Genome-wide analysis of mammalian promoter architecture and evolution

Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Frith, Martin C., Forrest, Alistair R. R., Ravasi, Timothy, Grimmond, Sean M., Wells, Christine A., Hume, David A. and Hayashizaki, Yoshihide (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics, 38 6: 626-635. doi:10.1038/ng1789

Author Carninci, Piero
Sandelin, Albin
Lenhard, Boris
Frith, Martin C.
Forrest, Alistair R. R.
Ravasi, Timothy
Grimmond, Sean M.
Wells, Christine A.
Hume, David A.
Hayashizaki, Yoshihide
Title Genome-wide analysis of mammalian promoter architecture and evolution
Journal name Nature Genetics   Check publisher's open access policy
ISSN 1061-4036
Publication date 2006
Sub-type Article (original research)
DOI 10.1038/ng1789
Volume 38
Issue 6
Start page 626
End page 635
Total pages 10
Place of publication New York
Publisher Nature Publishing Group
Collection year 2006
Language eng
Subject C1
270202 Genome Structure
780106 Political science and public policy
Abstract Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a welldefined 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.
Keyword Genetics & Heredity
Core Promoter
Transcriptional Regulation
Cap Analysis
Q-Index Code C1
Additional Notes Authors of this document: Carninci, P; Sandelin, A; Lenhard, B; Katayama, S; Shimokawa, K; Ponjavic, J; Semple, CAM; Taylor, MS; Engstrom, PG; Frith, MC; Forrest, ARR; Alkema, WB; Tan, SL; Plessy, C; Kodzius, R; Ravasi, T; Kasukawa, T; Fukuda, S; Kanamori-Katayama, M; Kitazume, Y; Kawaji, H; Kai, C; Nakamura, M; Konno, H; Nakano, K; Mottagui-Tabar, S; Arner, P; Chesi, A; Gustincich, S; Persichetti, F; Suzuki, H; Grimmond, SM; Wells, CA; Orlando, V; Wahlestedt, C; Liu, ET; Harbers, M; Kawai, J; Bajic, VB; Hume, DA; Hayashizaki, Y. DOI:10.1038/ng1789

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Created: Wed, 15 Aug 2007, 08:47:50 EST