MER41 repeat sequences contain inducible STAT1 binding sites.

PloS One
Christoph D Schmid, Philipp Bucher

Abstract

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we present novel approaches for the interpretation of ChIP-seq data.We compare recently developed approaches to determine STAT1 binding sites from ChIP-seq data. Assessing the content of the established consensus sequence for STAT1 binding sites, we find that the usage of "negative control" ChIP-seq data fails to provide substantial advantages. We derive a single refined probabilistic model of STAT1 binding sequences from these ChIP-seq data. Contrary to previous claims, we find no evidence that STAT1 binds to multiple distinct motifs upon interferon-gamma stimulation in vivo. While a large majority of genomic sites with high ChIP-seq signal is associated with a nucleotide sequence resembling a STAT1 binding site, only a very small subset of the over 5 million potential STAT1 binding sites in the human genome is covered by ChIP-seq data. Furthermore a surprisingly large fraction of the ChIP-seq signal (5%) is absorbed by a small family of repetitive sequences (MER41). The observ...Continue Reading

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Citations

Jan 15, 2014·Nature Immunology·Andreas BegittUwe Vinkemeier
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Methods Mentioned

BETA
immunoprecipitation
ChIP-chip
ChIP-seq
ChIP
SELEX
sequence-based
SGA

Software Mentioned

ORegAnno
RepeatMasker
peak
PeakSeq
cor
MACS
seq
UCSC Genome Browser
MArkow MOdeling Tool ( MAMOT
ChIP

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