Genomic instability can cause a wide range of diseases, including cancer and cellular senescence, which is also a major challenge in stem cell therapy. However, how a single event can cause extremely high levels of genomic instability remains unclear. Using our developed method, cell in situ electrophoresis (CISE), and models of normal, cancer, and embryonic stem cells, we found that cell rounding as a catastrophic source event ubiquitously observed in vivo and in vitro might lead to large-scale DNA deprotection, genomic instability, chromosomal shattering, cell heterogeneity, and senescent crisis by dissociation of single-stranded DNA-binding proteins (SSBs). Understanding the mechanism may facilitate the development of clinical strategies for cancer therapy, improve the safety of stem cell therapy, and prevent pathological aging.