Elevating RNA m5C methylation provides a promising strategy for crop productivity | 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 Elevating RNA m 5 C methylation provides a promising strategy for crop productivity Xiaofeng Gu, Xiulan Li, Cong Li, Xiangyu Wang, Liwen Yang, Weijun Guo, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5697502/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 RNA 5-methylcytidine (m5C) has been identified as a key epi-transcriptomic modification of mRNAs involved in regulating multiple post-transcriptional processes. Here, we found that knockout of the RNA m5C demethylase, OsNOP2, results in elevated m5C levels and positively influences numerous agronomic traits in rice. After verifying OsNOP2 RNA m5C demethylase function in vitro and in planta, we found that enhanced m5C levels arising from OsNOP2 knockout results in increased translation, particularly for transcripts involved in carbon assimilation and nitrogen metabolism. OsNOP2-KO boosts grain yield ~28% per plot in the Nipponbare genetic background in normal condition and maintains increased yield traits under both heat treatment and saline soil conditions. More importantly, knockout of OsNOP2 in the rice varieties Longgeng31 and Xiushui134, as well as its orthologs in wheat and tomato, also increases the RNA m5C level to enhance yield, supporting functional conservation of OsNOP2's regulatory impacts. Together, our findings unveil an RNA m5C elevating mechanism by OsNOP2 that epigenetically governs carbon assimilation and nitrogen utilization efficiency in plant, providing a potential strategy for genetic improvement in multiple crops. Biological sciences/Genetics/Epigenetics Biological sciences/Molecular biology/Epigenetics Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Additional Declarations There is NO Competing Interest. Supplementary Files nreditorialpolicychecklist.pdf Related Manuscript File nrreportingsummary.pdf Related Manuscript File Supplementaryinformation.pdf Supplementary information 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. 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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-5697502","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":403217230,"identity":"a08346b0-9ccf-4cbb-a8a7-92ed14dbd5a5","order_by":0,"name":"Xiaofeng Gu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA3UlEQVRIiWNgGAWjYJCCAwwMckCK+QBJWoyBFFsCSRaBtPAYEKdWPiLH8MCPCgM5c/41Hz/8qKlj4J/dgF+L4Y20hIM9ZwyMLWe83SzZc+wwg8SdAwS0zEg+cIC37U/ihhtntzHwsB1gMJBIIKQlseHg3zaD+g03zjxj/POvjrAWeYnkA4d52wwSDM73sDHztjET1mLA8yzhsMwZA8MNN9iMpWX7DvNI3CBkS3uO8cc3FQbyBucPP/z45ludHP8MQrYcgLGg7uHBrx5kSwOMxX8At6pRMApGwSgY2QAACphHzN+TfhgAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0003-1127-4261","institution":"Biotechnology Research Institute, Chinese Academy of Agricultural Sciences","correspondingAuthor":true,"prefix":"","firstName":"Xiaofeng","middleName":"","lastName":"Gu","suffix":""},{"id":403217231,"identity":"418b55fa-5ec2-4e78-9390-7f08247e7522","order_by":1,"name":"Xiulan Li","email":"","orcid":"","institution":"Biotechnology Research Institute, Chinese Academy of Agricultural 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Sciences","correspondingAuthor":false,"prefix":"","firstName":"Hanlin","middleName":"","lastName":"Liu","suffix":""},{"id":403217238,"identity":"4b764d56-ad2b-43cb-9204-dffcb42018e7","order_by":8,"name":"Dongwei Li","email":"","orcid":"","institution":"Biotechnology Research Institute, Chinese Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Dongwei","middleName":"","lastName":"Li","suffix":""},{"id":403217239,"identity":"80f770ec-d8de-4eda-9cd4-f1ad1f845ee8","order_by":9,"name":"Shuangyong Yan","email":"","orcid":"","institution":"Tianjin Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Shuangyong","middleName":"","lastName":"Yan","suffix":""}],"badges":[],"createdAt":"2024-12-23 07:40:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5697502/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5697502/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":74203344,"identity":"ffff59ee-aa95-4606-aed2-b3465f5e01a1","added_by":"auto","created_at":"2025-01-20 02:56:18","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":2160012,"visible":true,"origin":"","legend":"\u003cp\u003eOsNOP2 knockout boosts grain yield in Nipponbare background. a, Distribution of indica rice (XI) and japonica rice (GJ) after yield