The SIR2/3/4 complex promotes efficient break-induced replication by stabilizing recombination intermediates

Homologous recombination (HR) is one of the most effective pathways a cell can employ to repair DNA double strand breaks (DSBs). While most of the DNA repair machinery directly involved in HR has been characterized, less is known about how chromatin is reorganized and participates in repair. Here, we utilize a break-induced replication assay to explore a direct role of the SIR2/3/4 (SIR) silent chromatin complex in HR. Specifically, we measure an early step of break-induced replication (BIR), D-loop extension, and simultaneously monitor localization of the SIR complex at the initiating DSB and an ectopic donor locus. Interestingly, we observe a nearly four-fold increase in Sir2 and Sir3 protein levels upon DSB induction and detect an enrichment of all three SIR complex subunits at the DSB and donor loci during periods of active D-loop extension. ChIP-seq experiments reveal enrichment of SIR complex subunits that extend up to 15 kb from the DSB site. This enrichment is substantially reduced in rad51 null and rad52 null mutants that show defects in BIR. Lastly, we show that sir mutations confer slowed D-loop extension kinetics between divergent substrates and increase the rate of mutation during BIR. These data are consistent with a model in which the SIR complex acts to stabilize the extending D-loop during BIR, leading to more efficient, and thus less mutagenic repair.