Figure 6.

TOP2-mediated DSBs preferentially present at G4 structure regions and at the lost TAD boundary-associated CTCF binding sites. Etoposide (ETO) treatment significantly increases DSB enrichment at G4 consensus regions in GM13069 (A) and HeLa cells (B). Boxplot illustration of DSB coverage at the consensus G4 regions in GM13069 (C) and HeLa cells (D). (E) Mosaic plot shows lost CTCF binding sites at TAD boundaries are overrepresented among shared G4 CTCF binding sites, while gained CTCF binding sites are underrepresented among G4 CTCF binding sites (P = 2.13 × 10⁻¹², chi-square test). The lost CTCF binding sites at TAD boundaries, when compared to those at loops, are significantly more enriched with etoposide-induced DSBs in GM13069 (F) and HeLa cells (G), and maintain the strong DSB increase corresponding to the increased concentrations of etoposide. Boxes denote 25th and 75th percentiles, middle lines show medians and whiskers span from 5% to 95%; ***P < 0.001, ****P ∼ 0, and ns, not significant, Kruskal–Wallis followed by post-hoc Dunn test.