TY - JOUR
T1 - MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae
AU - Hung, I. Chen
AU - Hsiao, Yu Chuan
AU - Sun, H. Sunny
AU - Chen, Tsung Ming
AU - Lee, Shyh Jye
N1 - Funding Information:
This work was supported by the Ministry of Science and Technology, Taiwan (101-2321-B-002-054-, 102-2121-B-002-041, 103-2321-B-002-009) and National Taiwan University (NTU NTU CESRP-10R70602A5 and NTU ERP-10R80600 to SJL
Funding Information:
We thank Taiwan Zebrafish core facility for providing technical guidance and plasmids. We thank Technology Commons, College of Life Science, Center for Systems Biology, National Taiwan University for excellent technical assistance with NGS and qPCR experiments. We thank the Taiwan Bioinformatics Core at the National Cheng Kung University, supported by the Taiwan Ministry of Science for assisting with computational analyses and data mining. We thank the Center for Genomic Medicine, National Cheng Kung University, for the support of NGS analyses. The authors would also like to express great appreciation to the staffs of the zebrafish Core at National Taiwan University for providing assistance in fish maintenance. We are also grateful to Dr. Shih-Kuo Chen for the helpful discussion in the regulation of circadian rhythm.
Publisher Copyright:
© 2016 The Author(s).
PY - 2016/11/15
Y1 - 2016/11/15
N2 - Background: 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. Results: 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. Conclusions: 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.
AB - Background: 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. Results: 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. Conclusions: 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=84996528072&partnerID=8YFLogxK
U2 - 10.1186/s12864-016-3239-4
DO - 10.1186/s12864-016-3239-4
M3 - Article
C2 - 27846817
AN - SCOPUS:84996528072
SN - 1471-2164
VL - 17
JO - BMC genomics
JF - BMC genomics
IS - 1
M1 - 922
ER -