title: Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
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.
authors.affiliation: The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes vej 5, DK-2200, Denmark.
authors.forename: Eivind
authors.initials: E
authors.lastname: Valen
authors.forename: Giovanni
authors.initials: G
authors.lastname: Pascarella
authors.forename: Alistair
authors.initials: A
authors.lastname: Chalk
authors.forename: Norihiro
authors.initials: N
authors.lastname: Maeda
authors.forename: Miki
authors.initials: M
authors.lastname: Kojima
authors.forename: Chika
authors.initials: C
authors.lastname: Kawazu
authors.forename: Mitsuyoshi
authors.initials: M
authors.lastname: Murata
authors.forename: Hiromi
authors.initials: H
authors.lastname: Nishiyori
authors.forename: Dejan
authors.initials: D
authors.lastname: Lazarevic
authors.forename: Dario
authors.initials: D
authors.lastname: Motti
authors.forename: Troels Torben
authors.initials: TT
authors.lastname: Marstrand
authors.forename: Man-Hung Eric
authors.initials: MH
authors.lastname: Tang
authors.forename: Xiaobei
authors.initials: X
authors.lastname: Zhao
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
authors.forename: Ole
authors.initials: O
authors.lastname: Winther
authors.forename: Takahiro
authors.initials: T
authors.lastname: Arakawa
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Christine
authors.initials: C
authors.lastname: Wells
authors.forename: Carsten
authors.initials: C
authors.lastname: Daub
authors.forename: Matthias
authors.initials: M
authors.lastname: Harbers
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Stefano
authors.initials: S
authors.lastname: Gustincich
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
mesh_terms: D000818:Animals; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods; D015870:Gene Expression; D006624:Hippocampus / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D008954:Models, Biological; D009928:Organ Specificity / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors