A promoter-level mammalian expression atlas

Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J. Mungall; Terrence F. Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jorgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A. Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A. Semple; Yuri Ishizu; Robert S. Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M. Altschuler; Takahiro Arakawa; John A. C. Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J. Balwierz; Anthony G. Beckhouse; Swati Pradhan-Bhatt; Judith A. Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A. Maxwell Burroughs; Andrea Califano; Carlo V. Cannistraci; Daniel Carbajo; Yun Chen; Marco Chierici; Yari Ciani; Hans C. Clevers; Emiliano Dalla; Carrie A. Davis; Michael Detmar; Alexander D. Diehl; Taeko Dohi; Finn Drablos; Albert S. B. Edge; Matthias Edinger; Karl Ekwall; Mitsuhiro Endoh; Hideki Enomoto; Michela Fagiolini; Lynsey Fairbairn; Hai Fang; Mary C. Farach-Carson; Geoffrey J. Faulkner; Alexander V. Favorov; Malcolm E. Fisher; Martin C. Frith; Rie Fujita; Shiro Fukuda; Cesare Furlanello; Masaaki Furuno; Jun-ichi Furusawa; Teunis B. Geijtenbeek; Andrew P. Gibson; Thomas Gingeras; Daniel Goldowitz; Julian Gough; Sven Guhl; Reto Guler; Stefano Gustincich; Thomas J. Ha; Masahide Hamaguchi; Mitsuko Hara; Matthias Harbers; Jayson Harshbarger; Akira Hasegawa; Yuki Hasegawa; Takehiro Hashimoto; Meenhard Herlyn; Kelly J. Hitchens; Shannan J. Ho Sui; Oliver M. Hofmann; Ilka Hoof; Fumi Hori; Lukasz Huminiecki; Kei Iida; Tomokatsu Ikawa; Boris R. Jankovic; Hui Jia; Anagha Joshi; Giuseppe Jurman; Bogumil Kaczkowski; Chieko Kai; Kaoru Kaida; Ai Kaiho; Kazuhiro Kajiyama; Mutsumi Kanamori-Katayama; ArtemS Kasianov; Takeya Kasukawa; Shintaro Katayama; Sachi Kato; Shuji Kawaguchi; Hiroshi Kawamoto; Yuki I. Kawamura; Tsugumi Kawashima; Judith S. Kempfle; Tony J. Kenna; Juha Kere; Levon M. Khachigian; Toshio Kitamura; S. Peter Klinken; Alan J. Knox; Miki Kojima; Soichi Kojima; Naoto Kondo; Haruhiko Koseki; Shigeo Koyasu; Sarah Krampitz; Atsutaka Kubosaki; Andrew T. Kwon; Jeroen F. J. Laros; Weonju Lee; Andreas Lennartsson; Kang Li; Berit Lilje; Leonard Lipovich; Alan Mackay-sim; Ri-ichiroh Manabe; Jessica C. Mar; Benoit Marchand; Anthony Mathelier; Niklas Mejhert; Alison Meynert; Yosuke Mizuno; David A. de Lima Morais; Hiromasa Morikawa; Mitsuru Morimoto; Kazuyo Moro; Efthymios Motakis; Hozumi Motohashi; Christine L. Mummery; Mitsuyoshi Murata; Sayaka Nagao-Sato; Yutaka Nakachi; Fumio Nakahara; Toshiyuki Nakamura; Yukio Nakamura; Kenichi Nakazato; Erik Van Nimwegen; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Tadasuke Nozaki; Soichi Ogishima; Naganari Ohkura; Hiroko Ohmiya; Hiroshi Ohno; Mitsuhiro Ohshima; Mariko Okada-Hatakeyama; Yasushi Okazaki; Valerio Orlando; Dmitry A. Ovchinnikov; Arnab Pain; Robert Passier; Margaret Patrikakis; Helena Persson; Silvano Piazza; James G. D. Prendergast; Owen J. L. Rackham; Jordan A. Ramilowski; Mamoon Rashid; Timothy Ravasi; Patrizia Rizzu; Marco Roncador; Sugata Roy; Morten B. Rye; Eri Saijyo; Antti Sajantila; Akiko Saka; Shimon Sakaguchi; Mizuho Sakai; Hiroki Sato; Hironori Satoh; Suzana Savvi; Alka Saxena; Claudio Schneider; Erik A. Schultes; Gundula G. Schulze-Tanzil; Anita Schwegmann; Thierry Sengstag; Guojun Sheng; Hisashi Shimoji; Yishai Shimoni; Jay W. Shin; Christophe Simon; Daisuke Sugiyama; Takaaki Sugiyama; Masanori Suzuki; Naoko Suzuki; Rolf K. Swoboda; Peter A. C. 't Hoen; Michihira Tagami; Naoko Takahashi; Jun Takai; Hiroshi Tanaka; Hideki Tatsukawa; Zuotian Tatum; Mark Thompson; Hiroo Toyoda; Tetsuro Toyoda; Eivind Valen; Marc van de Wetering; Linda M. van den Berg; Roberto Verardo; Dipti Vijayan; Ilya E. Vorontsov; Wyeth W. Wasserman; Shoko Watanabe; Christine A. Wells; Louise N. Winteringham; Ernst Wolvetang; Emily J. Wood; Yoko Yamaguchi; Masayuki Yamamoto; Misako Yoneda; Yohei Yonekura; Shigehiro Yoshida; Susan E. Zabierowski; Peter G. Zhang; Xiaobei Zhao; Silvia Zucchelli; Kim M. Summers; Harukazu Suzuki; Carsten O. Daub; Jun Kawai; Peter Heutink; Winston Hide; Tom C. Freeman; Boris Lenhard; Vladimir B. Bajic; Martin S. Taylor; Vsevolod J. Makeev; Albin Sandelin; David A. Hume; Piero Carninci; Yoshihide Hayashizaki; FANTOM Consortium

