Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion [4C-seq]
Structural loops are known to collapse in the absence of cohesin, whereas regulatory loops largely persist with only minor transcriptional changes, leaving unresolved questions about cohesin's role in establishing regulatory interactions during cell state transitions. To investigate this, we degraded RAD21, a core cohesin subunit, in mouse embryonic stem cells (ESCs) transitioning from mitosis to G1 under self-renewal or differentiation conditions. We performed high-resolution in situ 4C-seq around the promoters of cohesin-sensitive genes (Klf4, Tbx3, Myc, and Fosl2) in ESCs and EpiLCs. Overall design: 4C-seq for selected genes in ESCs and EpiLCs with or without RAD21 depletion