Fig. 4
CGGBP1 affects CTCF occupancy and histone modifications at known CTCF-binding sites. a, b CTCF read distribution was plotted for CT, KD and OE at the LAD boundaries in the 50 kb flanks with bins of 1 kb. The average read density with standard error of the mean was plotted for LAD start sites (a) and LAD end sites (b). CTCF binding is reported to occur in 10 kb flanks of the LAD start and end sites. c Correlation heatmap was plotted for H3K4me3, H3K9me3 and H3K27me3 ChIP-seq peaks in CT and KD. The correlation values (r) corresponding to CT and KD are mentioned for each histone modification in the heatmap. Unlike H3K4me3 and H3K27me3, the CT and KD samples for H3K9me3 were significantly different from each other. d PCA analysis using input as control shows the distance between H3K9me3 CT and KD as the most affected in KD. CGGBP1 depletion minimizes the distinction of H3K9me3 from H3K4me3 and H3K27me3 along PC2 only while along PC1, the two repressing marks remain closer to each other than the activating mark. e Disturbances in the H3K9me3 is observed in KD compared to CT. Genome browser views (a 40 kb region on chr11 starting from approximately 1983 kb) showing reads of CTCF (data range on Y-axis 0–25), H3K9me3 (data range on Y-axis 0–25), H3K27me3 (data range on Y-axis 0–8) and H3K4me3 (data range on Y-axis 0–35) for CT and KD along with the CTCF-binding sites and repeats at the H19-ICR locus. The gain of CTCF binding upon CGGBP1 knockdown is highlighted by green arrow and changes in the histone modification profile in 10 kb flanks are highlighted by gray boxes. f Genome browser view (36 kb region on chr11 starting from approximately 5294 kb) of the beta-globin locus control region undergoing change in chromatin barrier function upon CGGBP1 depletion. The plot contains tracks of CTCF reads (data range on Y-axis 0–25), H3K9me3 (data range on Y-axis 0–25), H3K27me3 (data range on Y-axis 0–20) and H3K4me3 (data range on Y-axis 0–35) reads, hg38 genes, DNase hypersensitivity clusters and repeats. The gain and loss of CTCF binding upon CGGBP1 loss of function are highlighted with an arrowhead and an arrow, respectively