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

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, Anders Krogh, Ole Winther, Takahiro Arakawa, Jun Kawai, Christine Wells, Carsten Daub, Matthias HarbersYoshihide Hayashizaki, Stefano Gustincich, Albin Sandelin, Piero Carninci

Research output: Contribution to journalArticle


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
Pages (from-to)255-265
Number of pages11
JournalGenome Research
Issue number2
Publication statusPublished - Feb 2009


ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M. H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., ... Carninci, P. (2009). Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research, 19(2), 255-265.