On the origin of the integrity of a subset of Topologically Associating Domains upon Cohesin loss in Interphase Chromosomes

Interphase chromosomes undergo phase separation between active and inactive loci to form the A and B compartments on a multi-megabase scale. Below the megabase scale, Topologically Associating Domains (TADs), which are created by the motor protein cohesin in conjunction with the architectural protein CTCF, appear as squares along the diagonal in the contact matrix. Hi-C experiments have revealed that the majority of the TADs at the ensemble level are abolished upon cohesin depeletion, while recent super-resolution imaging studies exhibit cohesin-independent TAD-like domain structures at the single cell level. However, a closer examination of the Hi-C data shows a non-negligible fraction of TADs is preserved (P-TADs) even after cohesin loss. In this study, using polymer simulations, we uncovered that TADs with epigenetic mismatches across their boundaries or with physical boundaries in their 3D structures survive upon loop deletion. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and HCT-116, which corroborated that epigenetic mismatch plays an important role for P-TADs. Interestingly, the single-cell structures, calculated only from wild/cohesin-depleted Hi-C contact maps using the HIPPS method, display various TAD-like domains as in imaging experiments. We found that the preferential positioning of some single-cell domain boundaries is not lost after cohesin deletion, leading to the preservation of the ensemble TADs.