FIG. 7.

Interactions between CTCF sites are not associated with MHC-II gene activity. 3C assays were conducted between CTCF sites to determine the frequencies of interactions between the sites. Raji (MHC-II-expressing) and RJ2.2.5 (MHC-II-negative) cells were compared. EcoRI was used as the enzyme that allowed the majority of sites to be assessed. 3C assays were carried out as described above. The data were derived from three independent preparations of cross-linked chromatin. The shaded areas represent self-ligating restriction fragments that contained the anchor primer set for each panel, as indicated. These self-ligating 3C fragments demonstrate that restriction site accessibilities for these fragments were similar in the two cell lines tested. The error bars indicate standard errors.