抄録
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.
本文言語 | 英語 |
---|---|
ページ(範囲) | 462-470 |
ページ数 | 9 |
ジャーナル | Nature |
巻 | 507 |
号 | 7493 |
DOI | |
出版ステータス | 出版済み - 1 1月 2014 |
フィンガープリント
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In: Nature, Vol. 507, No. 7493, 01.01.2014, p. 462-470.
研究成果: ジャーナルへの寄稿 › 記事 › 査読
TY - JOUR
T1 - A promoter-level mammalian expression atlas
AU - Forrest, Alistair R.R.
AU - Kawaji, Hideya
AU - Rehli, Michael
AU - Baillie, J. Kenneth
AU - De Hoon, Michiel J.L.
AU - Haberle, Vanja
AU - Lassmann, Timo
AU - Kulakovskiy, Ivan V.
AU - Lizio, Marina
AU - Itoh, Masayoshi
AU - Andersson, Robin
AU - Mungall, Christopher J.
AU - Meehan, Terrence F.
AU - Schmeier, Sebastian
AU - Bertin, Nicolas
AU - Jørgensen, Mette
AU - Dimont, Emmanuel
AU - Arner, Erik
AU - Schmidl, Christian
AU - Schaefer, Ulf
AU - Medvedeva, Yulia A.
AU - Plessy, Charles
AU - Vitezic, Morana
AU - Severin, Jessica
AU - Semple, Colin A.
AU - Ishizu, Yuri
AU - Young, Robert S.
AU - Francescatto, Margherita
AU - Altschuler, Intikhab Alam
AU - Albanese, Davide
AU - Altschule, Gabriel M.
AU - Arakawa, Takahiro
AU - Archer, John A.C.
AU - Arner, Peter
AU - Babina, Magda
AU - Rennie, Sarah
AU - Balwierz, Piotr J.
AU - Beckhouse, Anthony G.
AU - Pradhan-Bhatt, Swati
AU - Blake, Judith A.
AU - Blumenthal, Antje
AU - Bodega, Beatrice
AU - Bonetti, Alessandro
AU - Briggs, James
AU - Brombacher, Frank
AU - Burroughs, A. Maxwell
AU - Califano, Andrea
AU - Cannistraci, Carlo V.
AU - Carbajo, Daniel
AU - Chen, Yun
AU - Chierici, Marco
AU - Ciani, Yari
AU - Clevers, Hans C.
AU - Dalla, Emiliano
AU - Davis, Carrie A.
AU - Detmar, Michael
AU - Diehl, Alexander D.
AU - Dohi, Taeko
AU - Drabløs, Finn
AU - Edge, Albert S.B.
AU - Edinger, Matthias
AU - Ekwall, Karl
AU - Endoh, Mitsuhiro
AU - Enomoto, Hideki
AU - Fagiolini, Michela
AU - Fairbairn, Lynsey
AU - Fang, Hai
AU - Farach-Carson, Mary C.
AU - Faulkner, Geoffrey J.
AU - Favorov, Alexander V.
AU - Fisher, Malcolm E.
AU - Frith, Martin C.
AU - Fujita, Rie
AU - Fukuda, Shiro
AU - Furlanello, Cesare
AU - Furuno, Masaaki
AU - Furusawa, Jun Ichi
AU - Geijtenbeek, Teunis B.
AU - Gibson, Andrew P.
AU - Gingeras, Thomas
AU - Goldowitz, Daniel
AU - Gough, Julian
AU - Guhl, Sven
AU - Guler, Reto
AU - Gustincich, Stefano
AU - Ha, Thomas J.
AU - Hamaguchi, Masahide
AU - Hara, Mitsuko
AU - Harbers, Matthias
AU - Harshbarger, Jayson
AU - Hasegawa, Akira
AU - Hasegawa, Yuki
AU - Hashimoto, Takehiro
AU - Herlyn, Meenhard
AU - Hitchens, Kelly J.
AU - Sui, Shannan J.Ho
AU - Hofmann, Oliver M.
AU - Hoof, Ilka
AU - Hori, Fumi
AU - Huminiecki, Lukasz
AU - Iida, Kei
AU - Ikawa, Tomokatsu
AU - Jankovic, Boris R.
AU - Jia, Hui
AU - Joshi, Anagha
AU - Jurman, Giuseppe
AU - Kaczkowski, Bogumil
AU - Kai, Chieko
AU - Kaida, Kaoru
AU - Kaiho, Ai
AU - Kajiyama, Kazuhiro
AU - Kanamori-Katayama, Mutsumi
AU - Kasianov, Artem S.
AU - Kasukawa, Takeya
AU - Katayama, Shintaro
AU - Kato, Sachi
AU - Kawaguchi, Shuji
AU - Kawamoto, Hiroshi
AU - Kawamura, Yuki I.
AU - Kawashima, Tsugumi
AU - Kempfle, Judith S.
AU - Kenna, Tony J.
AU - Kere, Juha
AU - Khachigian, Levon M.
AU - Kitamura, Toshio
AU - Klinken, S. Peter
AU - Knox, Alan J.
