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

Valen, E. et al. (2009) Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research, 19(2), pp. 255-265. (doi: 10.1101/gr.084541.108)

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 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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Wells, Dr Christine
• Authors: 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., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M., Hayashizaki, Y., Gustincich, S., Sandelin, A., and Carninci, P.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Genome Research
• ISSN: 1088-9051
• ISSN (Online): 1549-5469
• Copyright Holders: Copyright © 2009 Cold Spring Harbor Laboratory Press
• First Published: First Published in Genome Research 19(2):255-265
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher.