Projects per year
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 |
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Pages (from-to) | 462-470 |
Number of pages | 9 |
Journal | Nature |
Volume | 507 |
Issue number | 7493 |
Early online date | 26 Mar 2014 |
DOIs | |
Publication status | Published - 27 Mar 2014 |
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
Fingerprint
Dive into the research topics of 'A promoter-level mammalian expression atlas'. Together they form a unique fingerprint.Projects
- 4 Finished
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ISP1: Analysis and prediction in complex animal systems
Tenesa, A., Archibald, A., Beard, P., Bishop, S., Bronsvoort, M., Burt, D., Freeman, T., Haley, C., Hocking, P., Houston, R., Hume, D., Joshi, A., Law, A., Michoel, T., Summers, K., Vernimmen, D., Watson, M., Wiener, P., Wilson, A., Woolliams, J., Ait-Ali, T., Barnett, M., Carlisle, A., Finlayson, H., Haga, I., Karavolos, M., Matika, O., Paterson, T., Paton, B., Pong-Wong, R., Robert, C. & Robertson, G.
1/04/12 → 31/03/17
Project: Research
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Innate immunity and endemic diseases in livestock species
Collie, D., Beard, P., Bishop, S., Bronsvoort, M., Burt, D., Fitzgerald, R., Freeman, T., Gally, D., Gill, A., Glass, E., Hocking, P., Hope, J., Hume, D., Kaiser, P., Mabbott, N., McLachlan, G., Morrison, L., Stevens, J., Stevens, M. & Watson, M.
1/04/12 → 31/03/17
Project: Research
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A complete transcriptional map of the human body: systems Biology in toto (Japanese Partnering Grant)
Hume, D., Freeman, T. & Summers, K.
1/10/11 → 30/09/14
Project: Research
Profiles
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Kenneth Baillie
- Deanery of Clinical Sciences - Personal Chair of Experimental Medicine
- Centre for Inflammation Research
Person: Academic: Research Active
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Alison Meynert
- Deanery of Molecular, Genetic and Population Health Sciences - Senior Research Fellow
Person: Academic: Research Active
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James Prendergast
- Royal (Dick) School of Veterinary Studies - Senior Research Fellow
Person: Academic: Research Active