Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
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.
Valen
Eivind
E
The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes vej 5, DK-2200, Denmark.
Pascarella
Giovanni
G
Chalk
Alistair
A
Maeda
Norihiro
N
Kojima
Miki
M
Kawazu
Chika
C
Murata
Mitsuyoshi
M
Nishiyori
Hiromi
H
Lazarevic
Dejan
D
Motti
Dario
D
Marstrand
Troels Torben
TT
Tang
Man-Hung Eric
MH
Zhao
Xiaobei
X
Krogh
Anders
A
Winther
Ole
O
Arakawa
Takahiro
T
Kawai
Jun
J
Wells
Christine
C
Daub
Carsten
C
Harbers
Matthias
M
Hayashizaki
Yoshihide
Y
Gustincich
Stefano
S
Sandelin
Albin
A
Carninci
Piero
P
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
D014157:Transcription Factors