TOPBP1-Dependent DNA Damage Processing Promotes Centromere Loss in an Inviable Xenopus Hybrid

Hybrid incompatibility is associated with chromosome instability, DNA damage, and embryonic lethality, yet how cells respond to genome instability in hybrids is unclear. In inviable hybrids generated by fertilizing Xenopus tropicalis eggs with Xenopus laevis sperm, CENP-A is lost from paternal chromosomes, leading to elimination of two chromosome arms. Using hybrid Xenopus egg extract reactions, we show that CENP-A is removed from X. laevis chromosomes exposed to X. tropicalis cytoplasm through an RNA polymerase II-dependent process associated with DNA damage. Topoisomerase II Binding Protein 1 (TOPBP1) localized to damaged acentric chromosomes during metaphase, and its depletion impaired chromosome alignment, increased DNA damage, and blocked CENP-A removal. Inhibition of DNA polymerase theta increased DNA damage while promoting CENP-A retention, indicating that DNA damage processing rather than damage itself promotes CENP-A loss. Together, our findings reveal separable roles for TOPBP1 in chromosome organization and centromere destabilization, showing how a protective genome surveillance pathway can instead drive chromosome instability in an inviable hybrid.