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PMID: 19074369 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Validation Study

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

Genome research ·Vol. 19 ·No. 2 ·2009-02-00 ·Pages 255-65

Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P

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.

MeSH Terms
Animals Binding Sites Chromosome Mapping/methods Gene Expression Hippocampus/metabolism Mice Mice, Inbred C57BL Models, Biological Organ Specificity/genetics Promoter Regions, Genetic/genetics Protein Binding Sequence Analysis, DNA/methods Transcription Factors/metabolism
Chemicals
Transcription Factors
Authors & Affiliations
24 authors, click to expand affiliations / ORCID
Valen Eivind
The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes vej 5, DK-2200, Denmark.
Pascarella Giovanni
Chalk Alistair
Maeda Norihiro
Kojima Miki
Kawazu Chika
Murata Mitsuyoshi
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
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.084541.108
Published
2009-02-00
Epub
2008-00-11
Pages
255-65
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2652207
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.084541.108 PMC Full Text View journal details
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