title: Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish.
abstract: The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. However, the cis- and trans-factors governing cold responses are not well characterized. We profiled transcriptional changes in eight zebrafish tissues exposed to mildly and severely cold temperatures using RNA-Seq. A total of 1943 differentially expressed genes (DEGs) were identified, from which 34 clusters representing distinct tissue and temperature response expression patterns were derived using the k-means fuzzy clustering algorithm. The promoter regions of the clustered DEGs that demonstrated strong co-regulation were analysed for enriched cis-regulatory elements with a motif discovery program, DREME. Seventeen motifs, ten known and seven novel, were identified, which covered 23% of the DEGs. Two motifs predicted to be the binding sites for the transcription factors Bcl6 and Jun, respectively, were chosen for experimental verification, and they demonstrated the expected cold-induced and cold-repressed patterns of gene regulation. Protein interaction modeling of the network components followed by experimental validation suggested that Jun physically interacts with Bcl6 and might be a hub factor that orchestrates the cold response in zebrafish. Thus, the methodology used and the regulatory networks uncovered in this study provide a foundation for exploring the mechanisms of cold adaptation in teleosts.
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Hu
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Mingli
authors.initials: M
authors.lastname: Liu
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Niu
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Yimeng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Zhichao
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Bingshe
authors.initials: B
authors.lastname: Han
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China.
authors.forename: Wanying
authors.initials: W
authors.lastname: Zhai
authors.affiliation: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China lbchen@shou.edu.cn.
authors.forename: Liangbiao
authors.initials: L
authors.lastname: Chen
mesh_terms: D000818:Animals; D002460:Cell Line; D058639:Cold-Shock Response / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D008297:Male; D059372:Nucleotide Motifs; D009928:Organ Specificity; D011401:Promoter Regions, Genetic; D025941:Protein Interaction Mapping; D014157:Transcription Factors / Q000378:metabolism; D015027:Zebrafish / Q000235:genetics*
chemical_list: D014157:Transcription Factors