Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs.
Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs.
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识别和功能表征组织特异性和普遍表达的人类 lncRNA。
DOI：
10.18632/oncotarget.6859
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发表时间：
2016-02-09
期刊：
影响因子：
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通讯作者：
Li X
中科院分区：
文献类型：
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作者：
Jiang C;Li Y;Zhao Z;Lu J;Chen H;Ding N;Wang G;Xu J;Li X
转录组测序的最新进展使得区分普遍表达的长非编码RNA（UE lncRNA）和组织特异性lncRNA（TS lncRNA）成为可能，从而为它们的细胞功能提供线索。在这里，我们通过从16项独立研究中收集数百个正常人体组织的RNA-seq数据集，组装并功能性地表征了一个共有lncRNA转录组。总共鉴定了1，184个UE和2，583个TS lncRNA。这些不同的lncRNA群体具有几个不同的特征。具体而言，UE lncRNA与基因组压缩和高度保守的外显子和启动子区域相关。我们发现UE lncRNA在转录水平上受到调节（增强子的调节特别强），并且与表观遗传修饰和转录后调节相关。基于这些观察，我们提出了一种新的方法来预测UE和TS lncRNA的功能，通过分析它们的基因组位置和表观遗传修饰的相似性。我们对UE和TS lncRNA的表征可能为lncRNA基因组学和复杂疾病机制的描述提供基础。
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.