TY - JOUR
T1 - NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements
AU - Hirabayashi, Shigeki
AU - Bhagat, Shruti
AU - Matsuki, Yu
AU - Takegami, Yujiro
AU - Uehata, Takuya
AU - Kanemaru, Ai
AU - Itoh, Masayoshi
AU - Shirakawa, Kotaro
AU - Takaori-Kondo, Akifumi
AU - Takeuchi, Osamu
AU - Carninci, Piero
AU - Katayama, Shintaro
AU - Hayashizaki, Yoshihide
AU - Kere, Juha
AU - Kawaji, Hideya
AU - Murakawa, Yasuhiro
N1 - Funding Information:
We are grateful to all of the members of the RIKEN Genome Network Analaysis Support Facility and the K.K. DNAFORM genetic analysis department for library preparation, sequencing and primary data processing. We thank E. Arner, R. Andersson, K. Vitting-Seerup and A. Sandelin for helpful discussions. We thank I. Yamaguchi, K. Goto, M. Furuno and T. Kasukawa for assistance. We also thank M. Okada-Hatakeyama for guidance on performing the time-course experiment using MCF-7 cells. This work was supported by: JSPS Grants-in-Aid for Scientific Research (KAKENHI) (16H06153 and 18H03992) and grants from the Kanae Foundation for the Promotion of Medical Science, Ono Medical Research Foundation, Takeda Science Foundation, Japan Foundation for Applied Enzymology and Mochida Memorial Foundation for Medical and Pharmaceutical Research (to Y. Murakawa); JSPS Grants-in-Aid for Scientific Research (KAKENHI) (16H02902) (to H.K.); AMED under grant number 18ek0109282h0002 (to Y.H.); the RIKEN Junior Research Associate Program (to S.H.); the International Program Associate program and Karolinska Institutet (to S.B.); Invitational Fellowships for Research in Japan (F1606103) (to J.K. and P.C.); the Knut and Alice Wallenberg Foundation (Sweden) and The Royal Society Wolfson Research Merit Award (UK) (to J.K.).
Publisher Copyright:
© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2019/9/1
Y1 - 2019/9/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41588-019-0485-9
DO - 10.1038/s41588-019-0485-9
M3 - Article
C2 - 31477927
AN - SCOPUS:85071767071
VL - 51
SP - 1369
EP - 1379
JO - Nature Genetics
JF - Nature Genetics
SN - 1061-4036
IS - 9
ER -