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

• Published in: Nature genetics Vol. 51; no. 9; pp. 1369 - 1379
• Main Authors: Hirabayashi, Shigeki, Bhagat, Shruti, Matsuki, Yu, Takegami, Yujiro, Uehata, Takuya, Kanemaru, Ai, Itoh, Masayoshi, Shirakawa, Kotaro, Takaori-Kondo, Akifumi, Takeuchi, Osamu, Carninci, Piero, Katayama, Shintaro, Hayashizaki, Yoshihide, Kere, Juha, Kawaji, Hideya, Murakawa, Yasuhiro
• Format: Journal Article
• Language: English
• Published: United States Nature Publishing Group 01.09.2019
• Subjects: 5' Untranslated Regions - genetics; Binding sites; Bioinformatics; Cages; Chromatin; Computational Biology - methods; Enhancer Elements, Genetic; Enhancers; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Gene mapping; Genetic research; Genetic transcription; Genomes; HeLa Cells; Hep G2 Cells; Humans; MCF-7 Cells; Medicin och hälsovetenskap; Promoter Regions, Genetic; Regulatory sequences; Ribonucleic acid; RNA; RNA - genetics; RNA polymerase; Sensitivity enhancement; Synthesis; Topology; Transcription; Transcription factors; Transcription Initiation Site; Transcription, Genetic; Transcriptome
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/s41588-019-0485-9

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.