A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

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

	A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)
	Yang, Liandong 1,2; He, Shunping 1
刊名	GENE
	2014
卷号	533 期号:1 页码:261-269
关键词	Rainbow trout Comparative genomics MicroRNAs Targets
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.
中文摘要	MicroRNAs (miRNAs) participate in various vitally biological processes via controlling target genes activity and thousands of miRNAs have been identified in many species to date, including 18,698 known animal miRNA in miRBase. However, there are only limited studies reported in rainbow trout (Oncorhynchus mykiss) especially via the computational-based approaches. In present study, we systematically investigated the miRNAs in rainbow trout using a well-developed comparative genome-based homologue search. A total of 196 potential miRNAs, belonging to 124 miRNA families, were identified, most of which were firstly reported in rainbow trout. The length of miRNAs ranged from 17 to 24 nt with an average of 20 nt while the length of their precursors varied from 47 to 152 nt with an average of 85 nt The identified miRNAs were not evenly distributed in each miRNA family, with only one member per family for a majority, and multiple members were also identified for several families. Nucleotide U was dominant in the pre-miRNAs with a percentage of 30.04%. The rainbow trout pre-miRNAs had relatively high negative minimal folding free energy (MFE) and adjusted MFE (AMFE). Not only the mature miRNAs but their precursor sequences are conserved among the living organisms. About 2466 O. mykiss genes were predicted as potential targets for 189 miRNAs. Gene Ontology (GO) analysis showed that nearly 2093, 2107, and 2081 target genes are involved in cellular component, molecular function, and biological processes respectively. KEGG pathway enrichment analysis illuminated that these miRNAs targets might regulate 105 metabolic pathways, including those of purine metabolism, nitrogen metabolism, and oxidative phosphorylation. This study has provided an update on rainbow trout miRNAs and their targets, which represents a foundation for future studies. Crown Copyright (C) 2013 Published by Elsevier B.V. All rights reserved.
英文摘要	MicroRNAs (miRNAs) participate in various vitally biological processes via controlling target genes activity and thousands of miRNAs have been identified in many species to date, including 18,698 known animal miRNA in miRBase. However, there are only limited studies reported in rainbow trout (Oncorhynchus mykiss) especially via the computational-based approaches. In present study, we systematically investigated the miRNAs in rainbow trout using a well-developed comparative genome-based homologue search. A total of 196 potential miRNAs, belonging to 124 miRNA families, were identified, most of which were firstly reported in rainbow trout. The length of miRNAs ranged from 17 to 24 nt with an average of 20 nt while the length of their precursors varied from 47 to 152 nt with an average of 85 nt The identified miRNAs were not evenly distributed in each miRNA family, with only one member per family for a majority, and multiple members were also identified for several families. Nucleotide U was dominant in the pre-miRNAs with a percentage of 30.04%. The rainbow trout pre-miRNAs had relatively high negative minimal folding free energy (MFE) and adjusted MFE (AMFE). Not only the mature miRNAs but their precursor sequences are conserved among the living organisms. About 2466 O. mykiss genes were predicted as potential targets for 189 miRNAs. Gene Ontology (GO) analysis showed that nearly 2093, 2107, and 2081 target genes are involved in cellular component, molecular function, and biological processes respectively. KEGG pathway enrichment analysis illuminated that these miRNAs targets might regulate 105 metabolic pathways, including those of purine metabolism, nitrogen metabolism, and oxidative phosphorylation. This study has provided an update on rainbow trout miRNAs and their targets, which represents a foundation for future studies. Crown Copyright (C) 2013 Published by 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]	CELL-CYCLE PROGRESSION ; PLANT MICRORNAS ; COMPUTATIONAL IDENTIFICATION ; ARABIDOPSIS-THALIANA ; GENES ; EXPRESSION ; SEQUENCE ; SEARCH ; MIRNAS ; MOUSE
收录类别	SCI
资助信息	National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049]
语种	英语
WOS记录号	WOS:000327562700035
公开日期	2014-01-23
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/19751]
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
推荐引用方式 GB/T 7714	Yang, Liandong,He, Shunping. A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)[J]. GENE,2014,533(1):261-269.
APA	Yang, Liandong,&He, Shunping.(2014).A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss).GENE,533(1),261-269.
MLA	Yang, Liandong,et al."A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)".GENE 533.1(2014):261-269.