correlation analysis. b, Statistics of gene numbers in XI and GJ. c, Venn diagram showing overlap of yield-related genes in XI and GJ and epigenetic genes in rice. d, The expression of 9 genes in XI and GJ overlapped with epigenetic genes in panicles at different developmental stages. e-h, Field morphology, grain yield per plot (e), tillers (f), panicle (g), and root (h) of WT, KO1, and KO2 plants. Scale bars, 10 cm (e), 3 cm (f, h), and 5 cm (g). i-p Statistical analysis of grain yield per plant (i), grain yield per plot (j), tiller numbers per plant (k), 1,000-grain weight (l), panicle length (m), grain numbers per panicle (n), grain weight per panicle (o), and dry weight of roots (p) in WT, KO1, and KO2 plants. e, j, Yields in paddy fields between WT, KO1, and KO2 grown in the 4.5-m2 paddies (each paddy contained 10 × 15 plants) were harvested. Data are mean ± S.D. (i, k, n = 30 plants; j, n = 4 biological replicates; l, n = 7 biological replicates; m-o, n = 30 panicles; p, n = 10 plants). *P \u0026lt; 0.05, ***P \u0026lt; 0.001, ****P \u0026lt; 0.0001; P values are from one-way ANOVA (and nonparametric or mixed).\u003c/p\u003e","description":"","filename":"Fig.1.png","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/85ffa91e8331d4ce654d4eff.png"},{"id":74203345,"identity":"fabd8278-3285-4660-b65b-c8a7f9d98584","added_by":"auto","created_at":"2025-01-20 02:56:18","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1088954,"visible":true,"origin":"","legend":"\u003cp\u003eOsNOP2 knockout promotes photosynthetic capacity and nitrogen use efficiency. a-c, Statistical analysis of the SPAD value (a), photosynthetic rate (b), and the C content (c) of WT, KO1, and KO2 plants at filling stage grown in the field under the normal condition. d, Transmission electron micrographs of chloroplast ultrastructure from the flag leaves of WT, KO1, and KO2 plants. Scale bar, 5 μm. e-f, Statistical analysis of the number (e) and size (f) of chloroplasts in mesophyll cells in WT, KO1, and KO2 plants. g, Western blot analysis of the expression levels of proteins related to photosynthesis in WT, KO1, and KO2 plants. h-i, RubisCO content (h) and RubisCO activity (i) in the fourth leaf of WT, KO1, and KO2 seedlings. j, Single-plant phenotypes of WT, KO1, and KO2 under various nitrogen fertilization(no nitrogen (0 kg ha-1), low nitrogen (112.5 kg ha-1), and normal nitrogen (225 kg ha-1)). Scale bars, 25 cm. k, The N content of WT, KO1, and KO2 plants at anthesis stage grown in the field under the normal condition. l-n, Statistical analysis of the tiller numbers per plant (l), grain yield per plot (m), and nitrogen use efficiency (NUE) (n) of WT, KO1, and KO2 plants under various nitrogen fertilization. Data are mean ± S.D. (a-b, n ≥ 8 plants; c, k, and m-n, n = 3 biological replicates; e-f, n ≥ 6 biological replicates; h-i, n ≥ 3 biological replicates; l, n ≥ 15 plants). *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001, ****P \u0026lt; 0.0001; In a-b, e-f, and h-i, P values are from one-way ANOVA (and nonparametric or mixed). In c, k, and m-n, P values are from two-way ANOVA (and nonparametric or mixed).\u003c/p\u003e","description":"","filename":"Fig.2.png","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/40681c79f1dc3f2ddda256ff.png"},{"id":74203348,"identity":"d5ce5eee-46eb-4a33-9c41-241c45188ff0","added_by":"auto","created_at":"2025-01-20 02:56:18","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1352421,"visible":true,"origin":"","legend":"\u003cp\u003eOsNOP2 is an mRNA m5C demethylase in rice. a-b, Detection of total RNA m5C level from 3-week-old WT, KO1, and KO2 seedlings grown hydroponically by dot blot (a) and LC-MS/MS (b). c, The RNA m5C peak numbers within coding gene bodies in WT and KO2 seedlings. d, Consensus sequence motifs of RNA m5C peaks. P-value generated by HOMER. e, Detection of demethylation of RNA m5C by purified OsNOP2-GST protein in vitro and the quantification was shown on the right. f, Detection the levels of RNA m5C after that OsNOP2-GFP and GFP proteins were transiently expressed in rice protoplasts and the quantification was shown on the right. g, The location prediction of the key enzymatic active sites of OsNOP2 protein. h-i, Detection of the demethylase activity of the mutant proteins OsNOP2T422V and OsNOP2H375K (h) and OsNOP2A2G (i) in vitro, and the quantification was shown on the right. j, m, Phenotypes of the stable transgenic lines with site-directed