a, Hi-C contact matrices of the q-arm of chromosome 2 at 500-kb resolution. The corresponding compartment scores are plotted above. b, Genome-wide comparison of compartment scores for wild-type and CTCFY226A/F228A cells. Pearson correlation = 0.97. c, Saddle plots representing the interaction between A and B compartments. d, A region of chromosome 1 (55500000–59500000) at 10-kb resolution that contains no obvious CTCF-anchored loops. e, Relative contact probability profiles for wild-type and CTCFY226A/F228A mutant cells (left), compared to previously published12 contact profiles upon degradation of CTCF (middle) or SCC1 (right). The contact probability profile is affected only slightly in the CTCFY226A/F228A mutants, similar to the effects of CTCF depletion.