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Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish
Yang, Liandong1,2; Irwin, David M.3,4; He, Shunping1; He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
2015-05-01
Source PublicationGENE
ISSN0378-1119
Volume561Issue:2Pages:181-189
AbstractThe 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.
SubtypeArticle
KeywordTeleost Microrna Comparative Genomics Zebrafish Embryogenesis
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 ; [Irwin, David M.] Univ Toronto, Dept Lab Med & PathoBiol, Toronto, ON M5S 1A1, Canada ; [Irwin, David M.] Univ Toronto, Banting & Best Diabet Ctr, Toronto, ON M5S 1A1, Canada
DOI10.1016/j.gene.2015.02.055
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS KeywordRNA-SEQ ; TARGET RECOGNITION ; EVOLUTIONARY RATES ; ANIMAL DEVELOPMENT ; NONCODING RNAS ; GENE LOSS ; DUPLICATION ; FISH ; DIVERSIFICATION ; ANNOTATION
WOS IDWOS:000351802100002
Citation statistics
Cited Times:8[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/23832
Collection水生生物多样性与资源保护研究中心
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
3.Univ Toronto, Dept Lab Med & PathoBiol, Toronto, ON M5S 1A1, Canada
4.Univ Toronto, Banting & Best Diabet Ctr, Toronto, ON M5S 1A1, Canada
Recommended Citation
GB/T 7714
Yang, Liandong,Irwin, David M.,He, Shunping,et al. 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,&He, SP .(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.
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