Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse
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- dc.contributor.author Bogu, Gireesh K., 1984-ca
- dc.contributor.author Vizán, Pedroca
- dc.contributor.author Stanton, Lawrence W.ca
- dc.contributor.author Beato, Miguelca
- dc.contributor.author Di Croce, Lucianoca
- dc.contributor.author Marti-Renom, Marc A.ca
- dc.date.accessioned 2017-11-29T09:15:31Z
- dc.date.available 2017-11-29T09:15:31Z
- dc.date.issued 2015
- dc.description.abstract Discovering and classifying long noncoding RNAs (lncRNAs) across all mammalian tissues and cell lines remains a major challenge. Previously, mouse lncRNAs were identified using transcriptome sequencing (RNA-seq) data from a limited number of tissues or cell lines. Additionally, associating a few hundred lncRNA promoters with chromatin states in a single mouse cell line has identified two classes of chromatin-associated lncRNA. However, the discovery and classification of lncRNAs is still pending in many other tissues in mouse. To address this, we built a comprehensive catalog of lncRNAs by combining known lncRNAs with high-confidence novel lncRNAs identified by mapping and de novo assembling billions of RNA-seq reads from eight tissues and a primary cell line in mouse. Next, we integrated this catalog of lncRNAs with multiple genome-wide chromatin state maps and found two different classes of chromatin state-associated lncRNAs, including promoter-associated (plncRNAs) and enhancer-associated (elncRNAs) lncRNAs, across various tissues. Experimental knockdown of an elncRNA resulted in the downregulation of the neighboring protein-coding Kdm8 gene, encoding a histone demethylase. Our findings provide 2,803 novel lncRNAs and a comprehensive catalog of chromatin-associated lncRNAs across different tissues in mouse.
- dc.description.sponsorship This work was supported by the Spanish MINECO BFU2010-19310, BFU2013-47736-P, Spanish MINECO SAF2013-48926-P, Centro de Excelencia Severo Ochoa 2013-2017SEV-2012-0208
- dc.format.mimetype application/pdfca
- dc.identifier.citation Bogu GK, Vizán P, Stanton LW, Beato M, Di Croce L, Marti-Renom MA et al. Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse. Mol Cell Biol. 2015 Dec 28;36(5):809-19. DOI: 10.1128/MCB.00955-15
- dc.identifier.doi http://dx.doi.org/10.1128/MCB.00955-15
- dc.identifier.issn 0270-7306
- dc.identifier.uri http://hdl.handle.net/10230/33404
- dc.language.iso eng
- dc.publisher American Society for Microbiologyca
- dc.relation.ispartof Molecular and Cellular Biology. 2015 Dec 28;36(5):809-19
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2010-19310
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2013-47736-P
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2013-48926-P
- dc.rights © American Society for Microbiology
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.subject.other Cromatina -- Genètica
- dc.subject.other Ratolins (Animals de laboratori) -- Genètica
- dc.subject.other RNA
- dc.title Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouseca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/acceptedVersion