Fig. 5

Correlation between differential gene expression and disrupted CTCF binding of ZF mutants. a Schematic diagram of the integrative analysis of RNA-seq and differential binding of HA-CTCF-ZF mutants ChIP-seq. For each gene, initially, we considered all the peaks within [TSS − 50 kb, TES + 50 kb]. The RNA-seq and ChIP-seq fold changes were converted to z-score, then multiplied together for each gene-peak pair to get a combined score. Pareto optimization was performed to determine the most correlated peak-gene pairs. b Scatterplot representing the correlated distribution of DE genes and differentially bound peaks identified using Pareto optimization for ZF1, ZF10, and RBR mutants compared to CTCF WT. The x-axis shows the expression fold change of the differentially expressed genes. The y-axis represents the binding fold change of the gene-associated peaks. c HA ChIP-seq tracks from CTCF WT and mutants at the DDN locus showing disrupted CTCF binding in CTCF^AID2/dZF10 cells. d Differential expression of the DDN gene by RNA-seq (FKPM) in response to CTCF depletion. ***p ≤ 0.001 calculated by unpaired t-test. e HA ChIP-seq tracks from CTCF WT and mutants at the FGFBP2 locus showing disrupted CTCF binding in CTCF^AID2/dZF1 cells. f Differential expression of the FGFBP2 gene by RNA-seq (FKPM) in response to CTCF depletion. **p ≤ 0.01 calculated by unpaired t-test