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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 Jørgensen
  • , 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 Altschuler, Davide Albanese, Gabriel M. Altschule, 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 Drabløs, 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, Artem S. 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.Lima De 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 Tagami, 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, Lenhard Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki
  • RIKEN
  • University of Regensburg
  • Regensburg Centre for Interventional Immunology (RCI)
  • University of Edinburgh
  • University of Bergen
  • Imperial College London
  • RAS - Engelhardt Institute of Molecular Biology
  • Russian Academy of Sciences
  • University of Copenhagen
  • Lawrence Berkeley National Laboratory
  • Wellcome Trust
  • King Abdullah University of Science and Technology
  • Massey University
  • Harvard University
  • Research Center for Molecular Medicine of the Austrian Academy of Sciences
  • Institute of Predictive and Personalized Medicine of Cancer
  • Karolinska Institutet
  • Amsterdam University Medical Centers location VUmc
  • University of Porto
  • Fondazione Bruno Kessler
  • Charité – Universitätsmedizin Berlin
  • University of Basel
  • University of Queensland
  • University of Delaware
  • Jackson Laboratory
  • IRCCS Fondazione Santa Lucia - Roma
  • International Centre for Genetic Engineering and Biotechnology
  • University of Cape Town
  • Columbia University
  • Technische Universität Dresden
  • Albert Einstein College of Medicine
  • Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB)
  • Netherlands Institute for Developmental Biology
  • Royal Netherlands Academy of Arts and Sciences
  • Utrecht University
  • Cold Spring Harbor Laboratory
  • Swiss Federal Institute of Technology Zurich
  • SUNY Buffalo
  • National Center for Global Health and Medicine
  • Norwegian University of Science and Technology
  • Massachusetts Eye and Ear
  • Boston Children's Hospital
  • University of Bristol
  • Rice University
  • Mater Group
  • Johns Hopkins University
  • State Research Institute of Genetics and Selection of Industrial Microorganisms of NRC Kurchatov Institute
  • National Institute of Advanced Industrial Science and Technology
  • Tohoku University
  • Keio University
  • University of Amsterdam
  • Leiden University
  • University of British Columbia
  • International School for Advanced Studies
  • The University of Osaka
  • Wistar Institute
  • Wayne State University
  • The University of Tokyo
  • Science for Life Laboratory
  • University of New South Wales
  • University of Western Australia
  • University of Nottingham
  • Griffith University Queensland
  • Saitama Medical University
  • Japan Science and Technology Agency
  • Tokyo University of Pharmacy and Life Sciences
  • Institute of Science Tokyo
  • Ohu University
  • University of Helsinki
  • Guy's and St Thomas' NHS Foundation Trust
  • University of Udine
  • Kyushu University
  • Nagoya University
  • Nihon University
  • Moscow Institute of Physics and Technology

Research output: Contribution to journalArticlepeer-review

1555 Scopus citations

Abstract

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 â ̃ housekeepingâ ™, 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 reveals key 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.

Original languageEnglish
Pages (from-to)462-470
Number of pages9
JournalNature
Volume507
Issue number7493
DOIs
StatePublished - 1 Jan 2014

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