Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

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.长链非编码RNA（Long non-coding RNAs，lncRNAs）日益被视为调控多种组织与物种中各类生物学过程的关键因子。尽管已有研究在植物中报道了低温响应lncRNAs，但截至目前，尚无关于鱼类冷驯化过程中lncRNAs的筛选与功能预测的相关数据。本研究通过高通量测序技术，对比了在18℃条件下培养30天的冷驯化斑马鱼胚胎成纤维细胞（ZF4）与作为对照的28℃培养细胞的lncRNAs表达谱。研究共鉴定出8363条新型lncRNAs；在涵盖已知与新型lncRNAs的全部转录本中，冷驯化细胞内有347条lncRNAs表达上调、342条表达下调。在这些差异表达的lncRNAs中，分别有74条和61条仅在对照细胞或冷驯化细胞中被检测到。研究团队对差异表达lncRNAs的邻近基因开展基因本体论（GO）与京都基因与基因组百科全书（KEGG）富集分析，结果显示富集基因参与了电子传递、细胞黏附、氧化还原过程等生物学过程。本研究还通过探寻lncRNAs与信使RNA（mRNA）间的相互作用，预测了差异表达lncRNAs的靶基因，并构建了相互作用网络。综上，本研究对斑马鱼细胞中低温响应lncRNAs开展的全基因组系统性鉴定与功能预测，揭示了基因间长链非编码RNA（lincRNAs）在鱼类冷驯化过程中的关键作用。