Bogu, Gireesh K., 1984-Vizán, PedroStanton, Lawrence W.Beato, MiguelDi Croce, LucianoMarti-Renom, Marc A.2017-11-292017-11-292015Bogu 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.00955-150270-7306http://hdl.handle.net/10230/33404Discovering 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.application/pdfeng© American Society for MicrobiologyCromatina -- GenèticaRatolins (Animals de laboratori) -- GenèticaRNAinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1128/MCB.00955-15info:eu-repo/semantics/openAccess