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 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.

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE / 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, Stefano; Sandelin, A; Carninci, P.. - In: GENOME RESEARCH. - ISSN 1088-9051. - 19:2(2009), pp. 255-265. [10.1101/gr.084541.108]

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

Gustincich, Stefano;
2009

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 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.
19
2
255
265
http://www.genome.org/cgi/doi/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, Mh; Zhao, X; Krogh, A; Winther, O; Arakawa, T; Kawai, J; Wells, C; Daub, C; Harbers, M; Hayashizaki, Y; Gustincich, Stefano; Sandelin, A; Carninci, P.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/16607
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