title: Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.
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.
authors.affiliation: CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Bioinformatics and Genomics Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain gireesh.bogu@crg.eu martirenom@cnag.crg.eu.
authors.forename: Gireesh K
authors.initials: GK
authors.lastname: Bogu
authors.affiliation: Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Vizán
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore, Singapore Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Singapore, Singapore.
authors.forename: Lawrence W
authors.initials: LW
authors.lastname: Stanton
authors.affiliation: Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Beato
authors.affiliation: Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
authors.forename: Luciano
authors.initials: L
authors.lastname: Di Croce
authors.affiliation: CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain gireesh.bogu@crg.eu martirenom@cnag.crg.eu.
authors.forename: Marc A
authors.identifier: http://orcid.org/0000-0002-0151-4279
authors.initials: MA
authors.lastname: Marti-Renom
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D051379:Mice / Q000235:genetics*; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding