title: MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae.
abstract: MicroRNAs (miRNAs) are critical regulators responding to acute environmental stresses in both plants and animals. By modulating gene expression, miRNAs either restore or reconstitute a new expression program to enhance cell tolerance to stresses. Cold shock is one of the stresses that can induce acute physiological responses and transcriptional changes in aquatic creatures. Previous genomic studies have revealed many cold-affected genes in fish larvae and adults, however, the role of miRNAs in acute cold response is still ambiguous. To elucidate the regulatory roles of miRNAs in the cold-inducible responses, we performed small RNA-seq and RNA-seq analyses and found potential cold regulatory miRNAs and genes. We further investigated their interactions and involvements in cold tolerance.
  
  
  
  Small RNA-seq and RNA-seq identified 29 up-/26 down-regulated miRNAs and 908 up-/468 down-regulated genes, respectively, in responding to cold shock for 4 h at 18 °C. miRNA and transcriptomic analyses showed these miRNAs and mRNAs are involved in similar biological processes and pathways. Gene ontology enrichment analyses revealed the cold-induced genes were enriched in pathways, including melanogenesis, GnRH pathway, circadian rhythm, etc. We were particularly interested in the changes in circadian clock genes that affect daily metabolism. The enrichment of circadian clock genes was also observed in previous fish cold acclimation studies, but have not been characterized. To characterize the functional roles of circadian clock genes in cold tolerance, we individually overexpressed selected clock genes in zebrafish larvae and found one of the core clock genes per2 resulted in better recovery from cold shock. In addition, we validated the interaction of per2 with its associate miRNA, dre-mir-29b, which is also cold-inducible. It suggests the transcription of per2 can be modulated by miRNA upon cold shock.
  
  
  
  Collectively, our observations suggest that miRNAs are fine turners for regulating genomic plasticity against cold shock. We further showed that the fine tuning of core clock gene per2 via its associated miRNA, dre-mir-29b, can enhance the cold tolerance of zebrafish larvae.
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
authors.forename: I-Chen
authors.initials: IC
authors.lastname: Hung
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
authors.forename: Yu-Chuan
authors.initials: YC
authors.lastname: Hsiao
authors.affiliation: Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, 70456, Taiwan.|Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70456, Taiwan.
authors.forename: H Sunny
authors.initials: HS
authors.lastname: Sun
authors.affiliation: Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung 81157, Taiwan.
  tmtonychen@webmail.nkmu.edu.tw.
authors.forename: Tsung-Ming
authors.initials: TM
authors.lastname: Chen
authors.affiliation: Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan. jefflee@ntu.edu.tw.|Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan. jefflee@ntu.edu.tw.|Center for Biotechnology, National Taiwan University, Taipei, 10617, Taiwan. jefflee@ntu.edu.tw.|Center for Systems Biology, Taipei, 10617, Taiwan. jefflee@ntu.edu.tw.
authors.forename: Shyh-Jye
authors.identifier: 0000-0001-8452-9152
authors.initials: SJ
authors.lastname: Lee
mesh_terms: D000818:Animals; D057906:Circadian Clocks / Q000235:genetics; D058639:Cold-Shock Response / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D007814:Larva / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010641:Phenotype; D015203:Reproducibility of Results; D013312:Stress, Physiological; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs
keywords: Clock genes; Cold stress; Deep sequencing; Embryonic development; Zebrafish; miRNA