MER41 repeat sequences contain inducible STAT1 binding sites

Abstract

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChlP-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 ChlP-seq data. Assessing the content of the established consensus sequence for STAT1 binding sites, we find that the usage of ''negative control'' ChlP-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 ChlP-seq signal is associated with a nucleotide sequence ressembling 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 ChlP-seq data. Furthermore a surprisingly large fraction of the ChlP-seq signal (5%) is absorbed by a small family of repetitive sequences (MER41). The observation of the binding of activated STAT1 protein to a specific repetitive element bolsters similar reports concerning p53 and other TFs, and strengthens the notion of an involvement of repeats in gene regulation. lncidentally MER41 are specific to primates, consequently, regulatory mechanisms in the lFN-STAT pathway might fundamentally differ between primates and rodents. On a methodological aspect, the presence of large numbers of nearly identical binding sites in repetitive sequences may lead to wrong conclusions about intrinsic binding preferences of TF as illustrated by the spacing analysis STAT1 tandem motifs. Therefore, ChlP-seq data should be analyzed independently within repetitive and non-repetitive sequences. © 2010 Schmid, Bucher.