IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
Transcriptomic characterization of cold acclimation in larval zebrafish
Long, Yong1; Song, Guili1; Yan, Junjun1,2; He, Xiaozhen1,2; Li, Qing1; Cui, Zongbin1; Cui, ZB (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China.
2013-09-11
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume14Pages:612
AbstractBackground: 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.; 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.
SubtypeArticle
KeywordCold Stress Transcriptomic Analysis Zebrafish Rna-seq Gene Expression
Department[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
DOI10.1186/1471-2164-14-612
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationStrategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892] ; Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892] ; Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892] ; Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892]
Indexed BySCI
Language英语
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000324312500001
WOS KeywordARABIDOPSIS CIRCADIAN CLOCK ; GENE-EXPRESSION ; LOW-TEMPERATURE ; RNA-SEQ ; RAINBOW-TROUT ; HEAT-SHOCK ; DROSOPHILA-MELANOGASTER ; ENVIRONMENTAL-STRESS ; DIFFERENTIAL GENE ; UP-REGULATION
Funding OrganizationStrategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892] ; Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892] ; Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892] ; Strategic Priority Research Program - Innovation systems of molecular module design breeding of the Chinese Academy of Sciences; National Natural Science Foundation of China [31101892]
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/19609
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorCui, ZB (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China.
Affiliation1.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
GB/T 7714
Long, Yong,Song, Guili,Yan, Junjun,et al. Transcriptomic characterization of cold acclimation in larval zebrafish[J]. BMC GENOMICS,2013,14:612.
APA Long, Yong.,Song, Guili.,Yan, Junjun.,He, Xiaozhen.,Li, Qing.,...&Cui, ZB .(2013).Transcriptomic characterization of cold acclimation in larval zebrafish.BMC GENOMICS,14,612.
MLA Long, Yong,et al."Transcriptomic characterization of cold acclimation in larval zebrafish".BMC GENOMICS 14(2013):612.
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