Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

E Arner; CO Daub; K Vitting-Seerup; R Andersson; B Lilje; F Drabløs; A Lennartsson; M Rönnerblad; O Hrydziuszko; M Vitezic; TC Freeman; AMN Alhendi; P Arner; R Axton; JK Baillie; A Beckhouse; B Bodega; J Briggs; F Brombacher; M Davis; M Detmar; A Ehrlund; M Endoh; A Eslami; M Fagiolini; L Fairbairn; GJ Faulkner; C Ferrai; ME Fisher; L Forrester; D Goldowitz; R Guler; T Ha; M Hara; M Herlyn; T Ikawa; C Kai; H Kawamoto; LM Khachigian; SP Klinken; S Kojima; H Koseki; S Klein; N Mejhert; K Miyaguchi; Y Mizuno; M Morimoto; KJ Morris; C Mummery; Y Nakachi; S Ogishima; M Okada-Hatakeyama; Y Okazaki; V Orlando; D Ovchinnikov; R Passier; M Patrikakis; A Pombo; XY Qin; S Roy; H Sato; S Savvi; A Saxena; A Schwegmann; D Sugiyama; R Swoboda; H Tanaka; A Tomoiu; LN Winteringham; E Wolvetang; C Yanagi-Mizuochi; M Yoneda; S Zabierowski; P Zhang; I Abugessaisa; N Bertin; AD Diehl; S Fukuda; M Furuno; J Harshbarger; A Hasegawa; F Hori; S Ishikawa-Kato; Y Ishizu; M Itoh; T Kawashima; M Kojima; N Kondo; M Lizio; TF Meehan; CJ Mungall; M Murata; H Nishiyori-Sueki; S Sahin; S Nagao-Sato; J Severin; MJL De Hoon; J Kawai; T Kasukawa; T Lassmann

Journal article

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

E Arner, CO Daub, K Vitting-Seerup, R Andersson, B Lilje, F Drabløs, A Lennartsson, M Rönnerblad, O Hrydziuszko, M Vitezic, TC Freeman, AMN Alhendi, P Arner, R Axton, JK Baillie, A Beckhouse, B Bodega, J Briggs, F Brombacher, M Davis Show all

Science | Published : 2015

DOI: 10.1126/science.1259418

Abstract

Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data suppor..

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University of Melbourne Researchers

Christine Wells Author

Grants

Awarded by National Cancer Institute

Funding Acknowledgements

For a full list of acknowledgements and contributions, see supplementary text. FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT) to Y. Hayashizaki. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program to Y. Hayashizaki and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (from the MEXT, Japan). Additional funding is listed in the supplementary text. All CAGE data needed to reproduce the study have been deposited at the DNA Data Bank of Japan (DDBJ) under accession numbers DRA000991, DRA002711, DRA002747, and DRA002748. Additional visualizations of the data are available at http://fantom.gsc.riken.jp/5/. The human induced pluripotent stem cell lines that were subjected to cortical neuronal differentiation can be made available after completion of a materials transfer agreement with the Australian Institute for Bioengineering and Nanotechnology of The University of Queensland.