RIKEN Baton Zone Program, Yokohama, Japan.
Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Nat Genet. 2019 Sep;51(9):1369-1379. doi: 10.1038/s41588-019-0485-9. Epub 2019 Sep 2.
Promoters and enhancers are key cis-regulatory elements, but how they operate to generate cell type-specific transcriptomes is not fully understood. We developed a simple and robust method, native elongating transcript-cap analysis of gene expression (NET-CAGE), to sensitively detect 5' ends of nascent RNAs in diverse cells and tissues, including unstable transcripts such as enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site level, characterizing the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without the influence of RNA turnover, and show that enhancer-promoter pairs are generally activated simultaneously on stimulation. By integrating NET-CAGE data with chromatin interaction maps, we show that cis-regulatory elements are topologically connected according to their cell type specificity. We identified new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our NET-CAGE dataset derived from human and mouse cells expands the FANTOM5 atlas of transcribed enhancers, with broad applicability to biomedical research.
启动子和增强子是关键的顺式调控元件，但它们如何运作以产生细胞类型特异性转录组尚不完全清楚。我们开发了一种简单而强大的方法，即基因表达的天然延伸转录物 - 帽分析（NET-CAGE），以灵敏地检测不同细胞和组织中新生 RNA 的 5' 端，包括增强子衍生 RNA 等不稳定转录物。我们在转录起始位点水平研究了 RNA 合成和降解，描述了差异启动子使用对转录本稳定性的影响。我们在没有 RNA 周转影响的情况下定量了顺式调控元件的转录，并表明增强子 - 启动子对通常在刺激下同时激活。通过将 NET-CAGE 数据与染色质相互作用图谱整合，我们表明顺式调控元件根据其细胞类型特异性按拓扑方式连接。我们以高灵敏度识别了新的增强子，并描绘了超级增强子内转录的主要位置。我们从人类和小鼠细胞中获得的 NET-CAGE 数据集扩展了转录增强子的 FANTOM5 图谱，具有广泛的生物医学研究适用性。
