Fig. 3

CTCF-s competition causes the reduction of both CTCF and cohesin binding and alters CTCF-mediated chromatin looping. a Venn diagrams showing the overlap of RAD21 and CTCF peaks. b Venn diagrams showing the overlap of RAD21 binding sites with significantly decreased CTCF binding sites upon CTCF-s gain-of-function, from cluster 1 in Fig. 2f. c Heatmap and pileup for CTCF and RAD21 ChIP intensity in CTCF bound sites that decreased when FLAG-CTCF-s was overexpressed. d Raw interaction maps of CTCF HiChIP at a locus on chromosome 1 produced from FLAG control cells and cells with FLAG-CTCF-s overexpression and Hi-C data in HeLa-S3 cells drawn with the indicated resolutions and views. Numbers above the interaction maps correspond to maximum signal in the matrix. e Bar chart showing loop difference from HiChIP data in both FLAG control cells and cells with FLAG-CTCF-s overexpression. f Boxplot showing the distribution of loop intensities in average log2 counts per million (log2CPM) among the three loop classes (up, down and unchanged) from (e). The midline represents the second quartile, the bounds of box represent third quartile and first quartile. The whiskers indicate 1.5 × interquartile range and dots represent outliers. g Features of downregulated loops with distinct anchor features in FLAG control from (f). The loop anchor features were classified from the change of CTCF binding strength in FLAG control and FLAG-CTCF-s overexpressed samples. The midline represents the second quartile, while the bounds of box represent third quartile and first quartile, respectively. The whiskers indicate 1.5 × interquartile range and dots represent outliers. h Fold-change analysis of downregulated loops that were associated with distinct anchor features that were classified from FLAG control and FLAG-CTCF-s overexpressed samples after FLAG-CTCF-s gain-of-function. The midline represents the second quartile, the bounds of box represent third quartile and first quartile. The whiskers indicate 1.5 × interquartile range and dots represent outliers. i Example genomic view showing the changes of CTCF ChIP intensities and CTCF-mediated chromatin loops at the MDM2/CPM gene locus. The directionality of the motifs at CTCF loop anchors was indicated with red arrows