Additional file 10.

CTCF binds CpG promoters more frequently than non-CpG promoters. (a-f) CpG promoters are more frequently bound by CTCF than non-CpG promoters. The enrichment of CTCF at CpG promoters is independent of the definition of overlap (a, c, e). All comparisons have a chi-squared test P-value < 2.2e-16. To control for the correlation between CTCF binding and expression level, we split the two groups of genes into ten equally sized expression bins and counted the fraction of promoters overlapping CTCF binding sites in each expression bin (b, d, f). Error bars represent 95% confidence intervals of binomial proportions. (g-i) CTCF binding sites that overlap CpG promoters have similar levels of CTCF as intergenic CTCF binding sites. Here we show CTCF levels at all CpG promoters (g), CTCF levels at an equal number of distal CTCF binding sites (h) and CTCF levels at all intergenic CTCF binding sites (i). The CTCF profiles shown in (g-i) are centered on the CTCF peak mid-point.

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Vavouri and Lehner Genome Biology 2012 13:R110   doi:10.1186/gb-2012-13-11-r110