Extended Data Fig. 4: YAP recruits CTCF to modulate long-range enhancer-promoter interactions between human genes and TE MREEs.
a, RAD21 binding is detected at 81% of YAP/CTCF co-occupied TE loci. b, Box plot quantifying CTCF ChIP-seq signal at YAP/CTCF co-occupied TEs under stiff and soft conditions. n = 2 biologically independent experiments. c, d, (c) Heatmap and (d) box plot showing a reduction in RAD21 signal at YAP/CTCF co-occupied TEs under soft versus stiff conditions. n = 2 biologically independent experiments. e, MA scatter plot showing RAD21 ChIP-seq signal changes at YAP/CTCF co-occupied TE loci under soft versus stiff conditions. Loci with significantly reduced RAD21 binding in soft matrices are highlighted in blue, and those with increased binding are in red. f, Density plot showing the genomic distance of YAP/CTCF co-occupied TEs from the nearest TAD boundaries in hESCs. g, h, (g) Aggregated insulation scores of YAP/CTCF co-occupied TEs under soft and stiff conditions. The local maximal insulation scores indicate that these elements’ genome insulation function, if any, do not reduce in soft matrices. (h) Quantification of insulation score differences. n = 2 biologically independent experiments. i, Box plot quantifying H3K27ac signals at YAP/CTCF co-occupied TEs under soft versus stiff conditions. n = 2 biologically independent experiments. j, Density plot showing the genomic distance between YAP and CTCF peak summits at their co-occupied TE loci. k–m, (k) Heatmaps, (l) aggregated ChIP-seq signals, and (m) box plots comparing CTCF ChIP-seq signals at TE loci co-occupied by YAP and CTCF versus those bound by CTCF alone. n = 2 biologically independent experiments. In box plots(b, d, h, i, and m), center lines represent the median value, box limits the 25th and 75th percentiles, and whiskers denote minima and maxima (1.5× the interquartile range). Source numerical data are available in source data.
