Characterization of IncRNAs involved in cold acclimation of zebrafish ZF4 cells

Long non-coding RNAs (IncRNAs) are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. Although the cold responsive IncRNAs have been reported in plants, no data is available on screening and functional prediction of IncRNAs in cold acclimation in fish so far. Here we compared the expression profile of IncRNAs in cold acclimated zebrafish embryonic fibroblast cells (ZF4) cultured at 18 degrees C for 30 days with that of cells cultured at 28 degrees C as control by high-throughput sequencing. Totally 8,363 novel IncRNAs were identified. Including known and novel IncRNAs, there are 347 IncRNAs up-regulated and 342 IncRNAs down-regulated in cold acclimated cells. Among the differentially expressed IncRNAs, 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 IncRNAs 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 IncRNAs by looking for interactions between IncRNAs and mRNAs, and constructed an interaction network. In summary, our genome-wide systematic identification and functional prediction of cold responsive IncRNAs in zebrafish cells suggests a crucial role of lincRNAs in cold acclimation in fish.