A promoter-level mammalian expression atlas

Research output: Contribution to journalArticle


title = "A promoter-level mammalian expression atlas",
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.",
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",
author = "Forrest, {Alistair R R} and Hideya Kawaji and Michael Rehli and Baillie, {J Kenneth} and {de Hoon}, {Michiel J L} and Vanja Haberle and Timo Lassmann and Kulakovskiy, {Ivan V} and Marina Lizio and Masayoshi Itoh and Robin Andersson and Mungall, {Christopher J} and Meehan, {Terrence F} and Sebastian Schmeier and Nicolas Bertin and Mette J{\o}rgensen and Emmanuel Dimont and Erik Arner and Christian Schmidl and Ulf Schaefer and Medvedeva, {Yulia A} and Charles Plessy and Morana Vitezic and Jessica Severin and Semple, {Colin A} and Yuri Ishizu and Young, {Robert S} and Margherita Francescatto and Intikhab Alam and Davide Albanese and Altschuler, {Gabriel M} and Takahiro Arakawa and Archer, {John A C} and Peter Arner and Magda Babina and Sarah Rennie and Balwierz, {Piotr J} and Beckhouse, {Anthony G} and Swati Pradhan-Bhatt and Blake, {Judith A} and Antje Blumenthal and Beatrice Bodega and Alessandro Bonetti and James Briggs and Frank Brombacher and Burroughs, {A Maxwell} and Andrea Califano and Andreas Lennartsson and Helena Persson and Mark Thompson and {FANTOM Consortium and the RIKEN PMI and CLST (DGT)}",
year = "2014",
month = "3",
day = "27",
doi = "10.1038/nature13182",
language = "English",
volume = "507",
pages = "462--70",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7493",