Tissue-Specific RNA Expression Marks Distant Acting Developmental Enhancers

In this study, we explored the in vivo expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via in-depth transcriptome profiling. Overall, approximately 80% of validated in vivo enhancers show tissue-specific RNA expression that correlates with tissue-specific enhancer activity. Globally, we identified thousands of tissue-specifically transcribed non-coding regions (TSTRs) displaying various genomic hallmarks of bona fide enhancers. Together, our results demonstrate that tissue-specific eRNA expression is a common feature of in vivo enhancers, as well as a major source of extragenic transcription, and that eRNA expression signatures can be used to predict tissue-specific enhancers independent of known epigenomic enhancer marks. Examination of total RNA expression in mouse heart and limb tissues collected at mouse embryonic day 11.5.本研究通过深度转录组分析，探究了小鼠胚胎组织中组织特异性非编码RNA（non-coding RNAs）的体内表达动态特征。总体而言，经验证的体内增强子（enhancer）中约有80%表现出与组织特异性增强子活性相关的组织特异性RNA表达。本研究在全局尺度下共鉴定出数千个组织特异性转录非编码区域（tissue-specifically transcribed non-coding regions, TSTRs），这些区域展现出真实增强子的各类基因组标志性特征。综上，本研究结果表明，组织特异性增强子RNA（enhancer RNA, eRNA）表达是体内增强子的普遍特征，同时也是基因间转录的主要来源；此外，增强子RNA表达特征可在不依赖已知表观基因组增强子标记的情况下，用于预测组织特异性增强子。本研究检测了采集于小鼠胚胎发育第11.5天的小鼠心脏与肢体组织的总RNA表达情况。