Identification and analysis of mouse non-coding RNA using transcriptome data
Identification and analysis of mouse non-coding RNA using transcriptome data
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利用转录组数据鉴定和分析小鼠非编码RNA
DOI：
10.1007/s11427-015-4929-x
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发表时间：
2016-06-01
影响因子：
9.1
通讯作者：
Hu，Songnian
中科院分区：
文献类型：
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作者：
Zhao，Yuhui;Liu，Wanfei;Hu，Songnian
转录本的表达具有空间性和时间性，非常复杂、精确和具体；然而，大多数研究都集中在蛋白质编码相关基因上。近年来，大规模平行cDNA测序（RNA-seq）已成为转录组研究的一种新的有前途的工具，许多非编码rna，特别是lincRNAs，已被广泛鉴定并被充分表征为多种生物过程的重要调节因子。在本研究中，我们使用来自15只小鼠组织的超深RNA-seq数据来研究小鼠非编码rna的多样性和动态。利用我们自己的标准，我们在小鼠中共鉴定出16,249个非编码基因（21,569个非编码rna）。我们对这些非编码rna进行了不同性质的注释，发现与蛋白质编码基因相比，非编码rna通常更短，外显子更少，表达水平更低，具有更显著的组织特异性。此外，这些非编码rna表现出转录起始和延伸信号的显著富集，包括组蛋白修饰（H3K4me3、H3K27me3和H3K36me3）、RNAPII结合位点和CAGE标签。基因集富集分析（GSEA）结果揭示了与免疫效应过程、肌肉发育和有性生殖等多种生物过程相关的几组lincRNAs。综上所述，本研究为小鼠非编码rna提供了更全面的注释，为未来小鼠非编码rna的功能和进化研究提供了机会。
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.