Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- Eivind Valen1,
- Giovanni Pascarella2,
- Alistair Chalk3,
- Norihiro Maeda4,
- Miki Kojima4,
- Chika Kawazu4,
- Mitsuyoshi Murata4,
- Hiromi Mishiyori4,
- Dejan Lazarevich2,
- Dario Motti2,
- Troels Torben Marstrand1,
- Man-Hung Eric Tang1,
- Xiaobei Zhao1,
- Anders Krogh5,
- Ole Winther5,
- Takahiro Arakawa4,
- Jun Kawai4,
- Christine Wells3,
- Carsten Daub4,
- Matthias Harbers6,
- Yoshihide Hayashizaki4,
- Stefano Gustincich2,
- Albin Sandelin1, and
- Piero Carninci4,7
Abstract
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 which are preferentially used in hippocampus: this is the most comprehensive promoter dataset for any tissue to date. Using this 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.
Footnotes
-
- Received August 8, 2008.
- Accepted December 3, 2008.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
