Jiang Chunjie, Li Yongsheng, Zhao Zheng, Lu Jianping, Chen Hong, Ding Na, Wang Guangjuan, Xu Juan, Li Xia
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Oncotarget. 2016 Feb 9;7(6):7120-33. doi: 10.18632/oncotarget.6859.
Recent advances in transcriptome sequencing have made it possible to distinguish ubiquitously expressed long non-coding RNAs (UE lncRNAs) from tissue-specific lncRNAs (TS lncRNAs), thereby providing clues to their cellular functions. Here, we assembled and functionally characterized a consensus lncRNA transcriptome by curating hundreds of RNA-seq datasets across normal human tissues from 16 independent studies. In total, 1,184 UE and 2,583 TS lncRNAs were identified. These different lncRNA populations had several distinct features. Specifically, UE lncRNAs were associated with genomic compaction and highly conserved exons and promoter regions. We found that UE lncRNAs are regulated at the transcriptional level (with especially strong regulation of enhancers) and are associated with epigenetic modifications and post-transcriptional regulation. Based on these observations we propose a novel way to predict the functions of UE and TS lncRNAs through analysis of their genomic location and similarities in epigenetic modifications. Our characterization of UE and TS lncRNAs may provide a foundation for lncRNA genomics and the delineation of complex disease mechanisms.
转录组测序的最新进展使得区分普遍表达的长链非编码RNA（UE lncRNAs）和组织特异性lncRNAs（TS lncRNAs）成为可能，从而为它们的细胞功能提供了线索。在此，我们通过整理来自16项独立研究的数百个正常人组织的RNA-seq数据集，组装并对一个共识lncRNA转录组进行了功能表征。总共鉴定出1184个UE lncRNAs和2583个TS lncRNAs。这些不同的lncRNA群体具有几个明显的特征。具体而言，UE lncRNAs与基因组压缩以及高度保守的外显子和启动子区域相关。我们发现UE lncRNAs在转录水平受到调控（尤其是增强子的强烈调控），并且与表观遗传修饰和转录后调控相关。基于这些观察结果，我们提出了一种通过分析UE和TS lncRNAs的基因组位置和表观遗传修饰的相似性来预测其功能的新方法。我们对UE和TS lncRNAs的表征可能为lncRNA基因组学和复杂疾病机制的描绘提供基础。