doi:10.1038/nature13182

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A promoter-level mammalian expression atlas

Journal article

Peer reviewed

A promoter-level mammalian expression atlas

Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, …

Nature (London), Vol.507(7493), pp.462-470

27/03/2014

DOI: https://doi.org/10.1038/nature13182

PMCID: PMC4529748

PMID: 24670764

Abstract

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis revealskey transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

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Title: A promoter-level mammalian expression atlas
Creators - without role: Alistair R. R. Forrest - RIKEN
Hideya Kawaji - RIKEN
Michael Rehli - College Station Medical Center
J. Kenneth Baillie - University of Edinburgh
Michiel J. L. de Hoon - RIKEN
Vanja Haberle - University of Bergen
Timo Lassmann - RIKEN
Ivan V. Kulakovskiy - Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia
Marina Lizio - RIKEN
Masayoshi Itoh - RIKEN
Robin Andersson - University of Copenhagen
Christopher J. Mungall - Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA
Terrence F. Meehan - European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England
Sebastian Schmeier - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Nicolas Bertin - RIKEN
Mette Jorgensen - University of Copenhagen
Emmanuel Dimont - Harvard University
Erik Arner - RIKEN
Christian Schmidl - College Station Medical Center
Ulf Schaefer - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Yulia A. Medvedeva - Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia
Charles Plessy - RIKEN
Morana Vitezic - RIKEN
Jessica Severin - RIKEN
Colin A. Semple - University of Edinburgh
Yuri Ishizu - RIKEN
Robert S. Young - University of Edinburgh
Margherita Francescatto - University of Amsterdam
Intikhab Alam - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Davide Albanese - Fdn Bruno Kessler, I-38123 Trento, Italy
Gabriel M. Altschuler - Harvard University
Takahiro Arakawa - RIKEN
John A. C. Archer - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Peter Arner - Karolinska Institutet
Magda Babina - College Station Medical Center
Sarah Rennie - University of Edinburgh
Piotr J. Balwierz - University of Basel
Anthony G. Beckhouse - University of Queensland
Swati Pradhan-Bhatt - University of Delaware
Judith A. Blake - Jackson Memorial Hospital
Antje Blumenthal - University of Queensland
Beatrice Bodega - IRCCS Fdn Santa Lucia, I-00143 Rome, Italy
Alessandro Bonetti - RIKEN
James Briggs - University of Queensland
Frank Brombacher - Int Ctr Genet Engn & Biotechnol ICGEB Cape Town C, ZA-7925 Cape Town, South Africa
A. Maxwell Burroughs - RIKEN
Andrea Califano - Columbia University
Carlo V. Cannistraci - KAUST, Biol & Environm Sci & Engn Div, Thuwal 239556900, Saudi Arabia
Daniel Carbajo - Albert Einstein College of Medicine
Yun Chen - University of Copenhagen
Marco Chierici - Fdn Bruno Kessler, I-38123 Trento, Italy
Yari Ciani - LNCIB, I-34149 Trieste, Italy
Hans C. Clevers - Hubrecht Inst, NL-3584 CT Utrecht, Netherlands
Emiliano Dalla - LNCIB, I-34149 Trieste, Italy
Carrie A. Davis - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11797 USA
