Extended Data Fig. 6: Chromatin contacts at inserted CBSs.

a, K-R normalized Hi-C matrix (Observed/Expected) in the clone with the two forward Sox9-Kcnj2 TAD boundary CBSs inserted between the Sox2 promoter and super-enhancer (n = 2, replicates were merged). Hi-C reads were mapped to a customized chromosome 3 containing the insertion of the two forward CBSs. ChIP-seq signal of CTCF and orientations of the inserted CBSs and CBSs around the Sox2 promoter and super-enhancer were shown. The black arrow indicates the interactions between the inserted CBSs and the CBS on the Sox2 super-enhancer. b, Virtual 4C derived from Hi-C contacts in (a) at the viewpoint of the two inserted CBSs. Contacts were counted in each 5kb-bin. Contacts between the inserted CBSs and the Sox2 promoter or super-enhancer were compared to expected values, two-sided Poisson test. c, K-R normalized Hi-C matrix (Observed/Expected) in the clone with the four Sox9-Kcnj2 TAD boundary CBSs inserted between the Sox2 promoter and super-enhancer (n = 2, replicates were merged). Hi-C reads were mapped to a customized chromosome 3 containing the insertion of the four CBSs. ChIP-seq signal of CTCF and orientations of the inserted CBSs and CBSs around the Sox2 promoter and super-enhancer were shown. The black arrows indicate the interactions between the inserted CBSs and the CBS on the Sox2 promoter and super-enhancer. d, Virtual 4C derived from Hi-C contacts in (c) at the viewpoint of the two reverse-orientated CBSs inserted between the Sox2 promoter and super-enhancer. Contacts were counted in each 5kb-bin. Contacts between the two reverse CBSs and the Sox2 promoter or super-enhancer were compared to expected values, two-sided Poisson test.