Fig. 3

Differentially bound CTCF loci are found near genes, occur in shorter motifs, and have lower binding affinity and evolutionary conservation. a Differential CTCF binding sites were significantly enriched within promoters and gene bodies compared to stable CTCF binding sites (chi-square test, p = 4.9 × 10^− 10). b Stable CTCF peaks had a higher proportion of the longer (~ 33 bp) motif word compared to the differential sites. Multiple alignments of a randomly chosen subset of a hundred CTCF binding sites that are either stable or differential are shown. Each position in the alignment is colored corresponding to the nucleotide present, following the color scheme used in the CTCF motif logo shown at the top. c Binding sites susceptible to reduced CTCF concentration have significantly lower motif affinity (Mann-Whitney test, p < 2.2 × 10^− 16). d Regions bound by CTCF across the mouse lineage are less sensitive to Ctcf hemizygosity. Example tracks are shown of a stable CTCF binding site that is conserved in five species of mice, compared to a differential site that is found in only a subset of the species, M. = Mus. (M. musculus chr6:120,736,800 for the stable site and chr2:31,887,060 for the differential site). *** p value < 0.001