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A promoter-level mammalian expression atlas

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 and Itoh, Masayoshi, et al. (2014) In Nature 507(7493). p.70-462
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... (More)

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.

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keywords
Animals, Atlases as Topic, Cell Line, Cells, Cultured, Cluster Analysis, Conserved Sequence, Gene Expression Regulation, Gene Regulatory Networks, Genes, Essential, Genome, Humans, Mice, Molecular Sequence Annotation, Open Reading Frames, Organ Specificity, Promoter Regions, Genetic, RNA, Messenger, Transcription Factors, Transcription Initiation Site, Transcription, Genetic, Transcriptome
in
Nature
volume
507
issue
7493
pages
9 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:84897406127
ISSN
0028-0836
DOI
10.1038/nature13182
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English
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04e884ef-3083-458c-9a12-a7cdf9ea1c22
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2016-04-14 14:26:43
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2017-07-09 04:49:12
@article{04e884ef-3083-458c-9a12-a7cdf9ea1c22,
  abstract     = {<p>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.</p>},
  author       = {Forrest, Alistair R R and Kawaji, Hideya and Rehli, Michael and Baillie, J Kenneth and de Hoon, Michiel J L and Haberle, Vanja and Lassmann, Timo and Kulakovskiy, Ivan V and Lizio, Marina and Itoh, Masayoshi and Andersson, Robin and Mungall, Christopher J and Meehan, Terrence F and Schmeier, Sebastian and Bertin, Nicolas and Jørgensen, Mette and Dimont, Emmanuel and Arner, Erik and Schmidl, Christian and Schaefer, Ulf and Medvedeva, Yulia A and Plessy, Charles and Vitezic, Morana and Severin, Jessica and Semple, Colin A and Ishizu, Yuri and Young, Robert S and Francescatto, Margherita and Alam, Intikhab and Albanese, Davide and Altschuler, Gabriel M and Arakawa, Takahiro and Archer, John A C and Arner, Peter and Babina, Magda and Rennie, Sarah and Balwierz, Piotr J and Beckhouse, Anthony G and Pradhan-Bhatt, Swati and Blake, Judith A and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessandro and Briggs, James and Brombacher, Frank and Burroughs, A Maxwell and Califano, Andrea and Cannistraci, Carlo V and Carbajo, Daniel and Chen, Yun and Chierici, Marco and Ciani, Yari and Clevers, Hans C and Dalla, Emiliano and Davis, Carrie A and Detmar, Michael and Diehl, Alexander D and Dohi, Taeko and Drabløs, Finn and Edge, Albert S B and Edinger, Matthias and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and Fagiolini, Michela and Fairbairn, Lynsey and Fang, Hai and Farach-Carson, Mary C and Faulkner, Geoffrey J and Favorov, Alexander V and Fisher, Malcolm E and Frith, Martin C and Fujita, Rie and Fukuda, Shiro and Furlanello, Cesare and Furino, Masaaki and Furusawa, Jun-ichi and Geijtenbeek, Teunis B and Gibson, Andrew P and Gingeras, Thomas and Goldowitz, Daniel and Gough, Julian and Guhl, Sven and Guler, Reto and Gustincich, Stefano and Ha, Thomas J and Hamaguchi, Masahide and Hara, Mitsuko and Harbers, Matthias and Harshbarger, Jayson and Hasegawa, Akira and Hasegawa, Yuki and Hashimoto, Takehiro and Herlyn, Meenhard and Hitchens, Kelly J and Ho Sui, Shannan J and Hofmann, Oliver M and Hoof, Ilka and Hori, Furni and Huminiecki, Lukasz and Iida, Kei and Ikawa, Tomokatsu and Jankovic, Boris R and Jia, Hui and Joshi, Anagha and Jurman, Giuseppe and Kaczkowski, Bogumil and Kai, Chieko and Kaida, Kaoru and Kaiho, Ai and Kajiyama, Kazuhiro and Kanamori-Katayama, Mutsumi and Kasianov, Artem S and Kasukawa, Takeya and Katayama, Shintaro and Kato, Sachi