Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast

Abstract

Large-scale changes (gross chromosomal rearrangements [GCRs]) are common in genomes, and are often associated with pathological disorders. We report here that a specific pair of nearby inverted repeats in budding yeast fuse to form a dicentric chromosome intermediate, which then rearranges to form a translocation and other GCRs. We next show that fusion of nearby inverted repeats is general; we found that many nearby inverted repeats that are present in the yeast genome also fuse, as does a pair of synthetically constructed inverted repeats. Fusion occurs between inverted repeats that are separated by several kilobases of DNA and share >20 base pairs of homology. Finally, we show that fusion of inverted repeats, surprisingly, does not require genes involved in double-strand break (DSB) repair or genes involved in other repeat recombination events. We therefore propose that fusion may occur by a DSB-independent, DNA replication-based mechanism (which we term ''faulty template switching''). Fusion of nearby inverted repeats to form dicentrics may be a major cause of instability in yeast and in other organisms.[Keywords: Inverted repeats; acentric and dicentric chromosomes; breakage-fusion-bridge cycle; genome instability; large palindromes; template switch] Supplemental material is available at http://www.genesdev.org.

Genome rearrangements caused by interstitial telomeric sequences in yeast

“…We hypothesize that some sequence on this minichromosome might have a centromere-like activity, or that the segregation of the minichromosome is coupled to the segregation of other chromosomes (35). Paek et al (36) previously used PCR to demonstrate acentric fragments in yeast generated by template switching during DNA replication, although the stability of these fragments could not be quantitated.…”

Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans

“…Indeed, stalled forks have recently been shown to produce DSB-independent fusions of nearby inverted-repeats, which lead to the formation of palindromic chromosomes (Mizuno et al 2009;Paek et al 2009). The mechanisms by which these fusions take place remain a subject of debate, and three distinct possibilities have been proposed: faulty template switching, tandem inversion duplications, and replication U-turns (Mizuno et al 2009(Mizuno et al , 2013Paek et al 2009;Kugelberg et al 2010;Seier et al 2012).…”

Leaping forks at inverted repeats: Figure 1.

“…Since nearby inverted repeats separated by a few kilobases of DNA are unlikely to form cruciform structures as do palindromes, it is most probable that the mechanisms leading to formation of dicentric and acentric chromosomes in these situations are also different. The recent studies by Paek et al (2009) and Mizuno et al (2009) characterized the factors influencing the formation of acentric and dicentric chromosome intermediates at nearby inverted repeats or palindromic loci in budding and fission yeast, respectively.…”

“…In the December 15, 2009, issue of Genes & Development, Paek et al (2009) found that, in budding yeast, naturally occurring or synthetic inverted repeats separated by ;1.3-5.5 kb of DNA and having as few as ;20 base pairs (bp) of homology can fuse to form acentric or dicentric chromosomes (Paek et al 2009). This nearby inverted repeat fusion phenomenon has been reported previously in bacteria and in fission yeast (Bi and Liu 1996;Albrecht et al 2000).…”

“…S-phase checkpoints, recombination, and telomere maintenance pathways have been implicated in suppressing chromosome rearrangements, but little is known about the molecular mechanisms and the chromosome intermediates generating such genome-wide instability. In the December 15, 2009, issue of Genes & Development, two studies by Paek andcolleagues (2861-2875) and Mizuno andcolleagues (pp. 2876-2886), demonstrate that nearby inverted repeats in budding and fission yeasts recombine spontaneously and frequently to form dicentric and acentric chromosomes.…”