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PMID: 24670764 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A promoter-level mammalian expression atlas.

Nature ·Vol. 507 ·No. 7493 ·2014-03-27 ·Pages 462-70

FANTOM Consortium and the RIKEN PMI and CLST DGT, Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y

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.

MeSH Terms
Animals Atlases as Topic Cell Line Cells, Cultured Cluster Analysis Conserved Sequence/genetics Gene Expression Regulation/genetics Gene Regulatory Networks/genetics Genes, Essential/genetics Genome/genetics Humans Mice Molecular Sequence Annotation Open Reading Frames/genetics Organ Specificity Promoter Regions, Genetic/genetics RNA, Messenger/analysis,genetics Transcription Factors/metabolism Transcription Initiation Site Transcription, Genetic/genetics Transcriptome/genetics
Chemicals
RNA, Messenger Transcription Factors
Authors & Affiliations
262 authors, click to expand affiliations / ORCID
FANTOM Consortium and the RIKEN PMI and CLST (DGT)
Forrest Alistair R R
Kawaji Hideya
Rehli Michael
Baillie J Kenneth
de Hoon Michiel J L
Haberle Vanja
Lassmann Timo
Kulakovskiy Ivan V
Lizio Marina
Itoh Masayoshi
Andersson Robin
Mungall Christopher J
Meehan Terrence F
Schmeier Sebastian
Bertin Nicolas
Jørgensen Mette
Dimont Emmanuel
Arner Erik
Schmidl Christian
Schaefer Ulf
Medvedeva Yulia A
Plessy Charles
Vitezic Morana
Severin Jessica
Semple Colin A
Ishizu Yuri
Young Robert S
Francescatto Margherita
Alam Intikhab
Albanese Davide
Altschuler Gabriel M
Arakawa Takahiro
Archer John A C
Arner Peter
Babina Magda
Rennie Sarah
Balwierz Piotr J
Beckhouse Anthony G
Pradhan-Bhatt Swati
Blake Judith A
Blumenthal Antje
Bodega Beatrice
Bonetti Alessandro
Briggs James
Brombacher Frank
Burroughs A Maxwell
Califano Andrea
Cannistraci Carlo V
Carbajo Daniel
Chen Yun
Chierici Marco
Ciani Yari
Clevers Hans C
Dalla Emiliano
Davis Carrie A
Detmar Michael
Diehl Alexander D
Dohi Taeko
Drabløs Finn
Edge Albert S B
Edinger Matthias
Ekwall Karl
Endoh Mitsuhiro
Enomoto Hideki
Fagiolini Michela
Fairbairn Lynsey
Fang Hai
Farach-Carson Mary C
Faulkner Geoffrey J
Favorov Alexander V
Fisher Malcolm E
Frith Martin C
Fujita Rie
Fukuda Shiro
Furlanello Cesare
Furino Masaaki
Furusawa Jun-ichi
Geijtenbeek Teunis B
Gibson Andrew P
Gingeras Thomas
Goldowitz Daniel
Gough Julian
Guhl Sven
Guler Reto
Gustincich Stefano
Ha Thomas J
Hamaguchi Masahide
Hara Mitsuko
Harbers Matthias
Harshbarger Jayson
Hasegawa Akira
Hasegawa Yuki
Hashimoto Takehiro
Herlyn Meenhard
Hitchens Kelly J
Ho Sui Shannan J
Hofmann Oliver M
Hoof Ilka
Hori Furni
Huminiecki Lukasz
Iida Kei
Ikawa Tomokatsu
Jankovic Boris R
Jia Hui
Joshi Anagha
Jurman Giuseppe
Kaczkowski Bogumil
Kai Chieko
Kaida Kaoru
Kaiho Ai
Kajiyama Kazuhiro
Kanamori-Katayama Mutsumi
Kasianov Artem S
Kasukawa Takeya
Katayama Shintaro
Kato Sachi
Kawaguchi Shuji
Kawamoto Hiroshi
Kawamura Yuki I
Kawashima Tsugumi
Kempfle Judith S
Kenna Tony J
Kere Juha
Khachigian Levon M
Kitamura Toshio
Klinken S Peter
Knox Alan J
Kojima Miki
