Título:
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Chromatin and RNA maps reveal regulatory long noncoding RNAs in mouse
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Autor/a:
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Bogu, Gireesh K., 1984-; Vizán, Pedro; Stanton, Lawrence W.; Beato, Miguel; Di Croce, Luciano; Marti-Renom, Marc A.
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Abstract:
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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. |
Abstract:
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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 |
Materia(s):
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-Cromatina -- Genètica -Ratolins (Animals de laboratori) -- Genètica -RNA |
Derechos:
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© American Society for Microbiology
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Tipo de documento:
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Artículo Artículo - Versión aceptada |
Editor:
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American Society for Microbiology
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