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  • 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
    Griffith University Author(s)
    Wells, Christine
    Chalk, Alistair M.
    Year published
    2009
    Metadata
    Show full item record
    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 which ...
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    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.
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    Journal Title
    Genome Research
    Volume
    19
    Issue
    2
    DOI
    https://doi.org/10.1101/gr.084541.108
    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
    Genomics
    Biological Sciences
    Medical and Health Sciences
    Publication URI
    http://hdl.handle.net/10072/22543
    Collection
    • Journal articles

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