Fig. 2

Genome-wide binding profiles of MSH2 and MSH6 in mouse ESCs as revealed by Bio-ChIP-seq and ChIP-seq. a Pie chart showing the distribution of genomic elements within the DNA regions covered by MSH2 Bio-ChIP-seq peaks. MSH2 peaks were defined as DNA regions that were enriched in the Msh2-AviTag cells compared to mock-transfected BirA-expressing ESCs. For feature annotation, we used the plotAnnoPie function with annoDb = "org.Mm.eg.db" parameter". b Pie chart representing the percentage of MSH2 Bio-ChIP-seq peaks overlapping CpG islands (CpGI) and genomic regions not including CpGI (non CpGI). c Average Profile of MSH2 peaks overlapping Transcription Start Sites (TSS). The plot shows the peak frequency between −3000 bp and + 3000 bp from TSS. d Pie chart representing the percentile distribution of MSH2 peaks overlapping or not overlapping mask repetitive elements. e Bar plot showing the absolute frequency of repetitive elements covered by MSH2 peaks. f Heatmaps showing the read enrichment of MSH2 (2 replicates), MSH6 (2 replicates), ZFP57 and KAP1 in the genomic regions overlapping (± 1.5 kbp) the KAP1 ChIP-seq peaks. As controls, we added the Bio-ChIP-seq reads of untransfected E14 ESCs (MSH2 control) and input DNA reads of the MSH6 ChIP (MSH6 input). KAP1 peaks are sorted in descending order based on the mean read enrichment value per region