School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
Sci Rep. 2017 Nov 1;7(1):14817. doi: 10.1038/s41598-017-13844-9.
Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads from 59 publications together with RefSeq and UniGene annotated RNAs, we report 39,154 lincRNA transcripts encoded by 19,162 lincRNA genes in the rat. We reveal sequence and expression similarities in lincRNAs of rat, mouse and human. DNA methylation level of lincRNAs is higher than that of protein-coding genes across the transcription start sites (TSSs). And, three lincRNA genes overlap with differential methylation regions (DMRs) which associate with spontaneously hypertensive disease. In addition, there are similar binding trends for three transcription factors (HNF4A, CEBPA and FOXA1) between lincRNA genes and protein-coding genes, indicating that they harbour similar transcription regulatory mechanisms. To date, this is the most comprehensive assessment of lincRNAs in the rat genome. We provide valuable data that will advance lincRNA research using rat as a model.
长链非编码 RNA（lncRNAs）在许多生物过程中发挥着关键作用。大鼠是生物医学研究中的重要模式生物。最近的研究已经从多个样本中检测到了大鼠 lincRNA 基因。然而，利用大规模 RNA-seq 数据集鉴定大鼠 lincRNAs 的方法尚未见报道。在此，我们使用来自 59 篇文献的超过 1000 亿个 RNA-seq 读数，以及 RefSeq 和 UniGene 注释的 RNA，报告了大鼠中有 19162 个 lincRNA 基因编码的 39154 个 lincRNA 转录本。我们揭示了大鼠、小鼠和人类 lincRNAs 的序列和表达相似性。在转录起始位点（TSS）处，lincRNAs 的 DNA 甲基化水平高于蛋白质编码基因。并且，三个 lincRNA 基因与与自发性高血压疾病相关的差异甲基化区域（DMRs）重叠。此外，三个转录因子（HNF4A、CEBPA 和 FOXA1）在 lincRNA 基因和蛋白质编码基因之间具有相似的结合趋势，表明它们具有相似的转录调控机制。到目前为止，这是大鼠基因组中 lincRNAs 的最全面评估。我们提供了有价值的数据，将推进大鼠作为模型的 lincRNA 研究。
