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

Eivind Valen; Giovanni Pascarella; Alistair Chalk; Norihiro Maeda; Miki Kojima; Chika Kawazu; Mitsuyoshi Murata; Hiromi Nishiyori; Dejan Lazarevic; Dario Motti; Troels Torben Marstrand; Man-Hung Eric Tang; Xiaobei Zhao; Anders Krogh; Ole Winther; Takahiro Arakawa; Jun Kawai; Christine Wells; Carsten Daub; Matthias Harbers; Yoshihide Hayashizaki; Stefano Gustincich; Albin Sandelin; Piero Carninci

doi:10.1101/gr.084541.108

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

Eivind Valen, Giovanni Pascarella, Alistair Chalk, Norihiro Maeda, Miki Kojima, Chika Kawazu, Mitsuyoshi Murata, Hiromi Nishiyori, Dejan Lazarevic, Dario Motti, Troels Torben Marstrand, Man-Hung Eric Tang, Xiaobei Zhao, Anders Krogh, Ole Winther, Takahiro Arakawa, Jun Kawai, Christine Wells, Carsten Daub, Matthias HarbersYoshihide Hayashizaki, Stefano Gustincich, Albin Sandelin, Piero Carninci

121 Citations (Scopus)

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.

Original language	English
Journal	Genome Research
Volume	19
Issue number	2
Pages (from-to)	255-65
Number of pages	11
ISSN	1088-9051
DOIs	https://doi.org/10.1101/gr.084541.108
Publication status	Published - Feb 2009
Externally published	Yes

Keywords

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

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Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M.-H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., ... Carninci, P. (2009). Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research, 19(2), 255-65. https://doi.org/10.1101/gr.084541.108

Valen, E, Pascarella, G, Chalk, A, Maeda, N, Kojima, M, Kawazu, C, Murata, M, Nishiyori, H, Lazarevic, D, Motti, D, Marstrand, TT, Tang, M-HE, Zhao, X, Krogh, A, Winther, O, Arakawa, T, Kawai, J, Wells, C, Daub, C, Harbers, M, Hayashizaki, Y, Gustincich, S, Sandelin, A & Carninci, P 2009, 'Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE', Genome Research, vol. 19, no. 2, pp. 255-65. https://doi.org/10.1101/gr.084541.108

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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.",

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AU - Valen, Eivind

AU - Pascarella, Giovanni

AU - Chalk, Alistair

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AU - Kojima, Miki

AU - Kawazu, Chika

AU - Murata, Mitsuyoshi

AU - Nishiyori, Hiromi

AU - Lazarevic, Dejan

AU - Motti, Dario

AU - Marstrand, Troels Torben

AU - Tang, Man-Hung Eric

AU - Zhao, Xiaobei

AU - Krogh, Anders

AU - Winther, Ole

AU - Arakawa, Takahiro

AU - Kawai, Jun

AU - Wells, Christine

AU - Daub, Carsten

AU - Harbers, Matthias

AU - Hayashizaki, Yoshihide

AU - Gustincich, Stefano

AU - Sandelin, Albin

AU - Carninci, Piero

PY - 2009/2

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N2 - 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.

AB - 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.

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KW - Binding Sites

KW - Chromosome Mapping/methods

KW - Gene Expression

KW - Hippocampus/metabolism

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KW - Models, Biological

KW - Organ Specificity/genetics

KW - Promoter Regions, Genetic/genetics

KW - Protein Binding

KW - Sequence Analysis, DNA/methods

KW - Transcription Factors/metabolism

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VL - 19

SP - 255

EP - 265

JO - Genome Research

JF - Genome Research

IS - 2

ER -

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

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Keywords

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