Fig. 4

Genomic features of combinatorial TOP2B, CTCF, and RAD21 binding. a Overlap of TOP2B, CTCF, and RAD21 ChIP-seq binding regions defines seven different categories of peaks. b Comparison of CTCF, RAD21, and TOP2B ChIP-seq reads (RPKM) for each of the categories defined in (a). Outliers (>95th percentile) are not shown. c Pan-tissue analysis of CTCF binding for triple sites (black), double sites (dark gray), and CTCF-only sites (white). d DNA sequence constraint of triple (black), double (green), and CTCF only sites (yellow) as determined by average GERP score (y-axis). CTCF peaks were oriented based on the direction of CTCF motif (G-rich orientation is shown). e Cross-species comparison of mouse triple (n = 20,381), double (n = 20,049), and CTCF-only sites (n = 8301) with CTCF ChIP-seq peaks mapped in human, macaque, rat, and dog. Stacked bar plots show the proportion of peaks based on the degree of conservation (mouse only, mouse and rat only, and mouse plus one non-rodent (beyond rodents)). f Conservation of mouse triple (n = 1329), double (n = 6582), and singleton (n = 2957) CTCF sites that contain rodent-specific B2 SINE elements