Michael Detmar - ETH, Inst Pharmaceut Sci, CH-8093 Zurich, Switzerland
Alexander D. Diehl - University at Buffalo, State University of New York
Taeko Dohi - College Station Medical Center
Finn Drablos - College Station Medical Center
Albert S. B. Edge - Harvard University
Matthias Edinger - College Station Medical Center
Karl Ekwall - Karolinska Institutet
Mitsuhiro Endoh - RIKEN
Hideki Enomoto - RIKEN
Michela Fagiolini - Harvard University
Lynsey Fairbairn - University of Edinburgh
Hai Fang - University of Bristol
Mary C. Farach-Carson - Rice University
Geoffrey J. Faulkner - Mater Med Res Inst, Cancer Biol Program, South Brisbane, Qld 4101, Australia
Alexander V. Favorov - Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia
Malcolm E. Fisher - University of Edinburgh
Martin C. Frith - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Koto Ku, Tokyo 1350064, Japan
Rie Fujita - Tohoku University
Shiro Fukuda - RIKEN
Cesare Furlanello - Fdn Bruno Kessler, I-38123 Trento, Italy
Masaaki Furuno - RIKEN
Jun-ichi Furusawa - RIKEN
Teunis B. Geijtenbeek - University of Amsterdam
Andrew P. Gibson - Leiden University
Thomas Gingeras - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11797 USA
Daniel Goldowitz - University of British Columbia
Julian Gough - University of Bristol
Sven Guhl - College Station Medical Center
Reto Guler - Int Ctr Genet Engn & Biotechnol ICGEB Cape Town C, ZA-7925 Cape Town, South Africa
Stefano Gustincich - SISSA, I-34136 Trieste, Italy
Thomas J. Ha - University of British Columbia
Masahide Hamaguchi - Osaka University
Mitsuko Hara - RIKEN
Matthias Harbers - RIKEN
Jayson Harshbarger - RIKEN
Akira Hasegawa - RIKEN
Yuki Hasegawa - RIKEN
Takehiro Hashimoto - RIKEN
Meenhard Herlyn - The Wistar Institute
Kelly J. Hitchens - University of Queensland
Shannan J. Ho Sui - Harvard University
Oliver M. Hofmann - Harvard University
Ilka Hoof - University of Copenhagen
Fumi Hori - RIKEN
Lukasz Huminiecki - Karolinska Institutet
Kei Iida - RIKEN
Tomokatsu Ikawa - RIKEN
Boris R. Jankovic - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Hui Jia - Wayne State University
Anagha Joshi - University of Edinburgh
Giuseppe Jurman - Fdn Bruno Kessler, I-38123 Trento, Italy
Bogumil Kaczkowski - RIKEN
Chieko Kai - The University of Tokyo
Kaoru Kaida - RIKEN
Ai Kaiho - RIKEN
Kazuhiro Kajiyama - RIKEN
Mutsumi Kanamori-Katayama - RIKEN
ArtemS Kasianov - Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia
Takeya Kasukawa - DGT
Shintaro Katayama - RIKEN
Sachi Kato - RIKEN
Shuji Kawaguchi - RIKEN
Hiroshi Kawamoto - RIKEN
Yuki I. Kawamura - College Station Medical Center
Tsugumi Kawashima - RIKEN
Judith S. Kempfle - Harvard University
Tony J. Kenna - University of Queensland
Juha Kere - Karolinska Institutet
Levon M. Khachigian - Univ New S Wales, Ctr Vasc Res, Sydney, NSW 2052, Australia
Toshio Kitamura - The University of Tokyo
S. Peter Klinken - University of Western Australia
Alan J. Knox - University of Nottingham
Miki Kojima - RIKEN
Soichi Kojima - RIKEN
Naoto Kondo - RIKEN
Haruhiko Koseki - RIKEN
Shigeo Koyasu - RIKEN
Sarah Krampitz - ETH, Inst Pharmaceut Sci, CH-8093 Zurich, Switzerland
