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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Genome-wide analysis of mammalian promoter architecture and evolution
Nature Genetics, Volume 38, No. 6, Year 2006
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Description
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. © 2006 Nature Publishing Group.
Authors & Co-Authors
Carninci, Piero
Unknown Affiliation
Sandelin, Albin
Unknown Affiliation
Lenhard, Boris
Unknown Affiliation
Katayama, Shintaro
Unknown Affiliation
Shimokawa, Kazurou
Unknown Affiliation
Ponjavic, Jasmina
Unknown Affiliation
Semple, Colin A.M.
Unknown Affiliation
Taylor, Martin S.
Unknown Affiliation
Engström, Pär G.
Unknown Affiliation
Frith, Martin C.
Unknown Affiliation
Forrest, Alistair R.R.
Unknown Affiliation
Alkema, Wynand B.L.
Unknown Affiliation
Tan, Sinlam
Unknown Affiliation
Plessy, Charles
Unknown Affiliation
Kodzius, Rimantas
Unknown Affiliation
Ravasi, Timothy
Unknown Affiliation
Kasukawa, Takeya
Unknown Affiliation
Fukuda, Shiro
Unknown Affiliation
Kanamori-Katayama, Mutsumi
Unknown Affiliation
Kitazume, Yayoi
Unknown Affiliation
Kawaji, Hideya
Unknown Affiliation
Kai, Chikatoshi
Unknown Affiliation
Nakamura, Mari
Unknown Affiliation
Konno, Hideaki
Unknown Affiliation
Nakano, Kenji
Unknown Affiliation
Mottagui-Tabar, Salim
Unknown Affiliation
Arner, Peter
Unknown Affiliation
Chesi, Alessandra
Unknown Affiliation
Gustincich, Stefano
Unknown Affiliation
Persichetti, Francesca
Unknown Affiliation
Suzuki, Harukazu
Unknown Affiliation
Grimmond, Sean M.
Unknown Affiliation
Wells, Christine A.
Unknown Affiliation
Orlando, Valerio
Unknown Affiliation
Wahlestedt, Claes R.
Unknown Affiliation
Liu, Edison T.
Unknown Affiliation
Harbers, Matthias
Unknown Affiliation
Kawai, Jun
Unknown Affiliation
Bajic, Vladimir B.
Unknown Affiliation
Hume, David A.
Unknown Affiliation
Hayashizaki, Yoshihide
Unknown Affiliation
Statistics
Citations: 1,326
Authors: 41
Affiliations: 23
Identifiers
Doi:
10.1038/ng1789
ISSN:
10614036
e-ISSN:
15461718
Study Approach
Quantitative