Cohesin depleted cells rebuild active and inactive nuclear compartments after mitosis

Nuclear functions are essentially linked to nuclear compartmentalization. This study demonstrates that cohesin rings as anchors of chromatin loops are dispensable to rebuild a functional nuclear compartmentalization in cohesin depleted cells after passing through mitosis and formation of one daughter cell with a multilobulated nucleus (MLN). Super-resolved microscopy reveals co-aligned active and inactive nuclear compartments (ANC/INC) in these postmitotic nuclei, likely corresponding to A and B compartments, detected with Hi-C. MLN carry chromosome territories, built from chromatin domain clusters, pervaded by a system of interchromatin channels harboring splicing speckles. Channels are lined by transcriptionally competent chromatin, whereas repressed chromatin with higher compaction locates in the interior of chromatin clusters. MLN pass through S-phase with typical early and mid-to-late replication patterns. Sites of DNA synthesis become physically larger, consistent with a model where cohesin dependent loop extrusion tends to compact intervals of replicating chromatin, whereas their genomic boundaries are associated with compartmentalization. Overall design: Microscopy, Hi-C, and Repli-Seq in HCT-116 cmvOsTir1 RAD21-mAC cells