A promoter-level mammalian expression atlas

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

Research output: Contribution to journalArticlepeer-review

973 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 ‘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 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 (US)
Pages (from-to)462-470
Number of pages9
JournalNature
Volume507
Issue number7493
DOIs
StatePublished - Mar 27 2014

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