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.
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BibTeX (Download)
@article{Consortium2014,
title = {A promoter-level mammalian expression atlas},
author = {{FANTOM Consortium and RIKEN the PMI and CLST (DGT)} and Alistair R R Forrest and Hideya Kawaji and ... and Geoffrey J Faulkner and ... and David A Hume and Piero Carninci and Yoshihide Hayashizaki},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24670764},
doi = {10.1038/nature13182},
year = {2014},
date = {2014-03-26},
journal = {Nature},
volume = {507},
number = {7493},
pages = {462-470},
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 = {Faulknerlab},
pubstate = {published},
tppubtype = {article}
}