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题名: Transcriptomic characterization of cold acclimation in larval zebrafish
作者: Long, Yong1; Song, Guili1; Yan, Junjun1, 2; He, Xiaozhen1, 2; Li, Qing1; Cui, Zongbin1
通讯作者: Cui, ZB (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China.
关键词: Cold stress ; Transcriptomic analysis ; Zebrafish ; RNA-seq ; Gene expression
刊名: BMC GENOMICS
发表日期: 2013-09-11
DOI: 10.1186/1471-2164-14-612
卷: 14, 页:612
收录类别: SCI
文章类型: Article
部门归属: [Long, Yong ; Song, Guili ; Yan, Junjun ; He, Xiaozhen ; Li, Qing ; Cui, Zongbin] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China ; [Yan, Junjun ; He, Xiaozhen] Univ Chinese Acad Sci, Beijing, Peoples R China
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
资助者: Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892]
类目[WOS]: Biotechnology & Applied Microbiology ; Genetics & Heredity
研究领域[WOS]: Biotechnology & Applied Microbiology ; Genetics & Heredity
摘要: Background: Temperature is one of key environmental parameters that affect the whole life of fishes and an increasing number of studies have been directed towards understanding the mechanisms of cold acclimation in fish. However, the adaptation of larvae to cold stress and the cold-specific transcriptional alterations in fish larvae remain largely unknown. In this study, we characterized the development of cold-tolerance in zebrafish larvae and investigated the transcriptional profiles under cold stress using RNA-seq. Results: Pre-exposure of 96 hpf zebrafish larvae to cold stress (16 degrees C) for 24 h significantly increased their survival rates under severe cold stress (12 degrees C). RNA-seq generated 272 million raw reads from six sequencing libraries and about 92% of the processed reads were mapped to the reference genome of zebrafish. Differential expression analysis identified 1,431 up- and 399 down-regulated genes. Gene ontology enrichment analysis of cold-induced genes revealed that RNA splicing, ribosome biogenesis and protein catabolic process were the most highly overrepresented biological processes. Spliceosome, proteasome, eukaryotic ribosome biogenesis and RNA transport were the most highly enriched pathways for genes up-regulated by cold stress. Moreover, alternative splicing of 197 genes and promoter switching of 64 genes were found to be regulated by cold stress. A shorter isoform of stk16 that lacks 67 amino acids at the N-terminus was specifically generated by skipping the second exon in cold-treated larvae. Alternative promoter usage was detected for per3 gene under cold stress, which leading to a highly up-regulated transcript encoding a truncated protein lacking the C-terminal domains. Conclusions: These findings indicate that zebrafish larvae possess the ability to build cold-tolerance under mild low temperature and transcriptional and post-transcriptional regulations are extensively involved in this acclimation process.
英文摘要: Background: Temperature is one of key environmental parameters that affect the whole life of fishes and an increasing number of studies have been directed towards understanding the mechanisms of cold acclimation in fish. However, the adaptation of larvae to cold stress and the cold-specific transcriptional alterations in fish larvae remain largely unknown. In this study, we characterized the development of cold-tolerance in zebrafish larvae and investigated the transcriptional profiles under cold stress using RNA-seq.
关键词[WOS]: ARABIDOPSIS CIRCADIAN CLOCK ; GENE-EXPRESSION ; LOW-TEMPERATURE ; RNA-SEQ ; RAINBOW-TROUT ; HEAT-SHOCK ; DROSOPHILA-MELANOGASTER ; ENVIRONMENTAL-STRESS ; DIFFERENTIAL GENE ; UP-REGULATION
语种: 英语
WOS记录号: WOS:000324312500001
ISSN号: 1471-2164
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/19609
Appears in Collections:水生生物分子与细胞生物学研究中心_期刊论文

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作者单位: 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China

Recommended Citation:
Long, Yong; Song, Guili; Yan, Junjun; He, Xiaozhen; Li, Qing; Cui, Zongbin.Transcriptomic characterization of cold acclimation in larval zebrafish,BMC GENOMICS,2013,14():612
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