RNAi depletion of insulator proteins causes H3K27me3 depletion within domains but has no effect on H3K27me3 domain flanking genes. (A) Percentage of genes down-regulated (more than twofold) in Drosophila Kc cells after knockdown of insulator protein expression. Comparison of genes flanking H3K27me3 domains with genome-wide averages. (B) Average read intensity for H3K27me3 in Drosophila Kc cells at domain borders and surrounding domain centers. H3K27me3 levels were determined by ChIP-seq before and after dCTCF knockdown. For appropriate comparison, ChIP-seq data for H3K27me3 was rank normalized as previously described (Whyte et al. 2012) and represented as average read intensity.
