Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells.

Xiangqin Ji,Bingshe Han,Juntao Luo,Junfang Zhang,Mengjia Li,Yajing Bai,Penglei Jiang,Zongbin Cui

doi:10.1371/journal.pone.0226905

Abstract

MicroRNAs (miRNAs) play vital roles in various biological processes under multiple stress conditions by leading to mRNA cleavage or translational repression. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, high-throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28°C, 30 days) and cold-acclimation (18°C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the target genes of known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, both miR-100-3p inhibitor and miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. Further study showed that miR-100-3p and miR-16b could regulate inversely the expression of their target gene (atad5a, cyp2ae1, lamp1, rilp, atxn7, tnika, btbd9), and that overexpression of miR-100-3p disturbed the early embryonic development of zebrafish. In summary, the present data show that miRNAs are closely involved in cold acclimation in zebrafish ZF4 cells and provide information for further understanding of the roles of miRNAs in cold acclimation in fish.

Highlights

MicroRNAs are a class of endogenous non-coding RNAs in plants and animals, approximately 22 nucleotides in length, which play key roles in regulating gene expression by leading to cleavage or translational repression of their target mRNA [1, 2]
Zebrafish zebrafish embryonic fibroblast cells (ZF4) cells were maintained at 18 ̊C for 30 days for cold acclimation [22], 3 RNA samples from control group and 3 RNA samples from cold acclimation group were subjected to sequencing
Increasing evidence supports the involvement of miRNAs in cold stress of plants and animals. miR408 and its target genes show regulatory roles in cold response in arabidopsis [14]. miR319 is a potential marker for selection of cold-tolerant sugarcane cultivars [36]. miR-210-3p modulates expression of genes related to metabolism, apoptosis and proliferation in rat cells under acute cold stress conditions [16], and miRNAs play key roles in cold adaptation of Litopenaeus vannamei [17]

Summary

Introduction

MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs in plants and animals, approximately 22 nucleotides in length, which play key roles in regulating gene expression by leading to cleavage or translational repression of their target mRNA [1, 2].

Methods

Results

Discussion

Conclusion