Genome-wide analysis of mammalian promoter architecture and evolution.
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.
Carninci
Piero
P
Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Sandelin
Albin
A
Lenhard
Boris
B
Katayama
Shintaro
S
Shimokawa
Kazuro
K
Ponjavic
Jasmina
J
Semple
Colin A M
CA
Taylor
Martin S
MS
Engström
Pär G
PG
Frith
Martin C
MC
Forrest
Alistair R R
AR
Alkema
Wynand B
WB
Tan
Sin Lam
SL
Plessy
Charles
C
Kodzius
Rimantas
R
Ravasi
Timothy
T
Kasukawa
Takeya
T
Fukuda
Shiro
S
Kanamori-Katayama
Mutsumi
M
Kitazume
Yayoi
Y
Kawaji
Hideya
H
Kai
Chikatoshi
C
Nakamura
Mari
M
Konno
Hideaki
H
Nakano
Kenji
K
Mottagui-Tabar
Salim
S
Arner
Peter
P
Chesi
Alessandra
A
Gustincich
Stefano
S
Persichetti
Francesca
F
Suzuki
Harukazu
H
Grimmond
Sean M
SM
Wells
Christine A
CA
Orlando
Valerio
V
Wahlestedt
Claes
C
Liu
Edison T
ET
Harbers
Matthias
M
Kawai
Jun
J
Bajic
Vladimir B
VB
Hume
David A
DA
Hayashizaki
Yoshihide
Y
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
D020413:3' Untranslated Regions; D020543:Proteome; D004247:DNA