Complex Chromosomal Rearrangements Mediated by Break-Induced Replication Involve Structure-Selective Endonucleases

Abstract

DNA double-strand break (DSB) repair occurring in repeated DNA sequences often leads to the generation of chromosomal rearrangements. Homologous recombination normally ensures a faithful repair of DSBs through a mechanism that transfers the genetic information of an intact donor template to the broken molecule. When only one DSB end shares homology to the donor template, conventional gene conversion fails to occur and repair can be channeled to a recombination-dependent replication pathway termed break-induced replication (BIR), which is prone to produce chromosome non-reciprocal translocations (NRTs), a classical feature of numerous human cancers. Using a newly designed substrate for the analysis of DSB–induced chromosomal translocations, we show that Mus81 and Yen1 structure-selective endonucleases (SSEs) promote BIR, thus causing NRTs. We propose that Mus81 and Yen1 are recruited at the strand invasion intermediate to allow the establishment of a replication fork, which is required to complete BIR. Replication template switching during BIR, a feature of this pathway, engenders complex chromosomal rearrangements when using repeated DNA sequences dispersed over the genome. We demonstrate here that Mus81 and Yen1, together with Slx4, also promote template switching during BIR. Altogether, our study provides evidence for a role of SSEs at multiple steps during BIR, thus participating in the destabilization of the genome by generating complex chromosomal rearrangements.

Author Summary

Genome rearrangements consisting of non-reciprocal translocations (NRTs) seem to play an important role in carcinogenesis in humans. They are likely caused by intracellular mechanisms that are normally committed to repair breaks occurring in the DNA molecule. Failure of faithful repair of DNA double-strand breaks (DSBs) often leads to chromosomal rearrangements when repair occurs within repeated genomic regions. The break-induced replication (BIR) pathway of DSB repair is a major source of complex chromosomal rearrangements, the latter occurring when BIR involves template switching between dispersed repeated sequences. Given the deleterious consequences of such events for genomic stability, it is of great significance to understand the molecular bases of BIR. Here, we examined the role of different DNA nucleases in chromosomal rearrangements and uncovered the functional involvement of the structure-selective endonucleases (SSEs) subunits Mus81, Yen1, and Slx4 at different steps during BIR. Our work provides new clues to understand the origin of NRTs and the role of SSEs in their generation.