PUBLICATION

Transcriptomic characterization of cold acclimation in larval zebrafish

Authors
Long, Y., Song, G., Yan, J., He, X., Li, Q., and Cui, Z.
ID
ZDB-PUB-130918-19
Date
2013
Source
BMC Genomics   14(1): 612 (Journal)
Registered Authors
Cui, Zongbin, Li, Qing
Keywords
cold stress, transcriptomic analysis, zebrafish, RNA-seq, gene expression
MeSH Terms
  • Acclimatization/genetics*
  • Alternative Splicing
  • Animals
  • Cold Temperature*
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing
  • Larva/genetics
  • Promoter Regions, Genetic
  • Sequence Analysis, RNA
  • Transcriptome*
  • Zebrafish/genetics*
PubMed
24024969 Full text @ BMC Genomics
Abstract

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°C) for 24 h significantly increased their survival rates under severe cold stress (12°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.

Genes / Markers
Figures
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Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes