FIG. 3.

Methylation interferes with CTCF binding to the recognition sequence under study. Gel retardation experiments with a radiolabeled 50-bp fragment containing the putative CTCF-binding site either nonmethylated (C), fully methylated at all five CpGs (FM), or methylated at individual CpGs (M1 to M5). Nuclear protein extract (NPE) from HD3 cells was added to all reaction mixtures, except that shown in lane 1. In lane 3, a 10-fold molar excess of specific inhibitor (FII unlabeled DNA) was present in the reaction mixture along with poly(dI-dC) (note that the upper band was specifically competed). The sequence of the putative CTCF recognition site is presented below with the positions of CpG dinucleotides (M1 to M5) that were either totally or individually methylated.