mutagenesis of amino acids from OsNOP2T422V (j) and OsNOP2H375K (m). Scale bars, 5 cm. k, n, Statistical analysis of the plant height from stable transgenic lines (OsNOP2T422V) (k) and (OsNOP2H375K) (n) of T1 grown in the greenhouse. l, o, Detection of total RNA m5C level of 3-week-old stable transgenic lines(OsNOP2T422V) (l) and (OsNOP2H375K) (o), and the quantifications were displayed on the right of the figures, respectively. Data are shown as mean ± S.D. (a-b, e-f, h-i, l, and o, n = 3 biological replicates; k, n = 15 plants; n, n ≥ 12 plants). ns, no significance, **P \u0026lt; 0.01, ***P \u0026lt; 0.001, ****P \u0026lt; 0.0001; In a-b, P values are from one-way ANOVA (and nonparametric or mixed). In e-f, h-i, k-l, and n-o, P values are from two-tailed Student’s t-tests.\u003c/p\u003e","description":"","filename":"Fig.3.png","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/00b70b9ba16fdd4582749076.png"},{"id":74203351,"identity":"2d1de77d-8305-452e-9236-c2cd88ea5b6c","added_by":"auto","created_at":"2025-01-20 02:56:18","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1066654,"visible":true,"origin":"","legend":"\u003cp\u003eRNA m5C enhances translation efficiency of the target transcripts. a-b, The distribution (a) and number (b) of RNA m5C peaks within coding gene bodies divided into 5’UTR, CDS, and 3’UTR from 3-week-old WT and KO2 seedlings. c, Statistics of the number of genes bearing 1, 2, 3, and \u0026gt; 3 RNA m5C peaks. d, Scatter plot of transcripts modified by RNA m5C in WT and KO2 seedlings. Hyper-m5C-modified transcripts are in red; hypo-m5C-modified transcripts are in blue. e, KEGG analysis of hyper-m5C-modified transcripts. f-g, MeRIP-seq and proteomics analysis results were performed on transcripts related to carbon metabolism and nitrogen metabolism in WT and KO2 seedlings by Heat map. h, Browser representation of the m5C reads of RCA, PsbA, OsACS6, and PDIL1 detected in MeRIP-seq displaying by integrative genomics viewers (IGV) tracks. The red box marked with P1 and P2 represents the experimental verification regions. i, The relative RNA m5C level of RCA, PsbA, OsACS6, PDIL1, and Control detected by MeRIP-qPCR. j, RIP-qPCR showing that OsNOP2 bound to the RCA, PsbA, OsACS6, and PDIL1 by using anti-rabbit IgG and anti-OsNOP2 antibodies, respectively. k, The relative luciferase activity of RCA, PsbA, OsACS6, and PDIL1. l, Western blot analysis of the accumulation of RCA, PsbA, OsACS6, and PDIL1 of WT, KO1, and KO2 seedlings. The protein levels were normalized with HSP82 and imageJ was used for quantification. m, Schematic model summarizing the functions of OsNOP2 as an mRNA demethylase. Data are mean ± S.D.(i-l, n = 3 biological replicates). ns, no significance, *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001, ****P \u0026lt; 0.0001; P values are from two-way ANOVA (and nonparametric or mixed).\u003c/p\u003e","description":"","filename":"Fig.4.png","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/85cf97673d7646d289f285e1.png"},{"id":74203350,"identity":"9f3a2d44-b31a-490e-a54c-b79f516fcca4","added_by":"auto","created_at":"2025-01-20 02:56:18","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":1349050,"visible":true,"origin":"","legend":"\u003cp\u003eThe demethylase and yield regulation of OsNOP2 orthologs are conserved in different rice varieties, wheat and tomato. a, f, Detection of total RNA m5C level of flag leaves from rice of Longgeng 31 and Xiushui134 backgrounds by dot blot (top) and LC-MS/MS (bottom). b-c, Phenotype of single-plant (b) and panicle (c) from Longgeng 31 plants in Langfang in 2023. Scale bars, 20 cm (b) and 3 cm (top) and 1 cm (bottom) (c). d-e, Statistical analysis of the tiller numbers per plant (d) and grain yield per plant (e). g-h, Phenotype of single-plant (g) and panicle (h) from Xiushui134 plants in Langfang in 2023. Scale bars, 20 cm (g) and 3 cm (top) and 1 cm (bottom) (h). i-j, Statistical analysis of the tiller numbers per plant (i) and grain yield per plant (j). k, Phenotype of single-plant from wheat. Sale bar, 20 cm. l-m, Statistical analysis of the tiller numbers per plant (l) and grain yield per plant (m). n, Detection of total RNA m5C level of flag leaves from wheat by dot blot (top) and LC-MS/MS (bottom). o, The relative RNA m5C level of Ta-RCA, Ta-PsbA, Ta-OsACS6, Ta-PDIL1, and Ta-Control detected by MeRIP-qPCR. p, Phenotype of single-plant (top) and total fruit from a single plant (bottom) from