A promoter-level mammalian expression atlas

Forrest, Alistair R.R.; Kawaji, Hideya; Rehli, Michael; Kenneth Baillie, J.; de Hoon, Michiel J.L.; Haberle, Vanja; Lassmann, Timo; Kulakovskiy, Ivan V.; Lizio, Marina; Itoh, Masayoshi; Andersson, Robin; Mungall, Christopher J.; Meehan, Terrence F.; Schmeier, Sebastian; Bertin, Nicolas; J?rgensen, Mette; Dimont, Emmanuel; Arner, Erik; Schmidl, Christian; Schaefer, Ulf; Medvedeva, Yulia A.; Plessy, Charles; Vitezic, Morana; Severin, Jessica; Semple, Colin A.; Ishizu, Yuri; Young, Robert S.; Francescatto, Margherita; Alam, Intikhab; Albanese, Davide; Altschuler, Gabriel M.; Arakawa, Takahiro; Archer, John A.C.; Arner, Peter; Babina, Magda; Rennie, Sarah; Balwierz, Piotr J.; Beckhouse, Anthony G.; Pradhan-Bhatt, Swati; Blake, Judith A.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Maxwell Burroughs, A.; Califano, Andrea; Cannistraci, Carlo V.; Carbajo, Daniel; Chen, Yun; Chierici, Marco; Ciani, Yari; Clevers, Hans C.; Dalla, Emiliano; Davis,...

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.

Citation

Forrest, A. R., Kawaji, H., Rehli, M., Kenneth Baillie, J., 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., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., …Hayashizaki, Y. (2014). A promoter-level mammalian expression atlas. Nature, 507, 462-470. https://doi.org/10.1038/nature13182

• Journal Article Type: Article
• Acceptance Date: Feb 26, 2014
• Online Publication Date: Mar 26, 2014
• Publication Date: Mar 27, 2014
• Deposit Date: Aug 17, 2018
• Journal: Nature
• Print ISSN: 0028-0836
• Electronic ISSN: 1476-4687
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 507
• Pages: 462-470
• DOI: https://doi.org/10.1038/nature13182
• Keywords: Gene regulation, Gene regulatory networks, Multicellular systems, Transcriptomics
• Public URL: https://nottingham-repository.worktribe.com/output/1110917
• Publisher URL: https://www.nature.com/articles/nature13182
• PMID: 24670764