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A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)
Yang, Liandong1,2; He, Shunping1; He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
2014
Source PublicationGENE
ISSN0378-1119
Volume533Issue:1Pages:261-269
AbstractMicroRNAs (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.; 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.
SubtypeArticle
KeywordRainbow Trout Comparative Genomics Micrornas Targets
Department[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
DOI10.1016/j.gene.2013.09.060
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049] ; National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049] ; National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049] ; National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049]
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000327562700035
WOS KeywordCELL-CYCLE PROGRESSION ; PLANT MICRORNAS ; COMPUTATIONAL IDENTIFICATION ; ARABIDOPSIS-THALIANA ; GENES ; EXPRESSION ; SEQUENCE ; SEARCH ; MIRNAS ; MOUSE
Funding OrganizationNational Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049] ; National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049] ; National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049] ; National Natural Science Foundation of China [91131014]; State Key Program of National Natural Science of China [31130049]
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/19751
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorHe, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
Affiliation1.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
GB/T 7714
Yang, Liandong,He, Shunping,He, SP . 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,&He, SP .(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.
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