title: Identification and analysis of mouse non-coding RNA using transcriptome data.
abstract: Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel cDNA sequencing (RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially lincRNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes (21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications (H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis (GSEA) result revealed several sets of lincRNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Yuhui
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.|Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Riyadh, 11442, Saudi Arabia.
authors.forename: Wanfei
authors.initials: W
authors.lastname: Liu
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Jingyao
authors.initials: J
authors.lastname: Zeng
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Shoucheng
authors.initials: S
authors.lastname: Liu
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Tan
authors.affiliation: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Riyadh, 11442, Saudi Arabia.
authors.forename: Hasanawad
authors.initials: H
authors.lastname: Aljohi
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. husn@big.ac.cn.
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
mesh_terms: D000818:Animals; D015870:Gene Expression; D051379:Mice; D022661:RNA, Untranslated / Q000032:analysis* / Q000235:genetics; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D022661:RNA, Untranslated
keywords: RNA-seq; lincRNA; mouse; non-coding RNA; transcriptome