Genome-wide analysis of mammalian promoter architecture and evolution

Piero Carninci, 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 KitazumeHideya 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 R Wahlestedt, Edison T. Liu, Matthias Harbers, Jun Kawai, Vladimir B. Bajic, David A. Hume, Yoshihide Hayashizaki

Research output: Contribution to journalArticle

840 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)626-635
Number of pages10
JournalNature Genetics
Volume38
Issue number6
DOIs
StatePublished - Jun 1 2006
Externally publishedYes

Fingerprint

Transcription Initiation Site
Genome
TATA Box
3' Untranslated Regions
Human Genome
Plastics
Sequence Analysis
Exons
Genes
Proteins

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., ... Hayashizaki, Y. (2006). Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics, 38(6), 626-635. https://doi.org/10.1038/ng1789

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

In: Nature Genetics, Vol. 38, No. 6, 01.06.2006, p. 626-635.

Research output: Contribution to journalArticle

Carninci, P, Sandelin, A, Lenhard, B, Katayama, S, Shimokawa, K, Ponjavic, J, Semple, CAM, Taylor, MS, Engström, 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, CR, Liu, ET, Harbers, M, Kawai, J, Bajic, VB, Hume, DA & Hayashizaki, Y 2006, 'Genome-wide analysis of mammalian promoter architecture and evolution', Nature Genetics, vol. 38, no. 6, pp. 626-635. https://doi.org/10.1038/ng1789
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics. 2006 Jun 1;38(6):626-635. https://doi.org/10.1038/ng1789
Carninci, Piero ; Sandelin, Albin ; Lenhard, Boris ; Katayama, Shintaro ; Shimokawa, Kazuro ; Ponjavic, Jasmina ; Semple, Colin A M ; Taylor, Martin S. ; Engström, Pär G. ; Frith, Martin C. ; Forrest, Alistair R R ; Alkema, Wynand B. ; Tan, Sin Lam ; Plessy, Charles ; Kodzius, Rimantas ; Ravasi, Timothy ; Kasukawa, Takeya ; Fukuda, Shiro ; Kanamori-Katayama, Mutsumi ; Kitazume, Yayoi ; Kawaji, Hideya ; Kai, Chikatoshi ; Nakamura, Mari ; Konno, Hideaki ; Nakano, Kenji ; Mottagui-Tabar, Salim ; Arner, Peter ; Chesi, Alessandra ; Gustincich, Stefano ; Persichetti, Francesca ; Suzuki, Harukazu ; Grimmond, Sean M. ; Wells, Christine A. ; Orlando, Valerio ; Wahlestedt, Claes R ; Liu, Edison T. ; Harbers, Matthias ; Kawai, Jun ; Bajic, Vladimir B. ; Hume, David A. ; Hayashizaki, Yoshihide. / Genome-wide analysis of mammalian promoter architecture and evolution. In: Nature Genetics. 2006 ; Vol. 38, No. 6. pp. 626-635.
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