A promoter-level mammalian expression atlas

Forrest, 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.; Mungall, C.J.; Meehan, T.F.; Schmeier, S.; Bertin, N.; Jorgensen, M.; Dimont, E.; Arner, E.; Schmidl, C.; Schaefer, U.; Medvedeva, Y.A.; Plessy, C.; Vitezic, M.; Severin, J.; Semple, C.A.; Ishizu, Y.; Young, R.S.; Francescatto, M.; Altschuler, I.A.; Albanese, D.; Altschule, G.M.; Arakawa, T.; Archer, J.A.C.; Arner, P.; Babina, M.; Rennie, S.; Balwierz, P.J.; Beckhouse, A.G.; Pradhan-Bhatt, S.; Blake, J.A.; Blumenthal, A.; Bodega, B.; Bonetti, A.; Briggs, J.; Brombacher, F.; Burroughs, A.M.; Califano, A.; Cannistraci, C.V.; Carbajo, D.; Chen, Y.; Chierici, M.; Ciani, Y.; Clevers, H.C.; Dalla, E.; Davis, C.A.; Detmar, M.; Diehl, A.D.; Dohi, T.; Drablos, F.; Edge, A.S.B.; Edinger, M.; Ekwall, K.; Endoh, M.; Enomoto, H.; Fagiolini, M.; Fairbairn, L.; Fang, H.; Farach-Carson, M.C.; Faulkner, G.J.; Favorov, A.V.; Fisher, M.E.; Frith, M.C.; Fujita, R.; Fukuda, S.; Furlanello, C.; Furuno, M.; Furusawa, J.-.; Geijtenbeek, T.B.; Gibson, A.P.; Gingeras, T.; Goldowitz, D.; Gough, J.; Guhl, S.; Guler, R.; Gustincich, S.; T. J., H.; Hamaguchi, M.; Hara, M.; Harbers, M.; Harshbarger, J.; Hasegawa, A.; Hasegawa, Y.; Hashimoto, T.; Herlyn, M.; Hitchens, K.J.; Sui, S.J.H.; Hofmann, O.M.; Hoof, I.; Hori, F.; Huminiecki, L.; Iida, K.; Ikawa, T.; Jankovic, B.R.; Jia, H.; Joshi, A.; Jurman, G.; Kaczkowski, B.; Kai, C.; Kaida, K.; Kaiho, A.; Kajiyama, K.; Kanamori-Katayama, M.; Kasianov, A.S.; Kasukawa, T.; Katayama, S.; Kato, S.; Kawaguchi, S.; Kawamoto, H.; Kawamura, Y.I.; Kawashima, T.; Kempfle, J.S.; Kenna, T.J.; Kere, J.; Khachigian, L.M.; Kitamura, T.; Klinken, S.P.; Knox, A.J.; Kojima, M.; Kojima, S.; Kondo, N.; Koseki, H.; Koyasu, S.; Krampitz, S.; Kubosaki, A.; Kwon, A.T.; Laros, J.F.J.; Lee, W.; Lennartsson, A.; Li, K.; Lilje, B.; Lipovich, L.; Mackay-sim, A.; Manabe, R.