DNA structural properties of AF9 are similar to MLL and could act as recombination hot spots resulting in MLL/AF9 translocations and leukemogenesis

The human AF9 gene at 9p22 is one of the most common fusion partner genes w ith the MLL gene at 11q23, resulting in the t(9;11)(p22;q23). The MLL-AF9 f usion gene is associated with de novo acute myelogenous leukemia (AML), rar ely with acute lymphocytic leukemia (ALL) and with therapy related leukemia (t-AML). The AF9 gene is >100 kb and two patient breakpoint cluster region s (BCRs) have been identified; BCR1 is within intron 4, previously called s ite A, whereas BCR2 or site B spans introns 7 and 8, Patient breakpoint loc ations were determined previously by RT-PCR and by genomic DNA cloning. In this study, we defined the exon-intron boundaries and identified several di fferent structural elements in AF9 including a co-localizing in vivo DNA to po II cleavage site and an in vitro DNase I hypersensitive (DNase 1 HS) sit e in intron 7 in BCR2, Reversibility experiments demonstrated a religation of the topo II cleavage sites. The location of the in vivo topo II cleavage site was confirmed in vitro using a topo II cleavage assay. In addition, t wo scaffold associated regions (SARs) are located centromeric to the topo I I and DNase I HS cleavage sites and border both patient breakpoint regions: SAR1 is located in intron 4, whereas SAR2 encompasses parts of exons 5-7. This study demonstrates that the patient breakpoint regions of AF9 share th e same structural elements as the MLL BCR, We describe a DNA breakage and r epair model for non-homologous recombination between MLL and its partner ge nes, particularly AF9.