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 Kaida; Ai 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

doi:10.1038/nature13182

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 journal › Article › peer-review

1455 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 language	English (US)
Pages (from-to)	462-470
Number of pages	9
Journal	Nature
Volume	507
Issue number	7493
DOIs	https://doi.org/10.1038/nature13182
State	Published - Mar 27 2014

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y. Hayashizaki and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y. Hayashizaki. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program(RIKEN PMI) to Y. Hayashizaki and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan. Extended acknowledgements are provided in the Supplementary Information.

Access to Document

10.1038/nature13182

https://repository.kaust.edu.sa/bitstream/10754/565944/1/nihms607910.pdf

Cite this

Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Iida, K., Ikawa, T., Jankovic, B. R., Jia, H., Joshi, A. M., Jurman, G., Kaczkowski, B., Kai, C., ... Huminiecki, Ł. B. (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462-470. https://doi.org/10.1038/nature13182

@article{e2e6515a902e49b08f232e2947c59317,

title = "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 {\textquoteleft}housekeeping{\textquoteright}, 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.",

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

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y. Hayashizaki and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y. Hayashizaki. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program(RIKEN PMI) to Y. Hayashizaki and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan. Extended acknowledgements are provided in the Supplementary Information.",

year = "2014",

month = mar,

day = "27",

doi = "10.1038/nature13182",

language = "English (US)",

volume = "507",

pages = "462--470",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7493",

}

Forest, ARR, Kawaji, H, Rehli, M, Baillie, JK, De Hoon, MJL, Haberle, V, Lassmann, T, Kulakovskiy, IV, Lizio, M, Itoh, M, Andersson, R, Iida, K, Ikawa, T, Jankovic, BR, Jia, H, Joshi, AM, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Mungall, CJ, Kajiyama, K, Kanamori-Katayama, M, Kasianov, AS, Kasukawa, T, Katayama, S, Kato, S, Kawaguchi, S, Kawamoto, H, Kawamura, YI, Kawashima, T, Meehan, TF, Kempfle, JS, Kenna, TJ, Kere, J, Khachigian, LM, Kitamura, T, Klinken, SP, Knox, A, Kojima, M, Kojima, S, Kondo, N, Schmeier, S, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kwon, AT, Laros, JFJ, Lee, W, Lennartsson, A, Li, K, Lilje, B, Bertin, N, Lipovich, L, MacKay-Sim, A, Manabe, R, Mar, J, Marchand, B, Mathelier, A, Mejhert, N, Meynert, AM, Mizuno, Y, De Morais, DAL, Jørgensen, MC, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, CL, Murata, M, Nagao-Sato, S, Nakachi, Y, Nakahara, F, Dimont, E, Nakamura, T, Nakamura, Y, Nakazato, K, Van Nimwegen, E, Ninomiya, N, Nishiyori, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Arner, E, Ohmiya, H, Ohno, H, Ohshima, M, Okada-Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, DA, Pain, A, Passier, RCJJ, Patrikakis, M, Schmidl, C, Persson, HA, Piazza, S, Prendergast, JGD, Rackham, OJL, Ramilowski, JA, Rashid, M, Ravasi, T, Rizzu, P, Roncador, M, Roy, S, Schaefer, U, Rye, MB, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sato, H, Satoh, H, Savvi, S, Saxena, A, Medvedeva, Y, Schneider, CH, Schultes, EA, Schulze-Tanzil, GG, Schwegmann, A, Sengstag, T, Sheng, G, Shimoji, H, Shimoni, Y, Shin, JW, Simon, CM, Plessy, C, Sugiyama, D, Sugiyama, T, Suzuki, M, Suzuki, N, Swoboda, RK, 't Hoen, PAC, Tagami, M, Tagami, N, Takai, J, Tanaka, H, Vitezic, M, Tatsukawa, H, Tatum, Z, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, Van De Wetering, ML, Van Den Berg, LM, Verardo, R, Vijayan, D, Severin, JM, Vorontsov, IE, Wasserman, WW, Watanabe, S, Wells, CA, Winteringham, LN, Wolvetang, EJ, Wood, EJ, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Semple, CAM, Yonekura, Y, Yoshida, S, Zabierowski, SE, Zhang, P, Zhao, X, Zucchelli, S, Summers, KM, Suzuki, H, Daub, CO, Kawai, J, Ishizu, Y, Heutink, P, Hide, W, Freeman, TC, Lenhard, B, Bajic, VB, Taylor, MS, Makeev, VJ, Sandelin, A, Hume, DA, Carninci, P, Young, RS, Hayashizaki, YY, Francescatto, M, Alam, I, Albanese, D, Altschule, GM, Arakawa, T, Archer, JAC, Arner, P, Babina, M, Rennie, S, Balwierz, PJ, Beckhouse, AG, Pradhan-Bhatt, S, Blake, JA, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, JA, Brombacher, F, Burroughs, AM, Califano, AC, Cannistraci, C, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, HC, Dalla, E, Davis, CA, Detmar, MJ, Diehl, AD, Dohi, T, Drabløs, F, Edge, ASBB, Edinger, MG, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, LR, Fang, H, Farach-Carson, MC, Faulkner, GJ, Favorov, AV, Fisher, ME, Frith, MC, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, TBH, Gibson, AP, Gingeras, TR, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, S, Ha, T, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, MF, Hitchens, KJ, Sui, SJH, Hofmann, OM, Hoof, I, Hori, F & Huminiecki, ŁB 2014, 'A promoter-level mammalian expression atlas', Nature, vol. 507, no. 7493, pp. 462-470. https://doi.org/10.1038/nature13182

TY - JOUR

T1 - A promoter-level mammalian expression atlas

AU - Forest, Alistair R R

AU - Kawaji, Hideya

AU - Rehli, Michael

AU - Baillie, John Kenneth

AU - De Hoon, Michiel Jl L

AU - Haberle, Vanja

AU - Lassmann, Timo

AU - Kulakovskiy, Ivan V.

AU - Lizio, Marina

AU - Itoh, Masayoshi

AU - Andersson, Robin

AU - Iida, Kei

AU - Ikawa, Tomokatsu

AU - Jankovic, Boris R.

AU - Jia, Hui

AU - Joshi, Anagha Madhusudan

AU - Jurman, Giuseppe

AU - Kaczkowski, Bogumił

AU - Kai, Chieko

AU - Kaida, Kaoru

AU - Kaiho, Ai

AU - Mungall, Christopher J.

AU - Kajiyama, Kazuhiro

AU - Kanamori-Katayama, Mutsumi

AU - Kasianov, Artem S.

AU - Kasukawa, Takeya

AU - Katayama, Shintaro

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N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y. Hayashizaki and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y. Hayashizaki. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program(RIKEN PMI) to Y. Hayashizaki and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan. Extended acknowledgements are provided in the Supplementary Information.

PY - 2014/3/27

Y1 - 2014/3/27

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 ‘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.

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 ‘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.

UR - http://hdl.handle.net/10754/565944

UR - http://www.nature.com/articles/nature13182

UR - http://www.scopus.com/inward/record.url?scp=84897406127&partnerID=8YFLogxK

U2 - 10.1038/nature13182

DO - 10.1038/nature13182

M3 - Article

SN - 0028-0836

VL - 507

SP - 462

EP - 470

JO - Nature

JF - Nature

IS - 7493

ER -

A promoter-level mammalian expression atlas

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