Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

Cohesin subunits, the Nipped-B cohesin loader, the MED1 and MED30 subunits of the Mediator complex, and the Fs(1)h BET domain protein were mapped by ChIP-seq in ML-DmBG3-c2 cells and their effects on each other's association with promoters, enhancers, Polycomb Response Elements, and DNA replication origins were measured. DNA replication in early S phase was measured by ChIP-seq and correlated with functional element occupancy by cohesin. Overall design: Occupancy of functional features by different cohesin subunits and Nipped-B were compared, the effects on cohesin subunit and Nipped-B occupancy when different cohesin subunits and MED30 were depleted by RNAi relative to mock-treated controls were measured. The effects on cohesin subunit and Nipped-B occupancy when Fs(1)h chromosome binding was inhibited by the JQ1 inhibitor were measured relative to mock-treated controls.