Fig. 3.

The ICCE–DXZ4 and DXZ4–FIRRE superloops tend to occur simultaneously, forming a hub on the Xi chromosome. (A) Examination of a small region from the 3D contact tensor of the X chromosome, centered on ICCE, DXZ4, and FIRRE, reveals a peak relative to the local neighborhood. Five contacts are seen in the (300 kb)³ voxel (i.e., 3D pixel) associated with simultaneous colocation of all three loci. There are more than 2,000 other (300 kb)³ voxels in the region shown; the number of contacts in each is indicated by the color. Of these voxels, five contain two contacts each, 74 contain one contact each, and more than 2,000 voxels contain no contacts. Note that because of the fixed bin width, the voxel size presented in this figure, (300 kb)³, is slightly larger than (and has slightly more contacts than) the exact volume defined by ICCE–DXZ4–FIRRE boundaries, which was used for the analyses in the main text. (B) The average frequency of contact in various local neighborhoods surrounding the ICCE–DXZ4–FIRRE peak. The peak is strongly enriched with respect to every model. (C) Representative examples of direct-labeled three-color DNA FISH in GM12878, a female cell line, showing collocation of ICCE–DXZ4–FIRRE. FISH signals overlay DAPI (blue) and are merged in the panel at the far right. The white arrowhead indicates a three-way overlap on one X chromosome.