Kojima Soichi
Kondo Naoto
Koseki Haruhiko
Koyasu Shigeo
Krampitz Sarah
Kubosaki Atsutaka
Kwon Andrew T
Laros Jeroen F J
Lee Weonju
Lennartsson Andreas
Li Kang
Lilje Berit
Lipovich Leonard
Mackay-Sim Alan
Manabe Ri-ichiroh
Mar Jessica C
Marchand Benoit
Mathelier Anthony
Mejhert Niklas
Meynert Alison
Mizuno Yosuke
de Lima Morais David A
Morikawa Hiromasa
Morimoto Mitsuru
Moro Kazuyo
Motakis Efthymios
Motohashi Hozumi
Mummery Christine L
Murata Mitsuyoshi
Nagao-Sato Sayaka
Nakachi Yutaka
Nakahara Fumio
Nakamura Toshiyuki
Nakamura Yukio
Nakazato Kenichi
van Nimwegen Erik
Ninomiya Noriko
Nishiyori Hiromi
Noma Shohei
Noma Shohei
Noazaki Tadasuke
Ogishima Soichi
Ohkura Naganari
Ohimiya Hiroko
Ohno Hiroshi
Ohshima Mitsuhiro
Okada-Hatakeyama Mariko
Okazaki Yasushi
Orlando Valerio
Ovchinnikov Dmitry A
Pain Arnab
Passier Robert
Patrikakis Margaret
Persson Helena
Piazza Silvano
Prendergast James G D
Rackham Owen J L
Ramilowski Jordan A
Rashid Mamoon
Ravasi Timothy
Rizzu Patrizia
Roncador Marco
Roy Sugata
Rye Morten B
Saijyo Eri
Sajantila Antti
Saka Akiko
Sakaguchi Shimon
Sakai Mizuho
Sato Hiroki
Savvi Suzana
Saxena Alka
Schneider Claudio
Schultes Erik A
Schulze-Tanzil Gundula G
Schwegmann Anita
Sengstag Thierry
Sheng Guojun
Shimoji Hisashi
Shimoni Yishai
Shin Jay W
Simon Christophe
Sugiyama Daisuke
Sugiyama Takaai
Suzuki Masanori
Suzuki Naoko
Swoboda Rolf K
't Hoen Peter A C
Tagami Michihira
Takahashi Naoko
Takai Jun
Tanaka Hiroshi
Tatsukawa Hideki
Tatum Zuotian
Thompson Mark
Toyodo Hiroo
Toyoda Tetsuro
Valen Elvind
van de Wetering Marc
van den Berg Linda M
Verado Roberto
Vijayan Dipti
Vorontsov Ilya E
Wasserman Wyeth W
Watanabe Shoko
Wells Christine A
Winteringham Louise N
Wolvetang Ernst
Wood Emily J
Yamaguchi Yoko
Yamamoto Masayuki
Yoneda Misako
Yonekura Yohei
Yoshida Shigehiro
Zabierowski Susan E
Zhang Peter G
Zhao Xiaobei
Zucchelli Silvia
Summers Kim M
Suzuki Harukazu
Daub Carsten O
Kawai Jun
Heutink Peter
Hide Winston
Freeman Tom C
Lenhard Boris
Bajic Vladimir B
Taylor Martin S
Makeev Vsevolod J
Sandelin Albin
Hume David A
Carninci Piero
Hayashizaki Yoshihide
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Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
Published
2014-03-27
Pages
462-70
Language
English
Region
England
NLM ID
0410462
PMCID
PMC4529748
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BBS/E/D/20211550 · United Kingdom
NIDCR NIH HHS · R01 DE022969 · United States
Biotechnology and Biological Sciences Research Council · BB/G022771/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBS/E/D/20211551 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBS/E/D/20211552 · United Kingdom
NIGMS NIH HHS · R01 GM084875 · United States
Medical Research Council · MC_PC_U127597124 · United Kingdom
Medical Research Council · MC_UP_1102/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/I001107/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/F003722/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/I024801/1 · United Kingdom
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