Genome-wide analysis of mammalian promoter architecture and evolution - PubMed (original) (raw)
doi: 10.1038/ng1789. Epub 2006 Apr 28.
Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin A M Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair R R Forrest, Wynand B Alkema, Sin Lam Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki
Affiliations
- PMID: 16645617
- DOI: 10.1038/ng1789
Genome-wide analysis of mammalian promoter architecture and evolution
Piero Carninci et al. Nat Genet. 2006 Jun.
Erratum in
- Nat Genet. 2007 Sep;39(9):1174
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.
Comment in
- The multitasking genome.
Gingeras TR. Gingeras TR. Nat Genet. 2006 Jun;38(6):608-9. doi: 10.1038/ng0606-608. Nat Genet. 2006. PMID: 16736012 No abstract available.
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