RNA-Seq uncovers key to cold tolerance of zebrafish

A team at National Taiwan University, led by Prof Shyh-Jye Lee of the Department of Life Science and director of the Research Center for Developmental Biology and Regenerative Medicine, have demonstrated that microRNAs (miRNAs) regulate the cold response of fish. Using genomics methods, the team found that miRNAs fine tune circadian rhythm genes that help zebrafish withstand cold. The team’s study, “MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae”, was published in the journal BioMed Central Genomics.

Prof. H. Sunny Sun of National Cheng Kung University and Prof. Tsung-Ming Chen of National Kaohsiung Marine University cooperated with Prof. Lee in undertaking the study. NTU Master’s students I-Chen Hung and Yu-Chuan Hsiao served as the team’s main research personnel. The study was supported by a Ministry of Science and Technology program for the promotion of advanced agricultural biotechnology.

Every winter, cold fronts regularly lead to massive die-offs of aquatic animals, which results in enormous losses for Taiwan’s aquaculture sector. Unfortunately, fish farmers have no effective means to prevent this cold damage. The rapid decline in environmental temperatures causes the body temperature of fish to fall quickly, which leads to a series of physiological and stress responses called cold shock.

While previous research has shown that cold shock causes death and other physiological changes in fish, scientist have yet to explain the mechanisms of molecular regulation behind these changes. MiRNAs are small non-coding RNA molecules that regulate development, cell division, and metabolism. Existing studies show that miRNAs are an important factor in the regulation of environmental stresses, including temperature changes.

As miRNAs can inhibit the degree of expression of their target mRNA, Prof. Lee and his fellow researchers, working with zebrafish larvae, performed small RNA-seq and RNA-seq analysis to gain a better understanding of the overall changes in miRNA and mRNA in response to cold. Small RNA-seq and RNA-seq are high-throughput, next-generation sequencing methods used for miRNAome and transcriptome profiling.

Hung and Hsiao’s miRNAome profiling revealed 29 up-regulated and 26 down-regulated miRNAs in response to cold shock. Further analysis showed that these miRNAs and mRNAs are involved in many cellular physiological responses, among them circadian rhythm regulation.

As previous mammalian research has shown that the enrichment of circadian clock genes assists in the regulation of cold tolerance, the team set out to characterize the functional roles of circadian clock genes in the cold response of zebrafish larvae.

The researchers discovered that most of these genes were up-regulated under cold stress, especially per2, one of the core clock genes, which was overexpressed by a degree of ten times. Furthermore, they found that the overexpression of per2 in the zebrafish larvae resulted in significantly better recovery from cold shock compared to the control group. Also, glucose concentrations in the per2 overexpressing larvae were higher than in the control group, which shows that this gene might modulate the metabolism of glucose under cold shock to achieve the goal of cold tolerance.

Source – National Taiwan University

Hung IC, Hsiao YC, Sun HS, Chen TM, Lee SJ. (2016) MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae. BMC Genomics 17(1):922. [article]

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