A distinct population of therapy-related acute myeloid leukemia (t-AML) is strongly associated with prior administration of topoisomerase II (topo II) inhibitors. These t-AMLs display distinct cytogenetic alterations, most often disrupting the MLL gene on chromosome 11q23 within a breakpoint cluster region (bcr) of 8.3 kb. We recently identified a unique site within the MLL bcr that is highly susceptible to DNA double-strand cleavage by classic topo II inhibitors (e.g., etoposide and doxorubicin). Here, we report that site-specific cleavage within the MLL bcr can be induced by either catalytic topo II inhibitors, genotoxic chemotherapeutic agents which do not target topo II, or nongenotoxic stimuli of apoptotic cell death, suggesting that this site-specific cleavage is part of a generalized cellular response to an apoptotic stimulus. We also show that site-specific cleavage within the MLL bcr can be linked to the higher-order chromatin fragmentation that occurs during the initial stages of apoptosis, possibly through cleavage of DNA loops at their anchorage sites to the nuclear matrix. In addition, we show that site-specific cleavage is conserved between species, as specific DNA cleavage can also be demonstrated within the murine MLL locus. Lastly, site-specific cleavage during apoptosis can also be identified at the AML1 locus, a locus which is also frequently involved in chromosomal rearrangements present in t-AML patients. In conclusion, these results suggest the potential involvement of higher-order chromatin fragmentation which occurs as a part of a generalized apoptotic response in a mechanism leading to chromosomal translocation of the MLL and AML1 genes and subsequent t-AML.Nonrandom chromosomal aberrations, particularly chromosomal translocations, are frequently found in association with a wide spectrum of malignancies, most prominently leukemias and lymphomas (9,14,47). The available evidence suggests that these nonrandom chromosomal translocations are often causal events leading to malignant transformation (2, 40). However, the molecular mechanisms which cause these translocations remain largely unknown.In many cases, a powerful argument can be made that these translocations are the result of mistakes in normal V(D)J recombinase activity (4, 60). These arguments are based on identification of features that resemble normal V(D)J recombinase activity, such as cryptic heptamer sequences, nontemplated N-region nucleotide addition, and exonucleolytic deletion of germ line nucleotides at the translocation breakpoints (4, 60). Other factors that have been implicated in the generation of nonrandom translocations include homologous recombination events between Alu elements (52) and exposure to DNA-damaging agents (35,36). It has been recognized for some time that DNA-damaging cancer chemotherapeutic agents, such as the topoisomerase II (topo II) inhibitor etoposide (36) and the alkylating agent melphalan (35), can cause chromosomal translocations. For instance, phytohemagglutinin-stimulated peripheral blood ly...