An In Vivo Topoisomerase II Cleavage Site and a DNase I Hypersensitive Site Colocalize Near Exon 9in the MLL Breakpoint Cluster Region

The human myeloid-lymphoid leukemia gene, MLL (also calledALL-1, Htrx, or HRX ), maps to chromosomal band11q23. MLL is involved in translocations that result in de novoacute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML),mixed lineage leukemia, and also in therapy AML (t-AML) and therapy ALL(t-ALL) resulting from treatment with DNA topoisomerase II (topo II)targeting drugs. MLL can recombine with more than 30 otherchromosomal bands, of which 16 of the partner genes have been cloned.Breaks in MLL occur in an 8.3-kb breakpoint cluster region(BCR) encompassing exons 5 through 11. We recently demonstrated that75% of de novo patient breakpoints in MLL mapped in thecentromeric half of the BCR between two scaffold-associatedregions (SAR), whereas 75% of the t-AML patient breakpoints mapped tothe telomeric half of the BCR within a strong SAR. We have mappedadditional structural elements in the BCR. An in vivo DNA topo IIcleavage site (induced with several different drugs that target topoII) mapped near exon 9 in three leukemia cell lines. A strong DNase Ihypersensitive site (HS) also mapped near exon 9 in four leukemia celllines, including two in which MLL was rearranged a t(6;11)and a t(9;11)], and in two lymphoblastoid cell lines with normalMLL. Two of the leukemia cell lines also showed an in vivo topoII cleavage site. Our results suggest that the chromatin structure ofthe MLL BCR may influence the location of DNA breaks in both denovo and therapy-related leukemias. We propose that topo II is enrichedin the MLL telomeric SAR and that it cleaves the DNase I HSsite after treatment with topo II inhibitors. These events may beinvolved in recombination associated with t-AML/t-ALL breakpointsmapping in the MLL SAR.