ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells

Mammalian chromosomes are folded by the cohesin complex, which creates chromatin loops that are extruded as cohesin translocates along the chromatin fiber. This dynamic process regulates gene expression by controlling the frequency of contacts between enhancers and promoters. We analyzed where in the genome loop extrusion occurs to discover where extrusion initiates and whether particular regions are extruded more than others. We measured NIPBL/MAU2 binding in mouse embryonic stem cells and neural progenitor cells, and found that NIPBL/MAU2 is enriched at enhancers compared to promoters. We used the amount of cohesin binding at CTCF sites as a readout of cohesin traffic, and found that the NIPBL/MAU2 binding sites only modestly boost nearby cohesin levels. We measured NIPBL and MAU2 binding by performing spike-in calibrated HA ChIP-seq in cell lines in which NIPBL or MAU2 was tagged with an HA epitope and FKBP degron. Cells treated with dTAG for 24 hours to deplete NIPBL or MAU2 and untagged cell lines are used as negative controls. We also measured RAD21 and CTCF binding with endogenous antibodies. We used mouse embryonic stem cells and neural progenitor cells.