-.; Mar, J.C.; Marchand, B.; Mathelier, A.; Mejhert, N.; Meynert, A.; Mizuno, Y.; De Morais, D.A.L.; Morikawa, H.; Morimoto, M.; Moro, K.; Motakis, E.; Motohashi, H.; Mummery, C.L.; Murata, M.; Nagao-Sato, S.; Nakachi, Y.; Nakahara, F.; Nakamura, T.; Nakamura, Y.; Nakazato, K.; Van Nimwegen, E.; Ninomiya, N.; Nishiyori, H.; Noma, S.; Nozaki, T.; Ogishima, S.; Ohkura, N.; Ohmiya, H.; Ohno, H.; Ohshima, M.; Okada-Hatakeyama, M.; Okazaki, Y.; Orlando, V.; Ovchinnikov, D.A.; Pain, A.; Passier, R.; Patrikakis, M.; Persson, H.; Piazza, S.; Prendergast, J.G.D.; Rackham, O.J.L.; Ramilowski, J.A.; Rashid, M.; Ravasi, T.; Rizzu, P.; Roncador, M.; Roy, S.; Rye, M.B.; Saijyo, E.; Sajantila, A.; Saka, A.; Sakaguchi, S.; Sakai, M.; Sato, H.; Satoh, H.; Savvi, S.; Saxena, A.; Schneider, C.; Schultes, E.A.; Schulze-Tanzil, G.G.; Schwegmann, A.; Sengstag, T.; Sheng, G.; Shimoji, H.; Shimoni, Y.; Shin, J.W.; Simon, C.; Sugiyama, D.; Sugiyama, T.; Suzuki, M.; Suzuki, N.; Swoboda, R.K.; 'T Hoen, P.A.C.; Tagami, M.; Tagami, N.T.; Takai, J.; Tanaka, H.; Tatsukawa, H.; Tatum, Z.; Thompson, M.; Toyoda, H.; Toyoda, T.; Valen, E.; Van De Wetering, M.; Van Den Berg, L.M.; Verardo, R.; Vijayan, D.; Vorontsov, I.E.; Wasserman, W.W.; Watanabe, S.; Wells, C.A.; Winteringham, L.N.; Wolvetang, E.; Wood, E.J.; Yamaguchi, Y.; Yamamoto, M.; Yoneda, M.; Yonekura, Y.; Yoshida, S.; Zabierowski, S.E.; Zhang, P.G.; Zhao, X.; Zucchelli, S.; Summers, K.M.; Suzuki, H.; Daub, C.O.; Kawai, J.; Heutink, P.; Hide, W.; Freeman, T.C.; Lenhard, B.; Bajic, L.V.B.; Taylor, M.S.; Makeev, V.J.; Sandelin, A.; Hume, D.A.; Carninci, P.; Hayashizaki, Y.

