Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Erik Arner; Carsten O. Daub; Kristoffer Vitting-Seerup; Robin Andersson; Berit Lilje; Finn Drablos; Andreas Lennartsson; Michelle Roennerblad; Olga Hrydziuszko; Morana Vitezic; Tom C. Freeman; Ahmad M. N. Alhendi; Peter Arner; Richard Axton; J. Kenneth Baillie; Anthony Beckhouse; Beatrice Bodega; James Briggs; Frank Brombacher; Margaret Davis; Michael Detmar; Anna Ehrlund; Mitsuhiro Endoh; Afsaneh Eslami; Michela Fagiolini; Lynsey Fairbairn; Geoffrey J. Faulkner; Carmelo Ferrai; Malcolm E. Fisher; Lesley Forrester; Daniel Goldowitz; Reto Guler; Thomas Ha; Mitsuko Hara; Meenhard Herlyn; Tomokatsu Ikawa; Chieko Kai; Hiroshi Kawamoto; Levon M. Khachigian; S. Peter Klinken; Soichi Kojima; Haruhiko Koseki; Sarah Klein; Niklas Mejhert; Ken Miyaguchi; Yosuke Mizuno; Mitsuru Morimoto; Kelly J. Morris; Christine Mummery; Yutaka Nakachi; Soichi Ogishima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry Ovchinnikov; Robert Passier; Margaret Patrikakis; Ana Pombo; Xian-Yang Qin; Sugata Roy; Hiroki Sato; Suzana Savvi; Alka Saxena; Anita Schwegmann; Daisuke Sugiyama; Rolf Swoboda; Hiroshi Tanaka; Andru Tomoiu; Louise N. Winteringham; Ernst Wolvetang; Chiyo Yanagi-Mizuochi; Misako Yoneda; Susan Zabierowski; Peter Zhang; Imad Abugessaisa; Nicolas Bertin; Alexander D. Diehl; Shiro Fukuda; Masaaki Furuno; Jayson Harshbarger; Akira Hasegawa; Fumi Hori; Sachi Ishikawa-Kato; Yuri Ishizu; Masayoshi Itoh; Tsugumi Kawashima; Miki Kojima; Naoto Kondo; Marina Lizio; Terrence F. Meehan; Christopher J. Mungall; Mitsuyoshi Murata; Hiromi Nishiyori-Sueki; Serkan Sahin; Sayaka Nagao-Sato; Jessica Severin; Michiel J. L. de Hoon; Jun Kawai; Takeya Kasukawa; Timo Lassmann; Harukazu Suzuki; Hideya Kawaji; Kim M. Summers; Christine Wells; David A. Hume; Alistair R. R. Forrest; Albin Sandelin; Piero Carninci; Yoshihide Hayashizaki; FANTOM Consortium

doi:10.1126/science.1259418

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Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Journal article

Peer reviewed

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Erik Arner, Carsten O. Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drablos, Andreas Lennartsson, Michelle Roennerblad, Olga Hrydziuszko, Morana Vitezic, …

Science (American Association for the Advancement of Science), Vol.347(6225), pp.1010-1014

27/02/2015

DOI: https://doi.org/10.1126/science.1259418

PMCID: PMC4681433

PMID: 25678556

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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 support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.

