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A promoter-level mammalian expression atlas.


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.

SUBMITTER: FANTOM Consortium and the RIKEN PMI and CLST (DGT) 

PROVIDER: S-EPMC4529748 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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A promoter-level mammalian expression atlas.

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

Nature 20140301 7493


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 com  ...[more]

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