Rapid analysis of saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification

Aneuploidy and gross chromosomal rearrangements (gcrs) can lead to genetic diseases and the development of cancer. we previously demonstrated that introduction of the repetitive retrotransposon ty912 onto a nonessential chromosome arm of saccharomyces cerevisiae led to increased genome instability predominantly due to increased rates of formation of monocentric nonreciprocal translocations. in this study,we adapted multiplex ligation-dependent probe amplification (mlpa) to analyze a large numbers of these gcrs. using mlpa,we found that the distribution of translocations induced by the presence of ty912 in a wild-type strain was nonrandom and that the majority of these translocations were mediated by only six translocation targets on four different chromosomes,even though there were 254 potential ty-related translocation targets in the s. cerevisiae genome. while the majority of ty912-mediated translocations resulted from rad52-dependent recombination,we observed a number of nonreciprocal translocations mediated by rad52-independent recombination between ty1 elements. the formation of these rad52-independent translocations did not require the rad51 or rad59 homologous pairing proteins or the rad1-rad10 endonuclease complex that processes branched dnas during recombination. finally,we found that defects in asf1-rtt109-dependent acetylation of histone h3 lysine residue 56 (h3k56) resulted in increased accumulation of both gcrs and whole-chromosome duplications,and resulted in aneuploidy that tended to occur simultaneously with gcrs. overall,we found that mlpa is a versatile technique for the rapid analysis of gcrs and can facilitate the genetic analysis of the pathways that prevent and promote gcrs and aneuploidy. © 2012 chan,kolodner.