biostudies-literatureUnknown30(7)Ramasamy SEnhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a redistributiNature structural & molecular biology991-1000https://www.ebi.ac.uk/biostudies/studies/S-EPMC10352134biostudies-literatureThe Mediator complex regulates enhancer-promoter interactions.PMC10352134Lidschreiber MVelychko TCao TBNCruz JNAljahani AOudelaar AMRamasamy SKarpinska MAfalseThe Mediator complex regulates enhancer-promoter interactions.Enhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a redistributi2023-01-01T00:00:00Z2023 Jul2026-07-15T00:45:52.882Z2026-06-27T03:06:47.688ZS-EPMC103521343743006510.1038/s41594-023-01027-2