Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation

Enhancers and their target promoters often come into close physical proximity when activated. This may be explained by a variety of mechanisms, including cohesin-mediated chromatin loop extrusion. However, acute depletion of cohesin does not cause widespread changes in gene expression. We have tested the role of cohesin-mediated loop extrusion in gene expression at the mouse alpha-globin locus during erythropoiesis. Acute depletion of cohesin disrupts alpha-globin expression at early but not late stages of differentiation. Furthermore, when single or multiple CTCF sites, known to block cohesin, are placed between the alpha-globin enhancers and promoters, alpha-gene expression is disrupted. Importantly, the CTCF site's orientation is critical, suggesting that within this activated domain, in definitive erythroid cells, cohesin predominantly but not exclusively, translocates from the enhancers to the promoters. We find that loop extrusion does play an important role in establishing enhancer-promoter proximity and consequent expression of inducible genes during differentiation.