003cem\u003eFLM\u003c/em\u003e and \u003cem\u003eFLC\u003c/em\u003e, but with distinct dynamics: JMJ13 exhibited low-level, constitutive occupancy, whereas ELF6 recruitment was temperature and development dependent. Remarkably, ELF6 binding was detected earlier in development under low ambient temperature, coincident with increased ELF6 protein accumulation in germinating seedlings. Together, our data support a model in which low ambient temperature promotes early ELF6 recruitment to limit repressive histone H3 lysine 27 trimethylation (H3K27me3) accumulation at thermoresponsive floral repressors, thereby enabling appropriate gene expression and flowering-time control. These findings identify H3K27me3 demethylases as key components of the floral thermosensory pathway and highlight epigenetic mechanisms linking ambient temperature to flowering.\u003c/p\u003e","manuscriptTitle":"Cold-dependent ELF6 accumulation drives H3K27me3 demethylation to regulate flowering time response to low ambient temperature","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2026-04-14 17:30:41","doi":"10.21203/rs.3.rs-5893753/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2025-02-05 04:41:52","doi":"10.21203/rs.3.rs-5893753/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"4c6ab41f-93f8-4a87-9966-073fcef30a62","owner":[],"postedDate":"April 14th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":65272614,"name":"Biological sciences/Plant sciences/Plant development"},{"id":65272615,"name":"Biological sciences/Genetics/Epigenetics"}],"tags":[],"updatedAt":"2025-02-25T04:26:06+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-14 17:30:41","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-5893753","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5893753","identity":"rs-5893753","version":["v2"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}