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DNA end resection by Dna2–Sgs1–RPA and its stimulation by Top3–Rmi1 and Mre11–Rad50–Xrs2

Abstract

The repair of DNA double-strand breaks (DSBs) by homologous recombination requires processing of broken ends. For repair to start, the DSB must first be resected to generate a 3′-single-stranded DNA (ssDNA) overhang, which becomes a substrate for the DNA strand exchange protein, Rad51 (ref. 1). Genetic studies have implicated a multitude of proteins in the process, including helicases, nucleases and topoisomerases2,3,4. Here we biochemically reconstitute elements of the resection process and reveal that it requires the nuclease Dna2, the RecQ-family helicase Sgs1 and the ssDNA-binding protein replication protein-A (RPA). We establish that Dna2, Sgs1 and RPA constitute a minimal protein complex capable of DNA resection in vitro. Sgs1 helicase unwinds the DNA to produce an intermediate that is digested by Dna2, and RPA stimulates DNA unwinding by Sgs1 in a species-specific manner. Interestingly, RPA is also required both to direct Dna2 nucleolytic activity to the 5′-terminated strand of the DNA break and to inhibit 3′ to 5′ degradation by Dna2, actions that generate and protect the 3′-ssDNA overhang, respectively. In addition to this core machinery, we establish that both the topoisomerase 3 (Top3) and Rmi1 complex and the Mre11–Rad50–Xrs2 complex (MRX) have important roles as stimulatory components. Stimulation of end resection by the Top3–Rmi1 heterodimer and the MRX proteins is by complex formation with Sgs1 (refs 5, 6), which unexpectedly stimulates DNA unwinding. We suggest that Top3–Rmi1 and MRX are important for recruitment of the Sgs1–Dna2 complex to DSBs. Our experiments provide a mechanistic framework for understanding the initial steps of recombinational DNA repair in eukaryotes.

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Figure 1: Sgs1 and Dna2 resect DNA in a reaction dependent on yeast RPA.
Figure 2: Sgs1, Dna2 and RPA preferentially resect the 5′-terminated strand of a DNA break.
Figure 3: RPA promotes 5′ to 3′ degradation by Dna2 and inhibits 3′ to 5′ degradation.
Figure 4: Top3–Rmi1 and MRX complexes stimulate DNA resection by Dna2–Sgs1–RPA.

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Acknowledgements

We thank J.-B. Boulé, A. Nicolas, X. Veaute, B. Rad, J. L. Plank and P. Sung for purified proteins and DNA substrates, L. Symington for discussions, and W. D. Heyer and the members of the Kowalczykowski and Campbell laboratories for their comments on the manuscript. We are particularly grateful to P. Sung and colleagues for communicating their results to us before their publication. This work was supported by a Swiss National Science Foundation Fellowship (to P.C.), and National Institutes of Health grants GM-78666 (to J.L.C.), GM-41347 (to S.C.K.) and GM-62653 (to S.C.K.).

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P.C., J.L.C. and S.C.K. conceived the general ideas for this study. P.C., E.C., P.P., J.L.C. and S.C.K. planned experiments and interpreted data; P.C., E.C., P.P., T.M.-S. and S.P. performed experiments. P.C. and S.C.K. wrote the manuscript and all authors provided editorial input.

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Correspondence to Stephen C. Kowalczykowski.

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Cejka, P., Cannavo, E., Polaczek, P. et al. DNA end resection by Dna2–Sgs1–RPA and its stimulation by Top3–Rmi1 and Mre11–Rad50–Xrs2. Nature 467, 112–116 (2010). https://doi.org/10.1038/nature09355

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