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Title: Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Creators - without role: Erik Arner - RIKEN
Carsten O. Daub - RIKEN
Kristoffer Vitting-Seerup - University of Copenhagen
Robin Andersson - University of Copenhagen
Berit Lilje - University of Copenhagen
Finn Drablos - College Station Medical Center
Andreas Lennartsson - Karolinska Institutet
Michelle Roennerblad - Karolinska Institutet
Olga Hrydziuszko - Karolinska Institutet
Morana Vitezic - University of Copenhagen
Tom C. Freeman - University of Edinburgh
Ahmad M. N. Alhendi - UNSW Sydney
Peter Arner - Karolinska Institutet
Richard Axton - University of Edinburgh
J. Kenneth Baillie - University of Edinburgh
Anthony Beckhouse - University of Queensland
Beatrice Bodega - IRCCS Fnd Santa Lucia, Via Fosso Fiorano 64, I-00143 Rome, Italy
James Briggs - University of Queensland
Frank Brombacher - Int Ctr Genet Engn Biotechnol ICGEB Cape Town com, Immunol & Infect Dis, Anzio Rd, Cape Town, South Africa
Margaret Davis - University of Edinburgh
Michael Detmar - ETH Zurich
Anna Ehrlund - Karolinska Institutet
Mitsuhiro Endoh - College Station Medical Center
Afsaneh Eslami - College Station Medical Center
Michela Fagiolini - Franklin & Marshall College
Lynsey Fairbairn - University of Edinburgh
Geoffrey J. Faulkner - Mater Med Res Inst, Canc Biol Program, Raymond Terrace, South Brisbane, Qld 4101, Australia
Carmelo Ferrai - College Station Medical Center
Malcolm E. Fisher - University of Edinburgh
Lesley Forrester - University of Edinburgh
Daniel Goldowitz - University of British Columbia
Reto Guler - Int Ctr Genet Engn Biotechnol ICGEB Cape Town com, Immunol & Infect Dis, Anzio Rd, Cape Town, South Africa
Thomas Ha - University of British Columbia
Mitsuko Hara - RIKEN
Meenhard Herlyn - The Wistar Institute
Tomokatsu Ikawa - RIKEN
Chieko Kai - The University of Tokyo
Hiroshi Kawamoto - RIKEN
Levon M. Khachigian - UNSW Sydney
S. Peter Klinken - University of Western Australia
Soichi Kojima - RIKEN
Haruhiko Koseki - RIKEN
Sarah Klein
Niklas Mejhert - Karolinska Institutet
Ken Miyaguchi - College Station Medical Center
Yosuke Mizuno - College Station Medical Center
Mitsuru Morimoto - RIKEN
Kelly J. Morris - College Station Medical Center
Christine Mummery - Leiden University
Yutaka Nakachi - College Station Medical Center
Soichi Ogishima - College Station Medical Center
Mariko Okada-Hatakeyama - RIKEN
Yasushi Okazaki - College Station Medical Center
Valerio Orlando - King Abdullah Univ Sci & Technol KAUST, Biol & Environm Sci & Engn Div, Ibn Al Haytham Bldg-2, Thuwal, Saudi Arabia
Dmitry Ovchinnikov - University of Queensland
Robert Passier - Leiden University
Margaret Patrikakis - UNSW Sydney
Ana Pombo - College Station Medical Center
Xian-Yang Qin - RIKEN
Sugata Roy - RIKEN
Hiroki Sato - The University of Tokyo
Suzana Savvi - Int Ctr Genet Engn Biotechnol ICGEB Cape Town com, Immunol & Infect Dis, Anzio Rd, Cape Town, South Africa
Alka Saxena - RIKEN
Anita Schwegmann - Int Ctr Genet Engn Biotechnol ICGEB Cape Town com, Immunol & Infect Dis, Anzio Rd, Cape Town, South Africa
Daisuke Sugiyama - Kyushu University
Rolf Swoboda - The Wistar Institute
Hiroshi Tanaka - College Station Medical Center
Andru Tomoiu - University of Edinburgh
Louise N. Winteringham - University of Western Australia
Ernst Wolvetang - University of Queensland
Chiyo Yanagi-Mizuochi - Kyushu University
Misako Yoneda - The University of Tokyo
Susan Zabierowski - The Wistar Institute
Peter Zhang - University of British Columbia
Imad Abugessaisa - RIKEN
Nicolas Bertin - RIKEN
Alexander D. Diehl - University at Buffalo, State University of New York
Shiro Fukuda - RIKEN
Masaaki Furuno - RIKEN
Jayson Harshbarger - RIKEN
Akira Hasegawa - RIKEN
Fumi Hori - RIKEN
Sachi Ishikawa-Kato - RIKEN
Yuri Ishizu - RIKEN
Masayoshi Itoh - RIKEN
Tsugumi Kawashima - RIKEN
Miki Kojima - RIKEN
Naoto Kondo - RIKEN
Marina Lizio - RIKEN
Terrence F. Meehan - Wellcome Trust
Christopher J. Mungall - Cyclotron
Mitsuyoshi Murata - RIKEN
Hiromi Nishiyori-Sueki - RIKEN
Serkan Sahin - RIKEN
Sayaka Nagao-Sato - RIKEN
Jessica Severin - RIKEN
Michiel J. L. de Hoon - RIKEN
Jun Kawai - RIKEN
Takeya Kasukawa - RIKEN
Timo Lassmann - RIKEN
Harukazu Suzuki - RIKEN
Hideya Kawaji - RIKEN
Kim M. Summers - University of Edinburgh
Christine Wells - University of Queensland
David A. Hume - University of Edinburgh
Alistair R. R. Forrest - RIKEN
Albin Sandelin - University of Copenhagen
Piero Carninci - RIKEN
Yoshihide Hayashizaki - RIKEN
FANTOM Consortium
Publication Details: Science (American Association for the Advancement of Science), Vol.347(6225), pp.1010-1014
Publisher: Amer Assoc Advancement Science
Number of pages: 5
Grant note: BBS/E/D/20211552 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (from the MEXT, Japan) 24689042 / Grants-in-Aid for Scientific Research; Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT); Japan Society for the Promotion of Science; Grants-in-Aid for Scientific Research (KAKENHI) NNF10SA1016550 / Novo Nordisk Fonden; Novo Nordisk Foundation MC_U120061476 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) MC_U120061476 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC); European Commission P30CA010815 / NATIONAL CANCER INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI) BBS/E/D/20251969 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT); Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)
Identifiers: 9944343108331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article