CTCF mediates chromatin loops across the genome to regulate gene expression, particularly through enhancer-promoter (EP) interactions. Surprisingly, acute CTCF depletion has only modest effects on these interactions and gene expression, leaving much of its regulatory mechanism unclear. Using high-resolution chromatin interaction techniques within an acute CTCF degradation model, we found that promoter-bound CTCF enhances gene expression by increasing chromatin accessibility, driven by strengthening the binding of chromatin remodeler factors CHD4/CHD8 in a loop-independent manner. CTCF loops have a limited impact on EP or promoter-promoter (PP) interactions for the following reasons: CTCF strengthens these interactions when bound to one or both H3K27ac-marked regions and forming loops in the same direction; the functional impact of CTCF loops–whether promoting or insulating–requires substantial loop strength and appears to balance dual roles in activation or repression. Our data also show a poor correlation between changes in EP/PP interactions and gene expression alterations. Therefore, only a few differentially expressed genes are regulated via CTCF-mediated loops. In conclusion, CTCF’s loop-independent functions play a more dominant role in regulating gene expression than its mediation of chromatin loops.
 

CTCF,Enhancer-Promoter interaction,Loop-independent function,CHD4,CHD8