a Top: heatmap plot of distance matrices derived from the Si-C 10 kb structure of cell 1 for four genomic regions. In each region, two neighboring domains that are identified by separation score are indicated by black lines. Bottom: distributions of the separation score and gyration radius (Rg). b 3D structures of the genome regions associated with the two neighboring domains shown in (a). Structures corresponding to the boundary, domain 1 and domain 2 regions are shown in red, cyan, and green, respectively. c, d Loop and hairpin-like hyperfine structures visualized by beads of 10 kb size (left) and the 3D structures of the same regions visualized by beads of 100 kb size, inferred by Si-C (middle) and Nucdynamics(right).