The landscape of RNA-chromatin interaction reveals essential small non-coding RNAs as essential mediators of leukemia maintenance

The landscape of RNA-chromatin interaction reveals essential small non-coding RNAs as essential mediators of leukemia maintenance | 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 landscape of RNA-chromatin interaction reveals essential small non-coding RNAs as essential mediators of leukemia maintenance Carsten Müller-Tidow, Haiyang Yun, Julian Zoller, Fengbiao Zhou, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3715282/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 28 Jun, 2024 Read the published version in Leukemia → Version 1 posted 10 You are reading this latest preprint version Abstract RNA constitutes a large fraction of chromatin. Spatial distribution and functional relevance of RNA associating with chromatin remain largely elusive. We established a landscape analysis of RNA-chromatin interactions in human acute myeloid leukemia (AML). In total more than 50 million interactions were captured in an AML cell line. Protein-coding mRNAs and long non-coding RNAs (lncRNAs) exhibited a substantial number of cis -interactions with chromatin suggesting transcriptional activity. In contrast, small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs) associated with chromatin predominantly in trans indicating chromatin specific functions. Of note, snoRNA-chromatin interaction associates with chromatin modification and is independent of the classical snoRNA-RNP complexes. Two non-canonical C/D box snoRNAs, namely SNORD118 and SNORD3A , displayed high frequency of trans -association with chromatin. The transcription of SNORD118 and SNORD3A was increased upon leukemia transformation and enriched in leukemia stem cells, but decreased during myeloid differentiation. Suppression of SNORD118 and SNORD3A impaired leukemia cell proliferation and colony forming capacity in AML cells, but had minimal impact on healthy CD34+ hematopoietic stem and progenitor cells (HSPCs). These findings highlight the functional importance of chromatin-associated RNAs overall and in particular of SNORD118 and SNORD3A in maintaining leukemia propagation. Health sciences/Diseases/Haematological diseases/Haematological cancer/Leukaemia/Acute myeloid leukaemia Biological sciences/Genetics/Cancer genetics/Cancer epigenetics Full Text Additional Declarations There is NO conflict of interest to disclose. Supplementary Files Yunetal.SupplementaryTable1.xlsx Supplementary Table 1. Chromatin interactions associated with snRNAs and snoRNAs Yunetal.SupplementaryTable2.xlsx Supplementary Table 2. Trans-acting snRNAs and snoRNAs Yunetal.SupplementaryTable3.xlsx Supplementary Table 3. Chromatin regions associated with U1, SNORD3A, and SNORD118 revealed by ChIRP Yunetal.SupplementaryTable4.xlsx Supplementary Table 4. Active chromatin regions (C1) of snoRNA-chromatin interaction sites Yunetal.SupplementaryTable5.xlsx Supplementary Table 5. Fibrillarin-bound sites across genome in MV4-11 (shCtrl) cellsSupplementary Table 5. Yunetal.SupplementaryTable6.xlsx Supplementary Table 6. Normalized RNA-seq reads (in RPM) of SNORD118 and SNORD3A in AML patients with low or high LSC frequency Yunetal.SupplementaryTable7.xlsx Supplementary Table 7. Sequences of oligonucleotide used in this study Cite Share Download PDF Status: Published Journal Publication published 28 Jun, 2024 Read the published version in Leukemia → Version 1 posted Editorial decision: revise 12 Jan, 2024 Review # 2 received at journal 11 Jan, 2024 Review # 1 received at journal 02 Jan, 2024 Reviewer # 2 agreed at journal 28 Dec, 2023 Reviewer # 1 agreed at journal 27 Dec, 2023 Reviewers invited by journal 27 Dec, 2023 Editor assigned by journal 08 Dec, 2023 Submission checks completed at journal 08 Dec, 2023 First submitted to journal 08 Dec, 2023 Unknown event 07 Dec, 2023 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. 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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-3715282","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":263819087,"identity":"2350219f-e87f-473e-b5d8-b9ec467f7a11","order_by":0,"name":"Carsten Müller-Tidow","email":"data:image/png;base64,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","orcid":"","institution":"Heidelberg University Hospital","correspondingAuthor":true,"prefix":"","firstName":"Carsten","middleName":"","lastName":"Müller-Tidow","suffix":""},{"id":263819088,"identity":"d6fb08a6-8b05-4c8f-b6b1-e0e3c39eafd6","order_by":1,"name":"Haiyang Yun","email":"","orcid":"","institution":"Heidelberg University Hospital","correspondingAuthor":false,"prefix":"","firstName":"Haiyang","middleName":"","lastName":"Yun","suffix":""},{"id":263819089,"identity":"3b902293-3580-4567-9395-fdf4e7724c83","order_by":2,"name":"Julian Zoller","email":"","orcid":"","institution":"Heidelberg University Hospital","correspondingAuthor":false,"prefix":"","firstName":"Julian","middleName":"","lastName":"Zoller","suffix":""},{"id":263819090,"identity":"e085088e-8ce7-4f73-bfb8-c04caf715820","order_by":3,"name":"Fengbiao