Inverted DNA Repeats Channel Repair of Distant Double-Strand Breaks into Chromatid Fusions and Chromosomal Rearrangements

Abstract

Inverted DNA repeats are known to cause genomic instabilities. Here we demonstrate that double-strand DNA breaks (DSBs) introduced a large distance from inverted repeats in the yeast (Saccharomyces cerevisiae) chromosome lead to a burst of genomic instability. Inverted repeats located as far as 21 kb from each other caused chromosome rearrangements in response to a single DSB. We demonstrate that the DSB initiates a pairing interaction between inverted repeats, resulting in the formation of large dicentric inverted dimers. Furthermore, we observed that propagation of cells containing inverted dimers led to gross chromosomal rearrangements, including translocations, truncations, and amplifications. Finally, our data suggest that break-induced replication is responsible for the formation of translocations resulting from anaphase breakage of inverted dimers. We propose a model explaining the formation of inverted dicentric dimers by intermolecular single-strand annealing (SSA) between inverted DNA repeats. According to this model, anaphase breakage of inverted dicentric dimers leads to gross chromosomal rearrangements (GCR). This “SSA-GCR” pathway is likely to be important in the repair of isochromatid breaks resulting from collapsed replication forks, certain types of radiation, or telomere aberrations that mimic isochromatid breaks.

SUPPLEMENTAL MATERIAL

We thank James E. Haber for his support and suggestions (the project was originally started in his laboratory, where it was supported by NIH grant GM20056 to J.E.H.). We thank Dmitry Gordenin and Gregory Ira for their suggestions throughout this work and for comments on the manuscript. We are thankful to Carol Newlon and James Theis for their analysis of the structure of chromosome III and for helpful discussion pertinent to this subject.

This work was supported by ACS institutional grant IRG-84-002-22, IUPUI RSFG grant, and NIH grant 1R15GM074657-01A1 to A.M.; NIH grants GM24110 and GM52319 to T.D.P.; and NSF grant MCB-0417088 to K.L.