Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion [ChIP-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) under self-renewal or differentiation conditions. We performed ChIP-seq for H3K4me3, H3K27ac, RAD21 and HA. Overall design: Characterization of H3K4me3 and H3K27ac marked regions and RAD21 binding regions with ChIP-seq in ESCs and EpiLC