Journal Article

Genome-wide analysis of mammalian promoter architecture and evolution

Kai, Chikatoshi, Plessy, Charles, Harbers, Matthias, Arner, Peter, Persichetti, Francesca, Wells, Christine A, Carninci, Piero, Frith, Martin C, Engström, Pär G, Kitazume, Yayoi, Wahlestedt, Claes, Kodzius, Rimantas, Grimmond, Sean M, Ponjavic, Jasmina, Ravasi, Timothy, Konno, Hideaki, Suzuki, Harukazu, Tan, Sin Lam, Sandelin, Albin, Chesi, Alessandra, Gustincich, Stefano, Liu, Edison T, Orlando, Valerio, Kawai, Jun, Forrest, Alistair R R, Shimokawa, Kazuro, Hayashizaki, Yoshihide, Kasukawa, Takeya, Kanamori-Katayama, Mutsumi, Fukuda, Shiro, Katayama, Shintaro, Nakamura, Mari, Semple, Colin A M, Alkema, Wynand B, Lenhard, Boris, Hume, David A, Bajic, Vladimir B, Mottagui-Tabar, Salim, Kawaji, Hideya, Nakano, Kenji, Taylor, Martin S

2006

Overview

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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 3' Untranslated Regions / Agriculture / Animal Genetics and Genomics / Animals / Base Sequence / Biological and medical sciences / Biomedical and Life Sciences / Biomedicine / Cancer Research / DNA / Evolution, Molecular / Evolutionary biology / Fundamental and applied biological sciences. Psychology / Gene Function / Genetic aspects / Genetic regulation / Genetics of eukaryotes. Biological and molecular evolution / Genome / Genomics / Human Genetics / Mammals / Molecular and cellular biology / Molecular evolution / Molecular genetics / Physiological aspects / Promoter Regions, Genetic / Promoters (Genetics) / Proteins / Proteome / TATA Box / Tissues / Transcription. Transcription factor. Splicing. Rna processing