Mechanisms of MLL gene rearrangement: site-specific DNA cleavage within the breakpoint cluster region is independent of chromosomal context

The MLL gene at chromosome band 11q23 is specifically cleaved at a unique s ite within its breakpoint cluster region (bcr) during the higher order chro matin fragmentation associated with apoptosis. We now show that the same sp ecific DNA cleavage event can be detected in an exogenous MLL bcr fragment that is integrated into the genome outside of its normal chromosomal contex t, as well as in an extrachromosomal episome containing an MLL bcr fragment . We also show that episomal or randomly integrated copies of the MLL bcr b ehave similar to the endogenous MLL bcr when tested in a scaffold-associate d region (SAR) assay. Furthermore, an episomal murine MLL bcr introduced in to human cells is cleaved at the same site as the endogenous murine MLL bcr ; this episomal murine MLL bcr also functions as a SAR in human cells. We c onclude that both nuclear DNA scaffold attachment as well as site-specific DNA cleavage can be directed by sequences contained within the MLL bcr, and that it is feasible to study these events using episomal shuttle vectors.