Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Author(s)
Valen, Eivind
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
Year published
2009
Metadata
Show full item recordAbstract
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 ...
View more >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.
View less >
View more >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.
View less >
Journal Title
Genome Research
Volume
19
Issue
2
Copyright Statement
Self-archiving of the author-manuscript version is not yet supported by this publisher. Please refer to the journal link for access to the definitive, published version or contact the authors for more information.
Subject
Biological sciences
Genomics
Biomedical and clinical sciences