CTCF binding analysis. (A) MEME motif finder was executed on the CTCF binding locations identified by ChIP-seq in brain and compared with motifs identified using previously published ES cells and liver binding locations. Each data set found the canonical motif with high degrees of certainty. (B) The level of cytosine methylation within CTCF binding sites in the brain was compared with that across the whole genome using data from Xie et al. (2012). In both CpG and non-CpG context cytosine methylation, cytosines within CTCF binding sites are methylated less than those outside CTCF binding sites (χ2 contingency table tests, P < 0.001 for CpG and non-CpG context), confirming that CTCF prefers to bind to unmethylated DNA. (C) Genomic locations of CTCF binding are normalized to the proportion of the genome that constitutes each location (represented by the red line). This was considered for all CTCF peaks called with an FDR < 13 and separately for the 116 regions where CTCF binding was seen on one parental allele only (regions identified with a P < 0.001). CTCF is significantly enriched at genic regions, but depleted in distal intergenic regions. Parent-of-origin-specific CTCF binding locations are similar but show that binding is depleted in introns but not in intergenic regions.
