Translocations and gross deletions constitute an important cause of both cancer and inherited disease. Such gene rearrangements are non-randomly distributed in the human genome as a consequence of selection for growth advantage and/or the inherent potential of some DNA sequences to be frequently involved in breakage and recombination. Chromosomal rearrangements are generated by a variety of recombinational processes, each characterised by mechanism-specific DNA sequence features. Various types of recombinogenic motifs have been shown to promote non-homologous end joining whilst direct repeats may mediate homologous recombination. In addition, repetitive sequence elements can facilitate the formation of secondary structure between DNA ends at translocation or gross deletion breakpoints, and in so doing, may play a role in illegitimate recombination. Although results from DNA breakpoint studies are broadly consistent with a role for homologous unequal recombination in deletion mutagenesis and a role for non-homologous recombination in the generation of translocations, homologous recombination and non-homologous end joining are unlikely to be mutually exclusive mechanisms. Thus, chromosomal rearrangements will often represent the net result of multiple highly complex molecular interactions that are not always readily explicable.