AU - Kojima, Miki
AU - Kojima, Soichi
AU - Kondo, Naoto
AU - Koseki, Haruhiko
AU - Koyasu, Shigeo
AU - Krampitz, Sarah
AU - Kubosaki, Atsutaka
AU - Kwon, Andrew T.
AU - Laros, Jeroen F.J.
AU - Lee, Weonju
AU - Lennartsson, Andreas
AU - Li, Kang
AU - Lilje, Berit
AU - Lipovich, Leonard
AU - Mackay-sim, Alan
AU - Manabe, Ri Ichiroh
AU - Mar, Jessica C.
AU - Marchand, Benoit
AU - Mathelier, Anthony
AU - Mejhert, Niklas
AU - Meynert, Alison
AU - Mizuno, Yosuke
AU - De Morais, David A.Lima
AU - Morikawa, Hiromasa
AU - Morimoto, Mitsuru
AU - Moro, Kazuyo
AU - Motakis, Efthymios
AU - Motohashi, Hozumi
AU - Mummery, Christine L.
AU - Murata, Mitsuyoshi
AU - Nagao-Sato, Sayaka
AU - Nakachi, Yutaka
AU - Nakahara, Fumio
AU - Nakamura, Toshiyuki
AU - Nakamura, Yukio
AU - Nakazato, Kenichi
AU - Van Nimwegen, Erik
AU - Ninomiya, Noriko
AU - Nishiyori, Hiromi
AU - Noma, Shohei
AU - Nozaki, Tadasuke
AU - Ogishima, Soichi
AU - Ohkura, Naganari
AU - Ohmiya, Hiroko
AU - Ohno, Hiroshi
AU - Ohshima, Mitsuhiro
AU - Okada-Hatakeyama, Mariko
AU - Okazaki, Yasushi
AU - Orlando, Valerio
AU - Ovchinnikov, Dmitry A.
AU - Pain, Arnab
AU - Passier, Robert
AU - Patrikakis, Margaret
AU - Persson, Helena
AU - Piazza, Silvano
AU - Prendergast, James G.D.
AU - Rackham, Owen J.L.
AU - Ramilowski, Jordan A.
AU - Rashid, Mamoon
AU - Ravasi, Timothy
AU - Rizzu, Patrizia
AU - Roncador, Marco
AU - Roy, Sugata
AU - Rye, Morten B.
AU - Saijyo, Eri
AU - Sajantila, Antti
AU - Saka, Akiko
AU - Sakaguchi, Shimon
AU - Sakai, Mizuho
AU - Sato, Hiroki
AU - Satoh, Hironori
AU - Savvi, Suzana
AU - Saxena, Alka
AU - Schneider, Claudio
AU - Schultes, Erik A.
AU - Schulze-Tanzil, Gundula G.
AU - Schwegmann, Anita
AU - Sengstag, Thierry
AU - Sheng, Guojun
AU - Shimoji, Hisashi
AU - Shimoni, Yishai
AU - Shin, Jay W.
AU - Simon, Christophe
AU - Sugiyama, Daisuke
AU - Sugiyama, Takaaki
AU - Suzuki, Masanori
AU - Suzuki, Naoko
AU - Swoboda, Rolf K.
AU - 'T Hoen, Peter A.C.
AU - Tagami, Michihira
AU - Tagami, Naoko Takahashi
AU - Takai, Jun
AU - Tanaka, Hiroshi
AU - Tatsukawa, Hideki
AU - Tatum, Zuotian
AU - Thompson, Mark
AU - Toyoda, Hiroo
AU - Toyoda, Tetsuro
AU - Valen, Eivind
AU - Van De Wetering, Marc
AU - Van Den Berg, Linda M.
AU - Verardo, Roberto
AU - Vijayan, Dipti
AU - Vorontsov, Ilya E.
AU - Wasserman, Wyeth W.
AU - Watanabe, Shoko
AU - Wells, Christine A.
AU - Winteringham, Louise N.
AU - Wolvetang, Ernst
AU - Wood, Emily J.
AU - Yamaguchi, Yoko
AU - Yamamoto, Masayuki
AU - Yoneda, Misako
AU - Yonekura, Yohei
AU - Yoshida, Shigehiro
AU - Zabierowski, Susan E.
AU - Zhang, Peter G.
AU - Zhao, Xiaobei
AU - Zucchelli, Silvia
AU - Summers, Kim M.
AU - Suzuki, Harukazu
AU - Daub, Carsten O.
AU - Kawai, Jun
AU - Heutink, Peter
AU - Hide, Winston
AU - Freeman, Tom C.
AU - Lenhard, Boris
AU - Bajic, Lenhard Vladimir B.
AU - Taylor, Martin S.
AU - Makeev, Vsevolod J.
AU - Sandelin, Albin
AU - Hume, David A.
AU - Carninci, Piero
AU - Hayashizaki, Yoshihide
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84897406127&partnerID=8YFLogxK
U2 - 10.1038/nature13182
DO - 10.1038/nature13182
M3 - Article
C2 - 24670764
AN - SCOPUS:84897406127
SN - 0028-0836
VL - 507
SP - 462
EP - 470
JO - Nature
JF - Nature
IS - 7493
ER -