Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells.

Penglei Jiang,Yicheng Xu,Junfang Zhang,Bingshe Han,Weikang Fu,Yanwen Hou,Xiaofan Tao,Juntao Luo,Hanxu Lu,Yun Zheng

doi:10.1371/journal.pone.0195468

Abstract

Long non-coding RNAs (lncRNAs) are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. Although the cold responsive lncRNAs have been reported in plants, no data is available on screening and functional prediction of lncRNAs in cold acclimation in fish so far. Here we compared the expression profile of lncRNAs in cold acclimated zebrafish embryonic fibroblast cells (ZF4) cultured at 18°C for 30 days with that of cells cultured at 28°C as control by high-throughput sequencing. Totally 8,363 novel lncRNAs were identified. Including known and novel lncRNAs, there are 347 lncRNAs up-regulated and 342 lncRNAs down-regulated in cold acclimated cells. Among the differentially expressed lncRNAs, 74 and 61 were detected only in control cells or cold-acclimated cells, respectively. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses of adjacent genes to the differentially expressed lncRNAs showed that the enriched genes are involved in electron transport, cell adhesion, oxidation-reduction process, and so on. We also predicted the target genes of the differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNAs, and constructed an interaction network. In summary, our genome-wide systematic identification and functional prediction of cold responsive lncRNAs in zebrafish cells suggests a crucial role of lincRNAs in cold acclimation in fish.

Highlights

Long noncoding RNAs are generally defined as a class of transcripts with length more than 200 nucleotide but lack significant protein coding capacity [1]
We investigated the role of DNA methylation in zebrafish zebrafish embryonic fibroblast cells (ZF4) cells when experimentally acclimated at 18 ̊C for 30 days, suggesting that DNA methylation is involved in cold acclimation via regulation of genes related to anti-oxidant system, apoptosis, development, chromatin modifying and immune system [11]
We further studied the roles of long non-coding RNA (lncRNA) in cold acclimation of ZF4 cells

Summary

Introduction

Long noncoding RNAs (lncRNAs) are generally defined as a class of transcripts with length more than 200 nucleotide (nt) but lack significant protein coding capacity [1]. Accumulating studies suggest that lncRNAs play key roles in regulating development, tumorigenesis, and response to abiotic stresses [1,2]. Unlike the translational regulation mechanism of miRNA is well characterized, mechanism of lncRNAs is still far from a full understanding. They serve as transcriptional silencers, co-activators, and even competing endogenous RNAs by providing interaction sites for miRNAs [3]. LncRNAs play key roles in regulating gene and genome activity at various levels including serving as ligands or cofactors to mediate histone modification. They serve as transcriptional silencers, co-activators, and even competing endogenous RNAs by providing interaction sites for miRNAs [3]. lncRNAs play key roles in regulating gene and genome activity at various levels including serving as ligands or cofactors to mediate histone modification

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Results

Conclusion