Exploring the role of the SIR2/3/4 complex in maintaining accurate DNA repair by homologous recombination
Homologous recombination (HR) is one of the most effective pathways a cell can employ to repair DNA double strand breaks (DSBs). However, while HR sub-pathways such as synthesis-dependent strand annealing can seamlessly repair DSBs, other sub-pathways, such as break induced replication (BIR), can result in loss of heterozygosity and gross chromosomal rearrangements. While most of the DNA repair machinery directly involved in HR has been characterized, we know less about the processes of subnuclear movement and chromatin reorganization required for repair. Here, we utilize a BIR repair system, initiated by a single inducible DSB and explore a direct role of the Sir2/Sir3/Sir4 (SIR) complex in this process. Intriguingly, we observe a roughly four-fold increase in the levels of Sir2 and Sir3 proteins after induction of a single double-strand break. Seeking to characterize the role of the SIR complex more directly, we measure an early step of BIR, D-loop extension, and simultaneously monitor localization of the SIR complex at the initiating DSB and the ectopic donor locus. Strikingly, we detect enrichment of all three SIR complex subunits at the DSB and donor loci during periods of active D-loop extension; ChIP-seq experiments reveal a domain of enrichment extending 15-20kb distal from the DSB site. In the absence of the mismatch repair protein Msh2, we observe increased binding overall, and a shift in binding pattern proximal to the DSB. Assessing BIR efficiency by measuring D-loop extension, we note that the absence of the SIR complex during repair between divergent substrates results in slowed D-loop extension kinetics. Further, loss of the SIR complex appears to increase the rate of mutation during BIR, without affecting the pattern of said mutagenicity. 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. Whether the MMR protein Msh2 directly alters SIR complex localization or antagonizes SIR complex binding remains an intriguing question.