Fig. 6

Differential CTCF binding in CTCF-K20R regulates EP interactions and their associated gene expression. (A) Venn diagram showing the overlap between the downregulated CTCF sites and TAD boundaries. Two independent BL-Hi-C experiments were performed for each sample. (B) Scatter plot showing the insulation scores of the TAD boundaries between the WT and CTCF-K20R mutant in EB samples on day 4 after mESC differentiation. Red points represent TAD boundaries with downregulated CTCF sites. (C) Categories of significant chromatin loops extracted from BL-Hi-C data. (D) Scatter plot showing the change in chromatin loops. Loops were considered changed if the loops were up- or down-regulated at least twofold. (E) Heatmaps showing the APA analysis for up-, stable- and down-regulated chromatin loops, respectively. (F) Categories of up- and downregulated chromatin loops. (G) Scatter plots showing the expression of genes associated with CTCF-mediated EP interactions. The gene expression level is represented as normalized read counts. (H) Representative genomic locus showing CTCF, H3K27ac, RNA-seq and BL-Hi-C data at the Eomes gene locus. Chromatin interactions are shown at 10 kb resolution. Yellow tracks represent enhancers and promoters. Black arrows point to the decreased EP interactions