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题名: Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish
作者: Yang, Liandong1, 2; Irwin, David M.3, 4; 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: Teleost ; MicroRNA ; Comparative genomics ; Zebrafish embryogenesis
刊名: GENE
发表日期: 2015-05-01
DOI: 10.1016/j.gene.2015.02.055
卷: 561, 期:2, 页:181-189
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 ; [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
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
类目[WOS]: Genetics & Heredity
研究领域[WOS]: Genetics & Heredity
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.
关键词[WOS]: RNA-SEQ ; TARGET RECOGNITION ; EVOLUTIONARY RATES ; ANIMAL DEVELOPMENT ; NONCODING RNAS ; GENE LOSS ; DUPLICATION ; FISH ; DIVERSIFICATION ; ANNOTATION
语种: 英语
WOS记录号: WOS:000351802100002
ISSN号: 0378-1119
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/23832
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
3.Univ Toronto, Dept Lab Med & PathoBiol, Toronto, ON M5S 1A1, Canada
4.Univ Toronto, Banting & Best Diabet Ctr, Toronto, ON M5S 1A1, Canada
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