Fig. 1

The regulatory and topological domain organization at the Tfap2c–Bmp7 locus of the mouse. a The schema of the enhancer regulation at the Tfap2c–Bmp7 locus. The locus consists of two topological domains, separated by the action of the boundary region, TZ, in between. Allocation of the forebrain and heart enhancers to Tfap2c and Bmp7, respectively, follows the structural partition [11]. b Hi-C domains and CTCF bindings at the Tfap2c–Bmp7 locus of the mouse (chr2:172150000-172950000, mm9) genome. The left points to the centromere, while the right points to the telomere. The Hi-C heat maps are generated by the 3D Genome Browser [30] based on the data of CH12 cells at the resolution of 5 kb [6]. Contact domains called from the Hi-C data are depicted by blue bars [6]. Flags along the genomic positions represent non-tissue-specific CTCF-binding sites that are called as peaks in 14 or more out of the 31 ChIP-seq data sets generated from different biological samples by the ENCODE project listed in Additional file 2: Table S1 [32]. The orientation of the binding motifs is indicated by the pointing of the arrowheads as well as their color, with magenta and green indicating leftward and rightward orientations, respectively. As depicted, we named the four centromeric CTCF sites around the TZ as TZ-L1, L2, L3 and L4 and collectively referred to them as TZ-L. Also we named the three telomeric CTCF sites of the TZ as TZ-R1, R2 and R3 and collectively as TZ-R