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Journal article

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

In Genome Research — 2009, Volume 19, Issue 2, pp. 255-265

By Valen, Eivind¹; Pascarella, Giovanni²; Chalk, Alistair³; Maeda, Norihiro⁴; Kojima, Miki⁴; Kawazu, Chika⁴; Murata, Mitsuyoshi⁴; Nishiyori, Hiromi⁴; Lazarevic, Dejan²; Motti, Dario²; Marstrand, Troels Torben¹; Tang, Man-Hung Eric¹; Zhao, Xiaobei¹; Krogh, Anders¹; Winther, Ole¹; Arakawa, Takahiro⁴; Kawai, Jun⁴; Wells, Christine³; Daub, Carsten⁵; Harbers, Matthias⁷; Hayashizaki, Yoshihide⁴; Gustincich, Stefano²; Sandelin, Albin¹; Carninci, Piero⁴ ...and 14 more

From

The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes vej 5, DK-2200, Denmark;¹

The Giovanni Armenise-Harvard Foundation Laboratory, Sector of Neurobiology, International School for Advanced Studies (SISSA), Basovizza, 34012 Trieste, Italy;²

The National Centre for Adult Stem Cell Research, The Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan QLD 4111, Australia;³

LSA Technology Development Group, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045 Japan⁴

LSA Bioinformatics Team, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045 Japan;⁵

Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045 Japan;⁶

DNAFORM Inc., Yokohama, Kanagawa 230-0046, Japan;⁷

CBM Scrl–Consorzio per il Centro di Biomedicina Molecolare, Basovizza, 34012 Trieste, Italy⁸

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.

Language:	English
Publisher:	Cold Spring Harbor Laboratory Press
Year:	2009
Pages:	255-265
ISSN:	15495477 , 08909369 , 10889051 and 15495469
Types:	Journal article
DOI:	10.1101/gr.084541.108
ORCIDs:	Krogh, Anders , Winther, Ole and Sandelin, Albin

Keywords

Animals Binding Sites Chromosome Mapping Gene Expression Hippocampus Mice Mice, Inbred C57BL Models, Biological Organ Specificity Promoter Regions, Genetic Protein Binding Sequence Analysis, DNA Transcription Factors

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

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

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