Atsutaka Kubosaki - RIKEN
Andrew T. Kwon - RIKEN
Jeroen F. J. Laros - Leiden University
Weonju Lee - Supreme Council Of Health
Andreas Lennartsson - Karolinska Institutet
Kang Li - University of Copenhagen
Berit Lilje - University of Copenhagen
Leonard Lipovich - Wayne State University
Alan Mackay-sim - Griffith University
Ri-ichiroh Manabe - RIKEN
Jessica C. Mar - Albert Einstein College of Medicine
Benoit Marchand - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Anthony Mathelier - University of British Columbia
Niklas Mejhert - Karolinska Institutet
Alison Meynert - University of Edinburgh
Yosuke Mizuno - College Station Medical Center
David A. de Lima Morais - University of Bristol
Hiromasa Morikawa - Osaka University
Mitsuru Morimoto - RIKEN
Kazuyo Moro - RIKEN
Efthymios Motakis - RIKEN
Hozumi Motohashi - Tohoku University
Christine L. Mummery - Leiden University
Mitsuyoshi Murata - RIKEN
Sayaka Nagao-Sato - RIKEN
Yutaka Nakachi - College Station Medical Center
Fumio Nakahara - The University of Tokyo
Toshiyuki Nakamura - The University of Tokyo
Yukio Nakamura - RIKEN
Kenichi Nakazato - RIKEN
Erik Van Nimwegen - University of Basel
Noriko Ninomiya - RIKEN
Hiromi Nishiyori - RIKEN
Shohei Noma - RIKEN
Tadasuke Nozaki - Supreme Council Of Health
Soichi Ogishima - College Station Medical Center
Naganari Ohkura - Osaka University
Hiroko Ohmiya - RIKEN
Hiroshi Ohno - RIKEN
Mitsuhiro Ohshima - Ohu University
Mariko Okada-Hatakeyama - RIKEN
Yasushi Okazaki - College Station Medical Center
Valerio Orlando - IRCCS Fdn Santa Lucia, I-00143 Rome, Italy
Dmitry A. Ovchinnikov - University of Queensland
Arnab Pain - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Robert Passier - Leiden University
Margaret Patrikakis - Univ New S Wales, Ctr Vasc Res, Sydney, NSW 2052, Australia
Helena Persson - Karolinska Institutet
Silvano Piazza - LNCIB, I-34149 Trieste, Italy
James G. D. Prendergast - University of Edinburgh
Owen J. L. Rackham - University of Bristol
Jordan A. Ramilowski - RIKEN
Mamoon Rashid - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Timothy Ravasi - KAUST, Biol & Environm Sci & Engn Div, Thuwal 239556900, Saudi Arabia
Patrizia Rizzu - University of Amsterdam
Marco Roncador - Fdn Bruno Kessler, I-38123 Trento, Italy
Sugata Roy - RIKEN
Morten B. Rye - College Station Medical Center
Eri Saijyo - RIKEN
Antti Sajantila - University of Helsinki
Akiko Saka - RIKEN
Shimon Sakaguchi - Osaka University
Mizuho Sakai - RIKEN
Hiroki Sato - The University of Tokyo
Hironori Satoh - Tohoku University
Suzana Savvi - Int Ctr Genet Engn & Biotechnol ICGEB Cape Town C, ZA-7925 Cape Town, South Africa
Alka Saxena - RIKEN
Claudio Schneider - LNCIB, I-34149 Trieste, Italy
Erik A. Schultes - Leiden University
Gundula G. Schulze-Tanzil - Charité - Universitätsmedizin Berlin
Anita Schwegmann - Int Ctr Genet Engn & Biotechnol ICGEB Cape Town C, ZA-7925 Cape Town, South Africa
Thierry Sengstag - RIKEN
Guojun Sheng - RIKEN
Hisashi Shimoji - RIKEN
Yishai Shimoni - Columbia University
Jay W. Shin - RIKEN
Christophe Simon - RIKEN
Daisuke Sugiyama - Kyushu University
Takaaki Sugiyama - The University of Tokyo
Masanori Suzuki - RIKEN
