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

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.

• Authors: Jason E Chan, Richard D Kolodner
• Journal: PLoS genetics (PLoS Genet) Vol. 8 Issue 3 Pg. e1002539 ( 2012) ISSN: 1553-7404 [Electronic] United States
• PMID: 22396658 (Publication Type: Journal Article, Research Support, N.I.H., Extramural)

Chemical References

• ASF1 protein, S cerevisiae
• Cell Cycle Proteins
• Histones
• Molecular Chaperones
• RAD52 protein, S cerevisiae
• Rad52 DNA Repair and Recombination Protein
• Retroelements
• Saccharomyces cerevisiae Proteins
• Histone Acetyltransferases
• Rtt109 protein, S cerevisiae

Topics

• Acetylation
• Aneuploidy
• Base Sequence
• Cell Cycle Proteins (genetics, metabolism)
• Chromosome Duplication (genetics)
• Genome, Fungal
• Genomic Instability
• Histone Acetyltransferases (genetics, metabolism)
• Histones (genetics)
• Molecular Chaperones (genetics, metabolism)
• Molecular Sequence Data
• Multiplex Polymerase Chain Reaction (methods)
• Rad52 DNA Repair and Recombination Protein (genetics, metabolism)
• Recombination, Genetic
• Retroelements
• Saccharomyces cerevisiae (genetics)
• Saccharomyces cerevisiae Proteins (genetics, metabolism)
• Translocation, Genetic (genetics)