日本理化学研究所横滨综合医学中心Yasuhiro Murakawa和Hideya Kawaji课题组合作，利用NET-CAGE方法描述了人类顺式转录调控元件的动力学和拓扑结构。 2019年9月2日出版的《自然—遗传学》发表了这项成果。

研究人员开发了一种简单而稳定的方法，即基因表达的自然延伸转录本分析(NET-CAGE)，这种方法可以灵敏地检测不同细胞和组织中新生RNA的5'末端，包括不稳定的转录产物如增强子衍生的RNA。研究人员探究了转录起始位点RNA合成和降解，表征了在转录起始位点不同启动子的使用对转录产物稳定性的影响。在不影响RNA转录的情况下，研究人员量化了来自顺式调控元件的转录，表明增强子--启动子对通常在受到刺激时同时激活。通过将NET-CAGE数据与染色质相互作用图谱整合，研究证明顺式调节元件是根据其细胞类型特异性拓扑性连接的。研究人员确定了具有高灵敏度的新增强子，并描绘了原发性增强子在超级增强子内的转录位置。该研究的NET-CAGE数据集来源于人类和小鼠细胞并扩展到FANTOM5转录增强子图谱，广泛适用于生物医学研究。

据悉，启动子和增强子是关键的顺式调节元件，但它们如何调控产生细胞类型特异性转录组还没有完全明白。

附：英文原文

Title: NET-CAGE characterizes the dynamics and topology of human transcribed cis -regulatory elements

Author: Shigeki Hirabayashi, Shruti Bhagat, Yu Matsuki, Yujiro Takegami, Takuya Uehata, Ai Kanemaru, Masayoshi Itoh, Kotaro Shirakawa, Akifumi Takaori-Kondo, Osamu Takeuchi, Piero Carninci, Shintaro Katayama, Yoshihide Hayashizaki, Juha Kere, Hideya Kawaji, Yasuhiro Murakawa

Issue&Volume: Volume 51 Issue 9

Abstract: 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.

DOI: 10.1038/s41588-019-0485-9

Source:https://www.nature.com/articles/s41588-019-0485-9