Clustered DNA damage induced by ionizing radiation is refractory to repair and may trigger carcinogenic events for reasons that are not well understood. Here, we used an in situ method to directly monitor induction and repair of clustered DNA lesions in individual cells. We showed, consistent with biophysical modeling, that the kinetics of loss of clustered DNA lesions was substantially compromised in human fibroblasts. The unique spatial distribution of different types of DNA lesions within the clustered damages, but not the physical location of these damages within the subnuclear domains, determined the cellular ability to repair the damage. We then examined checkpoint arrest mechanisms and yield of gross chromosomal aberrations. Induction of nonrepairable clustered damage affected only G2 accumulation but not the early G2/M checkpoint. Further, cells that were released from the G2/M checkpoint with unrepaired clustered damage manifested a spectrum of chromosome aberrations in mitosis. Difficulties associated with clustered DNA damage repair and checkpoint release before the completion of clustered DNA damage repair appear to promote genome instability that may lead to carcinogenesis.heterochromatin | high linear energy transfer | high charge and energy particles | 53BP1 | ionizing radiation induced foci I onizing radiation (IR) may induce cancer and loss of neural function or death in humans. Low (e.g., γ-and X-rays) and high [i.e., high charge and energy (HZE)] linear energy transfer (LET) IR induces a plethora of DNA damage, and the damage complexity increases with an increase in the LET of the radiation (1-3). Isolated DNA lesions (mainly induced by low-LET radiation), including double-strand breaks (DSBs), single-strand breaks (SSBs), and damaged bases located at a distance from other damage, are generally repaired efficiently. Substantial evidence indicates that high-LET radiation induces complex DNA damage, a unique class of DNA lesions that includes two or more individual lesions within one or two helical turns of the DNA (4). These lesions can be abasic sites (apurinic/apyrimidinic sites or APs), damaged bases (oxidized purines or pyrimidines), SSBs, or DSBs (5). Convincing evidence indicates that complex DNA lesions are more difficult to repair than isolated lesions and in some instances are irreparable; however, it is unclear why clustered lesions are difficult to repair.The biological consequences of complex DNA damage range from point mutations and loss of genetic material to cellular lethality due to repair impairment and lesion or repair-intermediate persistency. Clustered lesions induce intra-and interchromosomal insertions, and inversions often in association with large deletions (6). FISH-painting methodologies were used to show that high-LET IR induces a high fraction of chromosome rearrangements (7). Recently, it has been suggested that non-DSB clusters, if unrepaired, can lead to the formation of mutations and chromosome abnormalities (8). After exposure to high-LET radiation, immortalized...