A promoter-level mammalian expression atlas

Autoria(s): Forrest, A. R.; Kawaji, H.; Rehli, M.; Baillie, J. K.; de Hoon, M. J.; 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.; Ishizu, Y.; Young, R. S.; Francescatto, M.; Alam, I.; Albanese, D.; Altschuler, G. M.; Arakawa, T.; Archer, J. A.; 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.; 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.; Furino, M.; Furusawa, J.; 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.; Ho Sui, S. J.; 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.; 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 Lima Morais, D. A.; 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.; Noma, S.; Noazaki, T.; Ogishima, S.; Ohkura, N.; Ohimiya, 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.; Rackham, O. J.; 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.; 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.; 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, L. M.; Verado, 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, V. B.; Taylor, M. S.; Makeev, V. J.; Sandelin, A.; Hume, D. A.; Carninci, P.; Hayashizaki, Y.
Data(s)

27/03/2014
Resumo

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.
Identificador

http://eprints.qut.edu.au/94055/
Publicador

Nature Publishing Group
Relação

DOI:10.1038/nature13182

Forrest, A. R., Kawaji, H., Rehli, M., Baillie, J. K., de Hoon, M. J., 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., Ishizu, Y., Young, R. S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G. M., Arakawa, T., Archer, J. A., 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., 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., Furino, M., Furusawa, J., 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., Ho Sui, S. J., 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., 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 Lima Morais, D. A., 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., Noma, S., Noazaki, T., Ogishima, S., Ohkura, N., Ohimiya, 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., Rackham, O. J., 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., 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., 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, L. M., Verado, 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, V. B., Taylor, M. S., Makeev, V. J., Sandelin, A., Hume, D. A., Carninci, P., & Hayashizaki, Y. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493), pp. 462-470.
Direitos

Copyright 2014 Macmillan Publishers Limited
Fonte

Faculty of Health; Institute of Health and Biomedical Innovation
Palavras-Chave #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
Tipo

Journal Article
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