Analysis of data on large-scale chromatin immunoprecipitation by recognition of transcription factor binding sites

Abstract

Chromatin immunoprecipitation followed by mass parallel sequencing of the precipitated fragments (ChIP-Seq) is broadly used for detailed investigation of the distribution of various transcription factor binding sites over the whole genome. The ChIP-Seq profiles obtained by immunoprecipitation of mouse liver chromatin with antibodies against the FoxA2 transcription factor [Wederell et al., 2008] were analyzed by our methods of recognition of FoxA binding sites. The following classification of locus profiles was proposed on the basis of analysis. (1)Unimodal loci (possessing a single peak) with length below 600 bp. These loci are likely to be formed by a single FoxA binding site. (2) Multimodal loci (possessing two or more distinct peaks) of lengths over 600 bp and all longer loci. Each locus of this group is likely to be composed of numerous single sites.