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题名: A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)
作者: Yang, Liandong1, 2; He, Shunping1
通讯作者: He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
关键词: Rainbow trout ; Comparative genomics ; MicroRNAs ; Targets
刊名: GENE
发表日期: 2014
DOI: 10.1016/j.gene.2013.09.060
卷: 533, 期:1, 页:261-269
收录类别: SCI
文章类型: Article
部门归属: [Yang, Liandong ; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China ; [Yang, Liandong] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
资助者: National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049]
类目[WOS]: Genetics & Heredity
研究领域[WOS]: Genetics & Heredity
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.
关键词[WOS]: CELL-CYCLE PROGRESSION ; PLANT MICRORNAS ; COMPUTATIONAL IDENTIFICATION ; ARABIDOPSIS-THALIANA ; GENES ; EXPRESSION ; SEQUENCE ; SEARCH ; MIRNAS ; MOUSE
语种: 英语
WOS记录号: WOS:000327562700035
ISSN号: 0378-1119
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/19751
Appears in Collections:水生生物多样性与资源保护研究中心_期刊论文

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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

Recommended Citation:
Yang, Liandong; He, Shunping.A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss),GENE,2014,533(1):261-269
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