Systematic characterization of the composition and dynamics of processing body-associated mRNAs

Systematic characterization of the composition and dynamics of processing body-associated mRNAs | 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 Systematic characterization of the composition and dynamics of processing body-associated mRNAs Wei Chen, Zhiyuan Sun, Xiaozhen Wen, Yanping Li, Xiaoxin Xie, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5354706/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Processing bodies (PBs) are dynamic, membraneless organelles consisting of RNAs and proteins. While PB proteins have been extensively characterized, the methods for systematically profiling PB-associated RNAs are limited. To address this, we developed PB-TRIBE-STAMP, a new tool based on two orthogonal RNA editing enzymes. Simultaneously applying APOBEC1-DDX6 and LSM14A-ADAR2dd, PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively. Further genetic perturbation demonstrated that these transcripts were translationally repressed by PBs. Integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails. Moreover, we established a TRIBE-ID-based tool to characterize the mRNA-PB association at high temporal resolution and unveiled a higher splicing efficiency of PB-associated XBP1 transcripts during unfolded protein response (UPR). Finally, based on single-cell LSM14A-TRIBE-ID (sc-LSM14A-TRIBE-ID), we demonstrated the dynamic pattern of mRNA-PB association during cell cycle progression. Biological sciences/Molecular biology/RNA metabolism Biological sciences/Systems biology Biological sciences/Cell biology/Organelles Biological sciences/Biological techniques/High-throughput screening Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryTables.zip Supplementary Table 1-10 ExtendedDataFigures.pdf Cite Share Download PDF Status: Published Journal Publication published 10 Nov, 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-5354706","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":385616009,"identity":"b9163c35-a884-4f43-8dce-8284cd48260a","order_by":0,"name":"Wei Chen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1klEQVRIiWNgGAWjYDACCRBRAWEzAzFjA3FazgAxG0laGNtI0cI/u/nYY955dYnz5zcf/FzAYCO74QDzswd4LblzLN2Yd9vhxA3H2JKlZzCkGW84wGZugE+LgUSOmXTutgOJG9h4zJh5GIB6D/CwSeDXkv9NOncO0GFt/N+AWv4ToyWHTTq3gTmx4RgPG1DLAcJaJG6kmUn/OXbYeMOxNGNpHoNk45mH2czwauGfkfxMckZNnez85sMPP/NU2Mn2HW9+hlcLujsZILEzCkbBKBgFo4AyAAARw0NjGZdoQQAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-3263-1627","institution":"Southern University of Science and Technology","correspondingAuthor":true,"prefix":"","firstName":"Wei","middleName":"","lastName":"Chen","suffix":""},{"id":385616010,"identity":"89ed79fe-7cd6-4a48-8528-3c61343f4fba","order_by":1,"name":"Zhiyuan Sun","email":"","orcid":"https://orcid.org/0000-0003-1779-9261","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Zhiyuan","middleName":"","lastName":"Sun","suffix":""},{"id":385616011,"identity":"687d7f76-e6d7-4e68-962f-a2a48265b857","order_by":2,"name":"Xiaozhen Wen","email":"","orcid":"https://orcid.org/0000-0002-0618-4571","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Xiaozhen","middleName":"","lastName":"Wen","suffix":""},{"id":385616012,"identity":"f7d5f6be-f9b0-4ad8-933f-1945a9835078","order_by":3,"name":"Yanping Li","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Yanping","middleName":"","lastName":"Li","suffix":""},{"id":385616013,"identity":"1e8e72c3-3ffe-4f02-a34f-4bb196cafb37","order_by":4,"name":"Xiaoxin Xie","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Xiaoxin","middleName":"","lastName":"Xie","suffix":""},{"id":385616014,"identity":"af14c019-edce-4ab1-a06d-ce8e6b2cafc1","order_by":5,"name":"Peng Dong","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Peng","middleName":"","lastName":"Dong","suffix":""},{"id":385616015,"identity":"0e7717c8-6de2-46ef-95c7-3c8a5a440c57","order_by":6,"name":"Yi Shu","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Yi","middleName":"","lastName":"Shu","suffix":""},{"id":385616016,"identity":"b2dedf51-638b-46c9-9963-bbce688701ab","order_by":7,"name":"Shuye Tian","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Shuye","middleName":"","lastName":"Tian","suffix":""},{"id":385616017,"identity":"83bffda9-75b6-44a4-99bd-5511a16d03d5","order_by":8,"name":"Jiao Yang","email":"","orcid":"","institution":"Department of Biology, Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Jiao","middleName":"","lastName":"Yang","suffix":""},{"id":385616018,"identity":"51a24bcf-dfa9-49d4-8f53-a47b70133f33","order_by":9,"name":"Yangfan Lin","email":"","orcid":"https://orcid.org/0009-0003-6551-8476","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Yangfan","middleName":"","lastName":"Lin","suffix":""},{"id":385616019,"identity":"5a09ff28-d28e-475e-8366-7a2640983b80","order_by":10,"name":"Mengran Wang","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Mengran","middleName":"","lastName":"Wang","suffix":""},{"id":385616020,"identity":"ee7066aa-53f6-46c3-ab05-2017b36f6f2f","order_by":11,"name":"Feifei Jiang","email":"","orcid":"","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Feifei","middleName":"","lastName":"Jiang","suffix":""},{"id":385616021,"identity":"4f282ec3-7b3d-410f-bb67-5107cfcb763d","order_by":12,"name":"Qionghua