title: Genome-wide analysis of mammalian promoter architecture and evolution.
abstract: Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
authors.affiliation: Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Piero
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authors.lastname: Carninci
authors.forename: Albin
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authors.lastname: Sandelin
authors.forename: Boris
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authors.lastname: Lenhard
authors.forename: Shintaro
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authors.forename: Sin Lam
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authors.forename: Rimantas
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authors.lastname: Kodzius
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authors.lastname: Ravasi
authors.forename: Takeya
authors.initials: T
authors.lastname: Kasukawa
authors.forename: Shiro
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authors.lastname: Fukuda
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Kanamori-Katayama
authors.forename: Yayoi
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authors.lastname: Kitazume
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Chikatoshi
authors.initials: C
authors.lastname: Kai
authors.forename: Mari
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authors.lastname: Nakamura
authors.forename: Hideaki
authors.initials: H
authors.lastname: Konno
authors.forename: Kenji
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authors.lastname: Nakano
authors.forename: Salim
authors.initials: S
authors.lastname: Mottagui-Tabar
authors.forename: Peter
authors.initials: P
authors.lastname: Arner
authors.forename: Alessandra
authors.initials: A
authors.lastname: Chesi
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
authors.forename: Francesca
authors.initials: F
authors.lastname: Persichetti
authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.forename: Christine A
authors.initials: CA
authors.lastname: Wells
authors.forename: Valerio
authors.initials: V
authors.lastname: Orlando
authors.forename: Claes
authors.initials: C
authors.lastname: Wahlestedt
authors.forename: Edison T
authors.initials: ET
authors.lastname: Liu
authors.forename: Matthias
authors.initials: M
authors.lastname: Harbers
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D004247:DNA; D019143:Evolution, Molecular; D016678:Genome; D011401:Promoter Regions, Genetic; D020543:Proteome; D016385:TATA Box
chemical_list: D020413:3' Untranslated Regions; D020543:Proteome; D004247:DNA