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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
language
English
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no
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04e884ef-3083-458c-9a12-a7cdf9ea1c22
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2016-04-14 14:26:43
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2018-07-15 04:30:32
@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 Lennartsson, Andreas and Persson, Helena and Thompson, Mark 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},
}