Abstract
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.
Highlights
Genome stability is important for normal cellular survival and growth
In this study we describe an adaptation of Multiplex Ligation–dependent Probe Amplification (MLPA) for use in the study of gross chromosomal rearrangements (GCRs) that occur in S. cerevisiae mutants with increased genome instability
Our results demonstrate that MLPA is a rapid, inexpensive method that allows the analysis of the large number of GCRs needed to understand the pathways that suppress or promote genome instability
Summary
Genome stability is important for normal cellular survival and growth. Genome instability is associated with abnormal cellular growth. Tumor cells often contain multiple genome rearrangements and/or exhibit aneuploidy, and such events are thought to contribute to the development and progression of cancer [1,2,3,4]. Genome rearrangements are associated with inborn genetic diseases. Copy number changes mediated by segmental duplications are associated with a diversity of genetic diseases [5] and whole chromosome aneuploidy can cause diseases like Down Syndrome [6]. While the association of genome rearrangements and aneuploidy with human genetic disease is well established, the genetic factors that suppress or enhance genome rearrangements and aneuploidy are less well understood
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