Aberrant splicing of key genes involved in R-loop processing underlies augmentation of cen-R-loop as overexpression of the normal isoform, but not the altered form, mitigates mitotic stress in SF3B1 mutant cells. Our study underscores the critical role of novel splice variants in linking RNA splicing dysregulation and CIN, and highlights cen-R-loop augmen-tation as a key mechanism for leukemogenesis.