doi:10.1038/nature13182

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. © 2014 Macmillan Publishers Limited.

A promoter-level mammalian expression atlas / A.R.R. Forrest, H. Kawaji, M. Rehli, J.K. Baillie, M.J.L. De Hoon, V. Haberle, T. Lassmann, I.V. Kulakovskiy, M. Lizio, M. Itoh, R. Andersson, C.J. Mungall, T.F. Meehan, S. Schmeier, N. Bertin, M. Jorgensen, E. Dimont, E. Arner, C. Schmidl, U. Schaefer, Y.A. Medvedeva, C. Plessy, M. Vitezic, J. Severin, C.A. Semple, Y. Ishizu, R.S. Young, M. Francescatto, I.A. Altschuler, D. Albanese, G.M. Altschule, T. Arakawa, J.A.C. Archer, P. Arner, M. Babina, S. Rennie, P.J. Balwierz, A.G. Beckhouse, S. Pradhan-Bhatt, J.A. Blake, A. Blumenthal, B. Bodega, A. Bonetti, J. Briggs, F. Brombacher, A.M. Burroughs, A. Califano, C.V. Cannistraci, D. Carbajo, Y. Chen, M. Chierici, Y. Ciani, H.C. Clevers, E. Dalla, C.A. Davis, M. Detmar, A.D. Diehl, T. Dohi, F. Drablos, A.S.B. Edge, M. Edinger, K. Ekwall, M. Endoh, H. Enomoto, M. Fagiolini, L. Fairbairn, H. Fang, M.C. Farach-Carson, G.J. Faulkner, A.V. Favorov, M.E. Fisher, M.C. Frith, R. Fujita, S. Fukuda, C. Furlanello, M. Furuno, J.-. Furusawa, T.B. Geijtenbeek, A.P. Gibson, T. Gingeras, D. Goldowitz, J. Gough, S. Guhl, R. Guler, S. Gustincich, T.J. Ha, M. Hamaguchi, M. Hara, M. Harbers, J. Harshbarger, A. Hasegawa, Y. Hasegawa, T. Hashimoto, M. Herlyn, K.J. Hitchens, S.J.H. Sui, O.M. Hofmann, I. Hoof, F. Hori, L. Huminiecki, K. Iida, T. Ikawa, B.R. Jankovic, H. Jia, A. Joshi, G. Jurman, B. Kaczkowski, C. Kai, K. Kaida, A. Kaiho, K. Kajiyama, M. Kanamori-Katayama, A.S. Kasianov, T. Kasukawa, S. Katayama, S. Kato, S. Kawaguchi, H. Kawamoto, Y.I. Kawamura, T. Kawashima, J.S. Kempfle, T.J. Kenna, J. Kere, L.M. Khachigian, T. Kitamura, S.P. Klinken, A.J. Knox, M. Kojima, S. Kojima, N. Kondo, H. Koseki, S. Koyasu, S. Krampitz, A. Kubosaki, A.T. Kwon, J.F.J. Laros, W. Lee, A. Lennartsson, K. Li, B. Lilje, L. Lipovich, A. Mackay-sim, R.-. Manabe, J.C. Mar, B. Marchand, A. Mathelier, N. Mejhert, A. Meynert, Y. Mizuno, D.A.L. De Morais, H. Morikawa, M. Morimoto, K. Moro, E. Motakis, H. Motohashi, C.L. Mummery, M. Murata, S. Nagao-Sato, Y. Nakachi, F. Nakahara, T. Nakamura, Y. Nakamura, K. Nakazato, E. Van Nimwegen, N. Ninomiya, H. Nishiyori, S. Noma, T. Nozaki, S. Ogishima, N. Ohkura, H. Ohmiya, H. Ohno, M. Ohshima, M. Okada-Hatakeyama, Y. Okazaki, V. Orlando, D.A. Ovchinnikov, A. Pain, R. Passier, M. Patrikakis, H. Persson, S. Piazza, J.G.D. Prendergast, O.J.L. Rackham, J.A. Ramilowski, M. Rashid, T. Ravasi, P. Rizzu, M. Roncador, S. Roy, M.B. Rye, E. Saijyo, A. Sajantila, A. Saka, S. Sakaguchi, M. Sakai, H. Sato, H. Satoh, S. Savvi, A. Saxena, C. Schneider, E.A. Schultes, G.G. Schulze-Tanzil, A. Schwegmann, T. Sengstag, G. Sheng, H. Shimoji, Y. Shimoni, J.W. Shin, C. Simon, D. Sugiyama, T. Sugiyama, M. Suzuki, N. Suzuki, R.K. Swoboda, P.A.C. 'T Hoen, M. Tagami, N.T. Tagami, J. Takai, H. Tanaka, H. Tatsukawa, Z. Tatum, M. Thompson, H. Toyoda, T. Toyoda, E. Valen, M. Van De Wetering, L.M. Van Den Berg, R. Verardo, D. Vijayan, I.E. Vorontsov, W.W. Wasserman, S. Watanabe, C.A. Wells, L.N. Winteringham, E. Wolvetang, E.J. Wood, Y. Yamaguchi, M. Yamamoto, M. Yoneda, Y. Yonekura, S. Yoshida, S.E. Zabierowski, P.G. Zhang, X. Zhao, S. Zucchelli, K.M. Summers, H. Suzuki, C.O. Daub, J. Kawai, P. Heutink, W. Hide, T.C. Freeman, B. Lenhard, L.V.B. Bajic, M.S. Taylor, V.J. Makeev, A. Sandelin, D.A. Hume, P. Carninci, Y. Hayashizaki. - In: NATURE. - ISSN 0028-0836. - 507:7493(2014 Mar 27), pp. 462-470. [10.1038/nature13182]