Naoko Suzuki - RIKEN
Rolf K. Swoboda - The Wistar Institute
Peter A. C. 't Hoen - Leiden University
Michihira Tagami - RIKEN
Naoko Takahashi - RIKEN
Jun Takai - Tohoku University
Hiroshi Tanaka - College Station Medical Center
Hideki Tatsukawa - Nagoya University
Zuotian Tatum - Leiden University
Mark Thompson - Leiden University
Hiroo Toyoda - Supreme Council Of Health
Tetsuro Toyoda - RIKEN
Eivind Valen - Harvard University
Marc van de Wetering - Hubrecht Inst, NL-3584 CT Utrecht, Netherlands
Linda M. van den Berg - University of Amsterdam
Roberto Verardo - LNCIB, I-34149 Trieste, Italy
Dipti Vijayan - University of Queensland
Ilya E. Vorontsov - Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia
Wyeth W. Wasserman - University of British Columbia
Shoko Watanabe - RIKEN
Christine A. Wells - University of Queensland
Louise N. Winteringham - University of Western Australia
Ernst Wolvetang - University of Queensland
Emily J. Wood - Wayne State University
Yoko Yamaguchi - Nihon University
Masayuki Yamamoto - Tohoku University
Misako Yoneda - The University of Tokyo
Yohei Yonekura - RIKEN
Shigehiro Yoshida - RIKEN
Susan E. Zabierowski - The Wistar Institute
Peter G. Zhang - University of British Columbia
Xiaobei Zhao - University of Copenhagen
Silvia Zucchelli - SISSA, I-34136 Trieste, Italy
Kim M. Summers - University of Edinburgh
Harukazu Suzuki - RIKEN
Carsten O. Daub - RIKEN
Jun Kawai - RIKEN
Peter Heutink - University of Amsterdam
Winston Hide - Harvard University
Tom C. Freeman - University of Edinburgh
Boris Lenhard - University of London
Vladimir B. Bajic - KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
Martin S. Taylor - University of Edinburgh
Vsevolod J. Makeev - Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia
Albin Sandelin - University of Copenhagen
David A. Hume - University of Edinburgh
Piero Carninci - RIKEN
Yoshihide Hayashizaki - RIKEN
FANTOM Consortium
Publication Details: Nature (London), Vol.507(7493), pp.462-470
Publisher: Springer Nature
Number of pages: 22
Grant note: R01DE022969 / NATIONAL INSTITUTE OF DENTAL & CRANIOFACIAL RESEARCH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Dental & Craniofacial Research (NIDCR) MC_PC_U127597124 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) NNF12OC1016371 / Novo Nordisk Fonden; Novo Nordisk Foundation RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan MEXT; Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) MC_PC_U127597124 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC); European Commission R82-2010-6779 / Lundbeck Foundation; Lundbeckfonden 103258/Z/13/Z / Wellcome Trust; European Commission Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program(RIKEN PMI) BBS/E/D/20211550 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) BBS/E/D/20211552 / BBSRC; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) MEXT, Japan; Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) R01GM084875 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS)
Identifiers: 9921459208331
Academic Unit: King Saud Bin Abdulaziz University for Health Sciences; King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article