Zhou","email":"","orcid":"https://orcid.org/0000-0002-9221-1096","institution":"University Hospital Heidelberg","correspondingAuthor":false,"prefix":"","firstName":"Fengbiao","middleName":"","lastName":"Zhou","suffix":""},{"id":263819091,"identity":"d09d4c09-3b2d-4fb0-ace8-0add179193a9","order_by":4,"name":"Christian Rohde","email":"","orcid":"","institution":"Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg","correspondingAuthor":false,"prefix":"","firstName":"Christian","middleName":"","lastName":"Rohde","suffix":""},{"id":263819092,"identity":"c908b686-fc66-4fbe-b8e4-65867cb7df33","order_by":5,"name":"Yi Liu","email":"","orcid":"","institution":"University Hospital Heidelberg","correspondingAuthor":false,"prefix":"","firstName":"Yi","middleName":"","lastName":"Liu","suffix":""},{"id":263819093,"identity":"ac16a140-4ea5-40a8-bea5-adcba58165bc","order_by":6,"name":"Maximilian Blank","email":"","orcid":"https://orcid.org/0000-0002-7524-4080","institution":"University Hospital Heidelberg","correspondingAuthor":false,"prefix":"","firstName":"Maximilian","middleName":"","lastName":"Blank","suffix":""},{"id":263819094,"identity":"69f3dbfc-e087-41b0-af20-98322eaf7940","order_by":7,"name":"Stefanie Göllner","email":"","orcid":"","institution":"Heidelberg University Hospital","correspondingAuthor":false,"prefix":"","firstName":"Stefanie","middleName":"","lastName":"Göllner","suffix":""}],"badges":[],"createdAt":"2023-12-06 13:40:54","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3715282/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3715282/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41375-024-02322-7","type":"published","date":"2024-06-28T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":59310913,"identity":"ae7e04d1-81b6-4aae-b63d-c5714d389dcc","added_by":"auto","created_at":"2024-06-29 07:06:52","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4651129,"visible":true,"origin":"","legend":"","description":"","filename":"Yunetal.Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1_covered_6df7db28-11c2-41d0-884f-2f21182ad363.pdf"},{"id":49020633,"identity":"a7b47645-cb26-465b-b97f-82a4527819c4","added_by":"auto","created_at":"2024-01-01 08:51:53","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":3856513,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 1. Chromatin interactions associated with snRNAs and snoRNAs\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/84395372a3af2190851b8a23.xlsx"},{"id":49020631,"identity":"3c92e771-254f-4806-8936-d527810684eb","added_by":"auto","created_at":"2024-01-01 08:51:53","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":17047,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 2. Trans-acting snRNAs and snoRNAs\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/09202859452f7a47c18756f6.xlsx"},{"id":49020728,"identity":"f363520c-962b-4392-84b7-d68f2679cc0e","added_by":"auto","created_at":"2024-01-01 08:59:53","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":153847,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 3. Chromatin regions associated with U1, SNORD3A, and SNORD118 revealed by ChIRP\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable3.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/2fd536a60fb160e5ebce23b0.xlsx"},{"id":49020635,"identity":"c4e9f6a4-4421-4ca1-86ef-53172e576418","added_by":"auto","created_at":"2024-01-01 08:51:53","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":12227,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 4. Active chromatin regions (C1) of snoRNA-chromatin interaction sites\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable4.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/1854fad5f03b16d8cbbfcaf2.xlsx"},{"id":49020632,"identity":"02af34ac-a4c3-49a6-ab17-3ba127cf67da","added_by":"auto","created_at":"2024-01-01 08:51:53","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":29769,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 5. Fibrillarin-bound sites across genome in MV4-11 (shCtrl) cellsSupplementary Table 5.\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable5.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/e0932bedaec4c0f71a40d3d0.xlsx"},{"id":49020727,"identity":"72161497-511e-4dcf-8112-33cf44d8d10f","added_by":"auto","created_at":"2024-01-01 08:59:53","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":31376,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 6. Normalized RNA-seq reads (in RPM) of SNORD118 and SNORD3A in AML patients with low or high LSC frequency\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable6.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/f45bf33e10b61cca70dffe3c.xlsx"},{"id":49020629,"identity":"1caee229-4cad-4a1a-96b2-b0a402126adb","added_by":"auto","created_at":"2024-01-01 08:51:53","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":10253,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 7. Sequences of oligonucleotide used in this study\u003c/p\u003e","description":"","filename":"Yunetal.SupplementaryTable7.