Evolutionary annotation of conserved long non-coding RNAs in major mammalian species

doi:10.1007/s11427-015-4881-9

	Evolutionary annotation of conserved long non-coding RNAs in major mammalian species
	Bu DeChao 1,2; Luo HaiTao 1,2; Jiao Fei 3; Fang ShuangSang 1,2; Tan ChengFu 1,2; Liu ZhiYong 1; Zhao Yi 1
	2015-08-01
发表期刊	SCIENCE CHINA-LIFE SCIENCES
ISSN	1674-7305
卷号	58 期号:8 页码:787-798
摘要	Mammalian genomes contain tens of thousands of long non-coding RNAs (lncRNAs) that have been implicated in diverse biological processes. However, the lncRNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lncRNA catalogs (4,142-42,558 lncRNAs) covering the major mammalian species. Compared to protein- coding RNAs, expression of lncRNAs exhibits striking lineage specificity. Notably, although 30%-99% human lncRNAs are conserved across different species on DNA locus level, only 20%-27% of these conserved lncRNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes (48%-80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lncRNAs. Moreover, we constructed lncRNA expression phylogenetic trees across nine mammals and demonstrated that lncRNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lncRNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lncRNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named PhyloNONCODE (http://www.bioinfo.org/phyloNoncode). Our work starts to place mammalian lncRNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.
关键词	lncRNA conservation evolution
DOI	10.1007/s11427-015-4881-9
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[91229120]
WOS研究方向	Life Sciences & Biomedicine - Other Topics
WOS类目	Biology
WOS记录号	WOS:000359146800008
出版者	SCIENCE PRESS
引用统计	被引频次：28[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/9509
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhao Yi
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Binzhou Med Coll, Dept Biochem & Mol Biol, Yantai 264003, Peoples R China
推荐引用方式 GB/T 7714	Bu DeChao,Luo HaiTao,Jiao Fei,et al. Evolutionary annotation of conserved long non-coding RNAs in major mammalian species[J]. SCIENCE CHINA-LIFE SCIENCES,2015,58(8):787-798.
APA	Bu DeChao.,Luo HaiTao.,Jiao Fei.,Fang ShuangSang.,Tan ChengFu.,...&Zhao Yi.(2015).Evolutionary annotation of conserved long non-coding RNAs in major mammalian species.SCIENCE CHINA-LIFE SCIENCES,58(8),787-798.
MLA	Bu DeChao,et al."Evolutionary annotation of conserved long non-coding RNAs in major mammalian species".SCIENCE CHINA-LIFE SCIENCES 58.8(2015):787-798.