tomato. Sale bars, 20 cm (top) and 3 cm (bottom). q-r, Statistical analysis of fruit numbers per plant (q) and fresh weight per fruit (r). s, Detection of total RNA m5C level of flag leaves from tomato by dot blot (top) and LC-MS/MS (bottom). t, The relative RNA m5C level of Sl-RCA, Sl-PsbA, Sl-OsACS6, Sl-PDIL1, and Sl-Control detected by MeRIP-qPCR. Data are mean ± S.D. (a, f, n-o, and s-t, n = 3 biological replicates; d-e, n ≥ 10 plants; d-e, n ≥ 10 plants; i-j, n ≥ 15 plants; l-m, n = 7 plants; q, n = 5 plants; r, n = 8 fruits). ns, no significance, *P \u0026lt; 0.05, **P \u0026lt; 0.01, ***P \u0026lt; 0.001, ****P \u0026lt; 0.0001; In a, d-f, i-j, l-n, and q-s, P values are from one-way ANOVA (and nonparametric or mixed). In o, and t, P values are from two-way ANOVA (and nonparametric or mixed).\u003c/p\u003e","description":"","filename":"Fig.5.png","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/95b1ce78fe54927a8281d728.png"},{"id":89024857,"identity":"29db41bc-efd8-4c00-8594-2e04ddc03bd0","added_by":"auto","created_at":"2025-08-13 22:28:30","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1897965,"visible":true,"origin":"","legend":"Article File","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1_covered_977afa4d-fa92-491b-8541-59b3e5105167.pdf"},{"id":74204485,"identity":"1e5160ba-4bfd-416f-97d6-e146666fc49a","added_by":"auto","created_at":"2025-01-20 03:12:18","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1682218,"visible":true,"origin":"","legend":"Related Manuscript File","description":"","filename":"nreditorialpolicychecklist.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/13b9ca4f93fd77d9dadcd468.pdf"},{"id":74203668,"identity":"97fba37b-d768-46e3-a6eb-ceadee09d83f","added_by":"auto","created_at":"2025-01-20 03:04:18","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":1667252,"visible":true,"origin":"","legend":"Related Manuscript File","description":"","filename":"nrreportingsummary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/60ee69cb0eef1812b8fc0b59.pdf"},{"id":74203352,"identity":"7753d285-f71d-4ff6-8807-127e62366f54","added_by":"auto","created_at":"2025-01-20 02:56:18","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":3864183,"visible":true,"origin":"","legend":"Supplementary information","description":"","filename":"Supplementaryinformation.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5697502/v1/6263e3bb60fbcf5893624fee.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"\u003cp\u003eElevating RNA m\u003csup\u003e5\u003c/sup\u003eC methylation provides a promising strategy for crop productivity\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":false,"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":"","lastPublishedDoi":"10.21203/rs.3.rs-5697502/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5697502/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eRNA 5-methylcytidine (m5C) has been identified as a key epi-transcriptomic modification of mRNAs involved in regulating multiple post-transcriptional processes. Here, we found that knockout of the RNA m5C demethylase, OsNOP2, results in elevated m5C levels and positively influences numerous agronomic traits in rice. After verifying OsNOP2 RNA m5C demethylase function in vitro and in planta, we found that enhanced m5C levels arising from OsNOP2 knockout results in increased translation, particularly for transcripts involved in carbon assimilation and nitrogen metabolism. OsNOP2-KO boosts grain yield ~28% per plot in the Nipponbare genetic background in normal condition and maintains increased yield traits under both heat treatment and saline soil conditions. More importantly, knockout of OsNOP2 in the rice varieties Longgeng31 and Xiushui134, as well as its orthologs in wheat and tomato, also increases the RNA m5C level to enhance yield, supporting functional conservation of OsNOP2's regulatory impacts. Together, our findings unveil an RNA m5C elevating mechanism by OsNOP2 that epigenetically governs carbon assimilation and nitrogen utilization efficiency in plant, providing a potential strategy for genetic improvement in multiple crops.\u003c/p\u003e","manuscriptTitle":"Elevating RNA m5C methylation provides a promising strategy for crop productivity","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-01-20 02:56:13","doi":"10.21203/rs.3.rs-5697502/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"
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