Frequency of DNA end joining in trans is not determined by the predamage spatial proximity of double-strand breaks in yeast

Proc Natl Acad Sci U S A. 2019 May 7;116(19):9481-9490. doi: 10.1073/pnas.1818595116. Epub 2019 Apr 24.


DNA double-strand breaks (DSBs) are serious genomic insults that can lead to chromosomal rearrangements if repaired incorrectly. To gain insight into the nuclear mechanisms contributing to these rearrangements, we developed an assay in yeast to measure cis (same site) vs. trans (different site) repair for the majority process of precise nonhomologous end joining (NHEJ). In the assay, the HO endonuclease gene is placed between two HO cut sites such that HO expression is self-terminated upon induction. We further placed an additional cut site in various genomic loci such that NHEJ in trans led to expression of a LEU2 reporter gene. Consistent with prior reports, cis NHEJ was more efficient than trans NHEJ. However, unlike homologous recombination, where spatial distance between a single DSB and donor locus was previously shown to correlate with repair efficiency, trans NHEJ frequency remained essentially constant regardless of the position of the two DSB loci, even when they were on the same chromosome or when two trans repair events were put in competition. Repair of similar DSBs via single-strand annealing of short terminal direct repeats showed substantially higher repair efficiency and trans repair frequency, but still without a strong correlation of trans repair to genomic position. Our results support a model in which yeast cells mobilize, and perhaps compartmentalize, multiple DSBs in a manner that no longer reflects the predamage position of two broken loci.

Keywords: genome rearrangement; homologous recombination; nonhomologous end joining; single-strand annealing; translocation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 3-Isopropylmalate Dehydrogenase / biosynthesis
  • 3-Isopropylmalate Dehydrogenase / genetics
  • DNA Breaks, Double-Stranded*
  • DNA End-Joining Repair / physiology*
  • Gene Expression Regulation, Fungal / physiology*
  • Genetic Loci / physiology*
  • Genome, Fungal / physiology*
  • Saccharomyces cerevisiae Proteins / biosynthesis
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae* / genetics
  • Saccharomyces cerevisiae* / metabolism


  • Saccharomyces cerevisiae Proteins
  • 3-Isopropylmalate Dehydrogenase
  • LEU2 protein, S cerevisiae