Global identification of the gene networks and cis-regulatory elements of the cold response in zebrafish

The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold-responsive transcriptional patterns have been determined in fishes, the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures, ranging from normal (28°C) to mild (18°C) and severe (10°C) cold, using RNA-seq. The tissues varied in the number of cold-responsive genes, of which the kidney appeared to be most sensitive, whereas the brain was the least. Fuzzy k-means clustering revealed 34 gene clusters of distinct expression patterns, demonstrating diverse tissue-specific responses in conjunction with multiple aspects of ubiquitous cross-tissue responses to cold. Thirty-one GO terms were over-represented upon cold treatment. These terms are involved in basic cellular processes, such as RNA splicing and proton transport, as well tissue-specific processes, such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis-regulatory elements governing the concerted cold responses, the promoters of the genes that demonstrated strong co-regulation were analyzed using an enriched motif discovery program, DREME. Eleven motifs, 6 known and 5 novel, were identified. These motifs belong to the genes corresponding to the 16 over-represented GO terms identified above. Some motifs, such as the AP-1 and STAT1 binding sites, are known to be stress responsive. By integrating comprehensive cold-induced transcriptional changes with a cis-motif identification tool, we identified genome-wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples (eight tissues at three temperatures)

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Hu P, Liu M, Zhang D, Wang J, Niu H, Liu Y, Wu Z, Han B, Zhai W, Shen Y, Chen L