Cohesin-dependent chromatin structure at a close view.

The cohesin complex is an important factor for the three-dimensional organization of chromatin. Hi-C studies have shown that chromatin loops cluster together into topological domains. Recently, we and others have used Hi-C to show how topological domains and subdomains change when the cohesin complex is depleted. Our study showed that topological domains are altered after cohesin depletion but not disrupted. However, the current resolution of Hi-C (40kb) is not sufficient to yield information about the inside of TADs, for instance which long range contacts are affected in particular and which regions remain unaffected, are only interactions involving cohesin sites affected and how does the chromatin fibre rearrange without cohesin. To address these question we have studied a 2.1 Mb region on the human chromosome 11 using our novel T2C technique which allows to generate a Hi-C type dataset at restriction fragment resolution (2-6 kb). Our selected region contains two topological domains and two imprinted gene clusters, H19/IGF2 and KCNQ1/KCNQ1OT1. We have generated T2C maps for two different cell types, a breast endothelial cell line and HEK293T cells, and also for cells where the cohesin complex was destroyed in interphase by proteolytic cleavage of its RAD21 subunit. We will present our results addressing the aforementioned questions. Further we have also reinvestigated previously published data concerning the interactions and potential co-regulation between the imprinted gene clusters and their imprinted control regions.