and Kawaguchi, Shuji and Kawamoto, Hiroshi and Kawamura, Yuki I and Kawashima, Tsugumi and Kempfle, Judith S and Kenna, Tony J and Kere, Juha and Khachigian, Levon M and Kitamura, Toshio and Klinken, S Peter and Knox, Alan J and Kojima, Miki and Kojima, Soichi and Kondo, Naoto and Koseki, Haruhiko and Koyasu, Shigeo and Krampitz, Sarah and Kubosaki, Atsutaka and Kwon, Andrew T and Laros, Jeroen F J and Lee, Weonju and Lennartsson, Andreas and Li, Kang and Lilje, Berit and Lipovich, Leonard and Mackay-Sim, Alan and Manabe, Ri-ichiroh and Mar, Jessica C and Marchand, Benoit and Mathelier, Anthony and Mejhert, Niklas and Meynert, Alison and Mizuno, Yosuke and de Lima Morais, David A and Morikawa, Hiromasa and Morimoto, Mitsuru and Moro, Kazuyo and Motakis, Efthymios and Motohashi, Hozumi and Mummery, Christine L and Murata, Mitsuyoshi and Nagao-Sato, Sayaka and Nakachi, Yutaka and Nakahara, Fumio and Nakamura, Toshiyuki and Nakamura, Yukio and Nakazato, Kenichi and van Nimwegen, Erik and Ninomiya, Noriko and Nishiyori, Hiromi and Noma, Shohei and Noma, Shohei and Noazaki, Tadasuke and Ogishima, Soichi and Ohkura, Naganari and Ohimiya, Hiroko and Ohno, Hiroshi and Ohshima, Mitsuhiro and Okada-Hatakeyama, Mariko and Okazaki, Yasushi and Orlando, Valerio and Ovchinnikov, Dmitry A and Pain, Arnab and Passier, Robert and Patrikakis, Margaret and Persson, Helena and Piazza, Silvano and Prendergast, James G D and Rackham, Owen J L and Ramilowski, Jordan A and Rashid, Mamoon and Ravasi, Timothy and Rizzu, Patrizia and Roncador, Marco and Roy, Sugata and Rye, Morten B and Saijyo, Eri and Sajantila, Antti and Saka, Akiko and Sakaguchi, Shimon and Sakai, Mizuho and Sato, Hiroki and Savvi, Suzana and Saxena, Alka and Schneider, Claudio and Schultes, Erik A and Schulze-Tanzil, Gundula G and Schwegmann, Anita and Sengstag, Thierry and Sheng, Guojun and Shimoji, Hisashi and Shimoni, Yishai and Shin, Jay W and Simon, Christophe and Sugiyama, Daisuke and Sugiyama, Takaai and Suzuki, Masanori and Suzuki, Naoko and Swoboda, Rolf K and 't Hoen, Peter A C and Tagami, Michihira and Takahashi, Naoko and Takai, Jun and Tanaka, Hiroshi and Tatsukawa, Hideki and Tatum, Zuotian and Thompson, Mark and Toyodo, Hiroo and Toyoda, Tetsuro and Valen, Elvind and van de Wetering, Marc and van den Berg, Linda M and Verado, Roberto and Vijayan, Dipti and Vorontsov, Ilya E and Wasserman, Wyeth W and Watanabe, Shoko and Wells, Christine A and Winteringham, Louise N and Wolvetang, Ernst and Wood, Emily J and Yamaguchi, Yoko and Yamamoto, Masayuki and Yoneda, Misako and Yonekura, Yohei and Yoshida, Shigehiro and Zabierowski, Susan E and Zhang, Peter G and Zhao, Xiaobei and Zucchelli, Silvia and Summers, Kim M and Suzuki, Harukazu and Daub, Carsten O and Kawai, Jun and Heutink, Peter and Hide, Winston and Freeman, Tom C and Lenhard, Boris and Bajic, Vladimir B and Taylor, Martin S and Makeev, Vsevolod J and Sandelin, Albin and Hume, David A and Carninci, Piero and Hayashizaki, Yoshihide and , },
  issn         = {0028-0836},
  keyword      = {Animals,Atlases as Topic,Cell Line,Cells, Cultured,Cluster Analysis,Conserved Sequence,Gene Expression Regulation,Gene Regulatory Networks,Genes, Essential,Genome,Humans,Mice,Molecular Sequence Annotation,Open Reading Frames,Organ Specificity,Promoter Regions, Genetic,RNA, Messenger,Transcription Factors,Transcription Initiation Site,Transcription, Genetic,Transcriptome},
  language     = {eng},
  month        = {03},
  number       = {7493},
  pages        = {70--462},
  publisher    = {Nature Publishing Group},
  series       = {Nature},
  title        = {A promoter-level mammalian expression atlas},
  url          = {http://dx.doi.org/10.1038/nature13182},
  volume       = {507},
  year         = {2014},
}