Zhu","email":"","orcid":"https://orcid.org/0000-0002-8057-202X","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Qionghua","middleName":"","lastName":"Zhu","suffix":""},{"id":385616022,"identity":"8eb29791-5fc9-4bf6-b2fd-cd4776206a48","order_by":13,"name":"Huanhuan Cui","email":"","orcid":"https://orcid.org/0000-0002-6190-6135","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Huanhuan","middleName":"","lastName":"Cui","suffix":""},{"id":385616023,"identity":"bb151ee6-148a-4cb2-a6a5-451250a2c423","order_by":14,"name":"Jixian Zhai","email":"","orcid":"https://orcid.org/0000-0002-0217-0666","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Jixian","middleName":"","lastName":"Zhai","suffix":""},{"id":385616024,"identity":"46549529-6190-478d-a070-860ddd480216","order_by":15,"name":"Yuhui Hu","email":"","orcid":"https://orcid.org/0000-0002-5210-5301","institution":"Southern University of Science and Technology, China","correspondingAuthor":false,"prefix":"","firstName":"Yuhui","middleName":"","lastName":"Hu","suffix":""},{"id":385616025,"identity":"9c26140b-c964-4161-a6d8-2c2df2e2e639","order_by":16,"name":"Liang Fang","email":"","orcid":"https://orcid.org/0000-0003-4502-1756","institution":"Southern University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Liang","middleName":"","lastName":"Fang","suffix":""}],"badges":[],"createdAt":"2024-10-29 13:35:46","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5354706/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5354706/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-025-64848-3","type":"published","date":"2025-11-10T05:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":95611295,"identity":"2387effc-bbc1-4e3d-a0a3-e90fe42fe2b7","added_by":"auto","created_at":"2025-11-11 08:08:01","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1799929,"visible":true,"origin":"","legend":"Article File","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5354706/v1_covered_e42b4622-d203-46f3-9f46-1314fec00372.pdf"},{"id":70618084,"identity":"546c3683-d401-4f8f-bf66-1fc12cd3ae2c","added_by":"auto","created_at":"2024-12-05 02:35:37","extension":"zip","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":94834116,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 1-10\u003c/p\u003e","description":"","filename":"SupplementaryTables.zip","url":"https://assets-eu.researchsquare.com/files/rs-5354706/v1/ae73a8c2b4a439b800cc1feb.zip"},{"id":70619262,"identity":"e96d0ffd-1a32-49f5-a44e-cb23d9e07153","added_by":"auto","created_at":"2024-12-05 02:51:32","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":4172583,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cbr\u003e\u003c/p\u003e","description":"","filename":"ExtendedDataFigures.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5354706/v1/2057eddb16be30a4ca7b8851.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Systematic characterization of the composition and dynamics of processing body-associated mRNAs","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":"","lastPublishedDoi":"10.21203/rs.3.rs-5354706/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5354706/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Processing bodies (PBs) are dynamic, membraneless organelles consisting of RNAs and proteins. While PB proteins have been extensively characterized, the methods for systematically profiling PB-associated RNAs are limited. To address this, we developed PB-TRIBE-STAMP, a new tool based on two orthogonal RNA editing enzymes. Simultaneously applying APOBEC1-DDX6 and LSM14A-ADAR2dd, PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively. Further genetic perturbation demonstrated that these transcripts were translationally repressed by PBs. Integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails. Moreover, we established a TRIBE-ID-based tool to characterize the mRNA-PB association at high temporal resolution and unveiled a higher splicing efficiency of PB-associated XBP1 transcripts during unfolded protein response (UPR). Finally, based on single-cell LSM14A-TRIBE-ID (sc-LSM14A-TRIBE-ID), we demonstrated the dynamic pattern of mRNA-PB association during cell cycle progression.","manuscriptTitle":"Systematic characterization of the composition and dynamics of processing body-associated mRNAs","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-12-05 02:35:27","doi":"10.21203/rs.3.rs-5354706/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":"99d55d60-ddc2-42db-a91f-47500e887448","owner":[],"postedDate":"December 5th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":41080938,"name":"Biological sciences/Molecular biology/RNA metabolism"},{"id":41080939,"name":"Biological sciences/Systems biology"},{"id":41080940,"name":"Biological sciences/Cell biology/Organelles"},{"id":41080941,"name":"Biological sciences/Biological techniques/High-throughput screening"}],"tags":[],"updatedAt":"2025-11-11T08:07:50+00:00","versionOfRecord":{"articleIdentity":"rs-5354706","link":"https://doi.org/10.1038/s41467-025-64848-3","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2025-11-10 05:00:00","publishedOnDateReadable":"November 10th, 2025"},"versionCreatedAt":"2024-12-05 02:35:27","video":"","vorDoi":"10.1038/s41467-025-64848-3","vorDoiUrl":"https://doi.org/10.1038/s41467-025-64848-3","workflowStages":[]},"version":"v1","identity":"rs-5354706","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5354706","identity":"rs-5354706","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}