Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

Research output: Contribution to journalJournal articleResearchpeer-review

  • Eivind Valen
  • Giovanni Pascarella
  • Alistair Chalk
  • Norihiro Maeda
  • Miki Kojima
  • Chika Kawazu
  • Mitsuyoshi Murata
  • Hiromi Nishiyori
  • Dejan Lazarevic
  • Dario Motti
  • Troels Torben Marstrand
  • Man-Hung Eric Tang
  • Xiaobei Zhao
  • Takahiro Arakawa
  • Jun Kawai
  • Christine Wells
  • Carsten Daub
  • Matthias Harbers
  • Yoshihide Hayashizaki
  • Stefano Gustincich
  • Piero Carninci
Finding and characterizing mRNAs, their transcription start sites (TSS), and their associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5-10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5' cDNA tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. We apply DeepCAGE to characterize 1.4 million sequenced TSS from mouse hippocampus and reveal a wealth of novel core promoters that are preferentially used in hippocampus: This is the most comprehensive promoter data set for any tissue to date. Using these data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.
Original languageEnglish
JournalGenome Research
Issue number2
Pages (from-to)255-65
Number of pages10
Publication statusPublished - 2009

ID: 10457656