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-3715282/v1/074332674654a6c9e5f18384.xlsx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e conflict of interest to disclose.","formattedTitle":"The landscape of RNA-chromatin interaction reveals essential small non-coding RNAs as essential mediators of leukemia maintenance","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"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":"leukemia","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"leu","sideBox":"Learn more about [Leukemia](http://www.nature.com/leu/)","snPcode":"41375","submissionUrl":"https://mts-leu.nature.com/cgi-bin/main.plex","title":"Leukemia","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-3715282/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3715282/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eRNA constitutes a large fraction of chromatin. Spatial distribution and functional relevance of RNA associating with chromatin remain largely elusive. We established a landscape analysis of RNA-chromatin interactions in human acute myeloid leukemia (AML). In total more than 50 million interactions were captured in an AML cell line. Protein-coding mRNAs and long non-coding RNAs (lncRNAs) exhibited a substantial number of \u003cem\u003ecis\u003c/em\u003e-interactions with chromatin suggesting transcriptional activity. In contrast, small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs) associated with chromatin predominantly in trans indicating chromatin specific functions. Of note, snoRNA-chromatin interaction associates with chromatin modification and is independent of the classical snoRNA-RNP complexes. Two non-canonical C/D box snoRNAs, namely \u003cem\u003eSNORD118 \u003c/em\u003eand \u003cem\u003eSNORD3A\u003c/em\u003e, displayed high frequency of \u003cem\u003etrans\u003c/em\u003e-association with chromatin. The transcription of \u003cem\u003eSNORD118 \u003c/em\u003eand \u003cem\u003eSNORD3A \u003c/em\u003ewas increased upon leukemia transformation and enriched in leukemia stem cells, but decreased during myeloid differentiation. Suppression of \u003cem\u003eSNORD118 \u003c/em\u003eand \u003cem\u003eSNORD3A \u003c/em\u003eimpaired leukemia cell proliferation and colony forming capacity in AML cells, but had minimal impact on healthy CD34+ hematopoietic stem and progenitor cells (HSPCs). These findings highlight the functional importance of chromatin-associated RNAs overall and in particular of \u003cem\u003eSNORD118 \u003c/em\u003eand \u003cem\u003eSNORD3A \u003c/em\u003ein maintaining leukemia propagation.\u003c/p\u003e","manuscriptTitle":"The landscape of RNA-chromatin interaction reveals essential small non-coding RNAs as essential mediators of leukemia maintenance","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-01-01 08:51:48","doi":"10.21203/rs.3.rs-3715282/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"revise","date":"2024-01-12T12:29:48+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"This content is not available.","date":"2024-01-11T19:39:37+00:00","index":2,"fulltext":"This content is not available."},{"type":"editorInvitedReview","content":"This content is not available.","date":"2024-01-02T16:04:40+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2023-12-28T12:11:42+00:00","index":2,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2023-12-27T21:57:27+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewersInvited","content":"","date":"2023-12-27T21:56:33+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2023-12-08T14:16:04+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2023-12-08T14:15:56+00:00","index":"","fulltext":""},{"type":"submitted","content":"Leukemia","date":"2023-12-08T12:27:00+00:00","index":"","fulltext":""},{"type":"checksFailed","content":"","date":"2023-12-07T11:44:36+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"leukemia","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"leu","sideBox":"Learn more about [Leukemia](http://www.nature.com/leu/)","snPcode":"41375","submissionUrl":"https://mts-leu.nature.com/cgi-bin/main.plex","title":"Leukemia","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"96bce168-395e-4cd9-91ac-43031b64db9d","owner":[],"postedDate":"January 1st, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":27821815,"name":"Health sciences/Diseases/Haematological diseases/Haematological cancer/Leukaemia/Acute myeloid leukaemia"},{"id":27821816,"name":"Biological sciences/Genetics/Cancer genetics/Cancer epigenetics"}],"tags":[],"updatedAt":"2024-06-29T07:06:42+00:00","versionOfRecord":{"articleIdentity":"rs-3715282","link":"https://doi.org/10.1038/s41375-024-02322-7","journal":{"identity":"leukemia","isVorOnly":false,"title":"Leukemia"},"publishedOn":"2024-06-28 04:00:00","publishedOnDateReadable":"June 28th, 2024"},"versionCreatedAt":"2024-01-01 08:51:48","video":"","vorDoi":"10.1038/s41375-024-02322-7","vorDoiUrl":"https://doi.org/10.1038/s41375-024-02322-7","workflowStages":[]},"version":"v1","identity":"rs-3715282","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3715282","identity":"rs-3715282","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}