CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression

Recent studies indicate that even a homogeneous population of cells display heterogeneity in gene expression and response to environmental stimuli. Although promoter structure critically influences the cell-to-cell variation of gene expression in bacteria and lower eukaryotes, it remains unclear what controls the gene expression noise in mammals. Here we report that CTCF decreases cell-to-cell variation of expression by stabilizing enhancer-promoter interaction. We show that CTCF binding sites are interwoven with enhancers within topologically-associated domains (TADs) and a positive correlation is found between CTCF binding and the activity of the associated enhancers. Deletion of CTCF sites using CRISPR/Cas9 compromises enhancer-promoter interactions. Using single-cell flow cytometry and single-molecule RNA-FISH assays, we demonstrate that knocking down of CTCF or deletion of a CTCF binding site results in increased cell-to-cell variation of gene expression, indicating that long-range promoter-enhancer interaction mediated by CTCF plays an important role in controlling the cell-to-cell variation of gene expression in mammalian cells. ¬ 3e Hi-C is a robust technique to measure genome-wide chromatin interactions ¬ CTCF binding is positively correlated with the activity of enhancers and their interaction with target promoters ¬ Knocking down CTCF expression or deletion of CTCF binding sites results in decreased enhancer-promoter interaction and increased cell-to-cell variation of gene expression ¬ CTCF stabilizes enhancer-promoter interaction and controls gene expression noise.