Complex Genomic Rearrangements by BIR and mmBIR

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Chromosomal rearrangements in tumor genomes and in disease-causing copy number variations (CNVs) are often highly complex. It has been suggested that these rearrangements in human cells result from repair pathways that are engaged when DNA replication forks stall or collapse. The repair pathways hypothesized to be involved are break-induced replication (classical BIR) and the error-prone microhomology-mediated break- induced replication (mmBIR) mechanism. It remains unclear what conditions prompt repair by mmBIR rather than the (relatively) conservative BIR pathway, and much remains to be understood about how mmBIR generates complex rearrangements. The aims of this proposal build on our previous work studying BIR in yeast. We will use the powerful genetic tools of the yeast model system to further compare and characterize these two repair pathways. In the first aim of this proposal, we will characterize conditions that promote mmBIR. We will study whether mmBIR can occur under “typical” cellular conditions, and whether it is employed more frequently under conditions of oxidative stress, which are known to lower the level of key proteins needed for classical BIR. We will also study whether processing of the broken end influences engagement of the mmBIR repair pathway. In the second aim, we will characterize template choice in the mmBIR pathway to determine how much homology is required and whether mmBIR is constrained by physical distances between templates involved. The experiments in both of these aims will test hypotheses about the models of mmBIR and will help us understand which situations and environments promote mmBIR-mediated complex genomic rearrangements in tumors and CNVs.