A promoter-level mammalian expression atlas

Forrest 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.;Mungall C. J.;Meehan T. F.;Schmeier S.;Bertin N.;Jorgensen M.;Dimont E.;Arner E.;Schmidl C.;Schaefer U.;Medvedeva Y. A.;Plessy C.;Vitezic M.;Severin J.;Semple C. A.;Ishizu Y.;Young R. S.;Francescatto M.;Altschuler I. A.;Albanese D.;Altschule G. M.;Arakawa T.;Archer J. A. C.;Arner P.;Babina M.;Rennie S.;Balwierz P. J.;Beckhouse A. G.;Pradhan-Bhatt S.;Blake J. A.;Blumenthal A.;B. Bodega^{Membro del Collaboration Group};Bonetti A.;Briggs J.;Brombacher F.;Burroughs A. M.;Califano A.;Cannistraci C. V.;Carbajo D.;Chen Y.;Chierici M.;Ciani Y.;Clevers H. C.;Dalla E.;Davis C. A.;Detmar M.;Diehl A. D.;Dohi T.;Drablos F.;Edge A. S. B.;Edinger M.;Ekwall K.;Endoh M.;Enomoto H.;Fagiolini M.;Fairbairn L.;Fang H.;Farach-Carson M. C.;Faulkner G. J.;Favorov A. V.;Fisher M. E.;Frith M. C.;Fujita R.;Fukuda S.;Furlanello C.;Furuno M.;Furusawa J. -I.;Geijtenbeek T. B.;Gibson A. P.;Gingeras T.;Goldowitz D.;Gough J.;Guhl S.;Guler R.;Gustincich S.;Ha T. J.;Hamaguchi M.;Hara M.;Harbers M.;Harshbarger J.;Hasegawa A.;Hasegawa Y.;Hashimoto T.;Herlyn M.;Hitchens K. J.;Sui S. J. H.;Hofmann O. M.;Hoof I.;Hori F.;Huminiecki L.;Iida K.;Ikawa T.;Jankovic B. R.;Jia H.;Joshi A.;Jurman G.;Kaczkowski B.;Kai C.;Kaida K.;Kaiho A.;Kajiyama K.;Kanamori-Katayama M.;Kasianov A. S.;Kasukawa T.;Katayama S.;Kato S.;Kawaguchi S.;Kawamoto H.;Kawamura Y. I.;Kawashima T.;Kempfle J. S.;Kenna T. J.;Kere J.;Khachigian L. M.;Kitamura T.;Klinken S. P.;Knox A. J.;Kojima M.;Kojima S.;Kondo N.;Koseki H.;Koyasu S.;Krampitz S.;Kubosaki A.;Kwon A. T.;Laros J. F. J.;Lee W.;Lennartsson A.;Li K.;Lilje B.;Lipovich L.;Mackay-sim A.;Manabe R. -I.;Mar J. C.;Marchand B.;Mathelier A.;Mejhert N.;Meynert A.;Mizuno Y.;De Morais D. A. L.;Morikawa H.;Morimoto M.;Moro K.;Motakis E.;Motohashi H.;Mummery C. L.;Murata M.;Nagao-Sato S.;Nakachi Y.;Nakahara F.;Nakamura T.;Nakamura Y.;Nakazato K.;Van Nimwegen E.;Ninomiya N.;Nishiyori H.;Noma S.;Nozaki T.;Ogishima S.;Ohkura N.;Ohmiya H.;Ohno H.;Ohshima M.;Okada-Hatakeyama M.;Okazaki Y.;Orlando V.;Ovchinnikov D. A.;Pain A.;Passier R.;Patrikakis M.;Persson H.;Piazza S.;Prendergast J. G. D.;Rackham O. J. L.;Ramilowski J. A.;Rashid M.;Ravasi T.;Rizzu P.;Roncador M.;Roy S.;Rye M. B.;Saijyo E.;Sajantila A.;Saka A.;Sakaguchi S.;Sakai M.;Sato H.;Satoh H.;Savvi S.;Saxena A.;Schneider C.;Schultes E. A.;Schulze-Tanzil G. G.;Schwegmann A.;Sengstag T.;Sheng G.;Shimoji H.;Shimoni Y.;Shin J. W.;Simon C.;Sugiyama D.;Sugiyama T.;Suzuki M.;Suzuki N.;Swoboda R. K.;'T Hoen P. A. C.;Tagami M.;Tagami N. T.;Takai J.;Tanaka H.;Tatsukawa H.;Tatum Z.;Thompson M.;Toyoda H.;Toyoda T.;Valen E.;Van De Wetering M.;Van Den Berg L. M.;Verardo R.;Vijayan D.;Vorontsov I. E.;Wasserman W. W.;Watanabe S.;Wells C. A.;Winteringham L. N.;Wolvetang E.;Wood E. J.;Yamaguchi Y.;Yamamoto M.;Yoneda M.;Yonekura Y.;Yoshida S.;Zabierowski S. E.;Zhang P. G.;Zhao X.;Zucchelli S.;Summers K. M.;Suzuki H.;Daub C. O.;Kawai J.;Heutink P.;Hide W.;Freeman T. C.;Lenhard B.;Bajic L. V. B.;Taylor M. S.;Makeev V. J.;Sandelin A.;Hume D. A.;Carninci P.;Hayashizaki Y.

2014

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 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. © 2014 Macmillan Publishers Limited.

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Scheda completa

Scheda completa (DC)

	Settori scientifico-disciplinari dell'articolo
	
			Settore BIO/11 - Biologia Molecolare
		
	Data di pubblicazione
	
			27-mar-2014
		
	Rivista in ANCE
	
			NATURE
		
	DOI
	
			https://dx.doi.org/10.1038/nature13182
		
	Tipologia
	
			Article (author)
		
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			01 - Articolo su periodico

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