Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish

CORC > 水生生物研究所 > 中科院水生所知识产出（2009年前） > 水生生物多样性与资源保护研究中心 > 期刊论文

	Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish
	Yang, Liandong 1,2; Irwin, David M.3,4; He, Shunping 1
刊名	GENE
	2015-05-01
卷号	561 期号:2 页码:181-189
关键词	Teleost MicroRNA Comparative genomics Zebrafish embryogenesis
ISSN号	0378-1119
通讯作者	He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
英文摘要	The molecular genetic basis of teleost phenotypic diversity remains poorly understood, despite the increasing availability of genome and transcriptome data. Changes in gene expression, resulting from regulatory mutations, contribute to many or even most phenotypic innovations. In this study, we performed comparative genomic analyses to identify 44 Conserved Teleost-Specific MicroRNAs (CTSMs). An analysis of the sequences of CTSMs demonstrated that their sequence variability is significantly higher than that of Evolutionarily Conserved microRNAs (ECs - microRNAs conserved throughout vertebrates), and that this difference primarily results from variation in the loop regions. We computationally predicted target genes for CTSMs and found that the targets of CTSMs show significantly lower SNP density compared with targets of ECs as well as non-targets of CTSMs. The temporal expression profile of targets of CTSMs obtained from RNA-seq data revealed that the targets of CTSMs are specifically enriched in early-stage embryos and exhibit a broader expression spectrum. Finally, functional enrichment analysis (GO and KEGG) indicated that the targets of CTSMs play diverse functional roles, with a significantly enriched category being the "immune response". Our study provides the first systematic identification and characterization of conserved teleost-specific microRNAs and their targets and presents valuable foundation for a better understanding the genomic basis for the diversification of teleosts. (C) 2015 Elsevier B.V. All rights reserved.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Genetics & Heredity
研究领域[WOS]	Genetics & Heredity
关键词[WOS]	RNA-SEQ ; TARGET RECOGNITION ; EVOLUTIONARY RATES ; ANIMAL DEVELOPMENT ; NONCODING RNAS ; GENE LOSS ; DUPLICATION ; FISH ; DIVERSIFICATION ; ANNOTATION
收录类别	SCI
语种	英语
WOS记录号	WOS:000351802100002
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/23832]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
作者单位	1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Univ Toronto, Dept Lab Med & PathoBiol, Toronto, ON M5S 1A1, Canada 4.Univ Toronto, Banting & Best Diabet Ctr, Toronto, ON M5S 1A1, Canada
推荐引用方式 GB/T 7714	Yang, Liandong,Irwin, David M.,He, Shunping. Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish[J]. GENE,2015,561(2):181-189.
APA	Yang, Liandong,Irwin, David M.,&He, Shunping.(2015).Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish.GENE,561(2),181-189.
MLA	Yang, Liandong,et al."Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish".GENE 561.2(2015):181-189.