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

Valen, Eivind, Pascarella, Giovanni, Chalk, Alistair, Maeda, Norihiro, Kojima, Miki, Kawazu, Chika, Murata, Mistuyoshi, Nishiyori, Hiromi, Lazarevic, Dejan, Motti, Dario, Marstrand, Troels Torben, Tang, Man-Hung Eric, Zhao, Xiaobei, Krogh, Anders, Winther, Ole, Arakawa, Takahiro, Kawai, Jun, Wells, Christine, Daub, Carsten, Harbers, Matthias, Hayashizaki, Yoshihide, Gustincich, Stefano, Sandelin, Albin and Carninci, Piero (2009) Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research, 19 2: 255-265. doi:10.1101/gr.084541.108


Author Valen, Eivind
Pascarella, Giovanni
Chalk, Alistair
Maeda, Norihiro
Kojima, Miki
Kawazu, Chika
Murata, Mistuyoshi
Nishiyori, Hiromi
Lazarevic, Dejan
Motti, Dario
Marstrand, Troels Torben
Tang, Man-Hung Eric
Zhao, Xiaobei
Krogh, Anders
Winther, Ole
Arakawa, Takahiro
Kawai, Jun
Wells, Christine
Daub, Carsten
Harbers, Matthias
Hayashizaki, Yoshihide
Gustincich, Stefano
Sandelin, Albin
Carninci, Piero
Title Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2009-02-01
Year available 2009
Sub-type Article (original research)
DOI 10.1101/gr.084541.108
Open Access Status DOI
Volume 19
Issue 2
Start page 255
End page 265
Total pages 11
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
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 59 cDNA tags—DeepCAGE: merging the Cap Analysis of Gene Expression method with ultrahigh-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.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
BIOCHEMISTRY & MOLECULAR BIOLOGY
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
GENETICS & HEREDITY
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID FP7/20072013
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
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Created: Thu, 10 Mar 2011, 00:35:10 EST