4C-seq for wild type and rearranged alleles at the Tfap2c-Bmp7 locus in mouse ES cells

To analyze how the binding patterns of CTCF organize the chromatin conformation of the Tfap2c-Bmp7 locus, thorough deletion and inversion of CTCF binding regions were introduced around the locus in the mouse embryonic cells. Then the outcome of these mutations for the chromatin conformation was analyzed by 4C-seq (Circular Chromatin Conformation Capture followed by high-throughput sequencing). The locus harbors two contact domains (TADs) separated by a boundary region called TZ. The TZ consists of two arrays of CTCF binding sites, one consisting of four sites orienting toward the Tfap2c side and the other of three sites orienting to the Bmp7 side, in divergent configuration. When the arrays were deleted and inverted, the degree of the inter-domain contacts was increased. Also the influence of the non-boundary CTCF binding sites at the Tfap2c promoter was analyzed.