Fig. 2.

Concatemers produced by proximity ligation indicate simultaneous colocation of three or more loci. (A) In COLA, concatemers spanning three or more fragments are created by cutting chromatin using CviJI, followed by DNA–DNA proximity ligation in intact nuclei. (B) Contact triples visualized as a 3D contact tensor. Broad patterns of contacts can be revealed by slicing the tensor and examining the results at low resolution. (C) A planar cut of the contact tensor enables the examination of all triples containing DXZ4. Enlargement: Enrichment is seen in the plane at x75(–DXZ4)–FIRRE. (Resolution: 800 kb.) (D) A different cut makes it possible to study triples in the vicinity of ICCE. Superloop triples (ICCE–)DXZ4–FIRRE and (ICCE–)x75–FIRRE are highlighted. (Resolution: 2 Mb.)