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DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9

Abstract

In response to genotoxic stress, a transient arrest in cell-cycle progression enforced by the DNA-damage checkpoint (DDC) signalling pathway positively contributes to genome maintenance1. Because hyperactivated DDC signalling can lead to a persistent and detrimental cell-cycle arrest2,3, cells must tightly regulate the activity of the kinases involved in this pathway. Despite their importance, the mechanisms for monitoring and modulating DDC signalling are not fully understood. Here we show that the DNA-repair scaffolding proteins Slx4 and Rtt107 prevent the aberrant hyperactivation of DDC signalling by lesions that are generated during DNA replication in Saccharomyces cerevisiae. On replication stress, cells lacking Slx4 or Rtt107 show hyperactivation of the downstream DDC kinase Rad53, whereas activation of the upstream DDC kinase Mec1 remains normal. An Slx4–Rtt107 complex counteracts the checkpoint adaptor Rad9 by physically interacting with Dpb11 and phosphorylated histone H2A, two positive regulators of Rad9-dependent Rad53 activation. A decrease in DDC signalling results from hypomorphic mutations in RAD53 and H2A and rescues the hypersensitivity to replication stress of cells lacking Slx4 or Rtt107. We propose that the Slx4–Rtt107 complex modulates Rad53 activation by a competition-based mechanism that balances the engagement of Rad9 at replication-induced lesions. Our findings show that DDC signalling is monitored and modulated through the direct action of DNA-repair factors.

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Figure 1: Slx4 counteracts Rad9-dependent Rad53 activation.
Figure 2: Slx4 binding to Dpb11 counteracts the Dpb11–Rad9 interaction and Rad53 activation.
Figure 3: Rtt107 counteracts Rad9-dependent Rad53 activation by binding to phosphorylated histone H2A.
Figure 4: Slx4 sensitizes mrc1 Δ cells to hydroxyurea-induced replication stress.

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Acknowledgements

This work was supported by grants from the National Institutes of Health (RO1-GM097272 to M.B.S. and F31-GM093588 to P.Y.O.). F.M.B.O. was supported by a Cornell Fleming Research Fellowship. C.J.M. was supported by an HHMI Institutional Undergraduate Education Grant to Cornell. The authors thank B. Almeida for technical assistance and R. Weiss, S. Emr, A. Bretscher, G. Balmus and P. Russell for comments on the manuscript.

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P.Y.O., F.M.B.O. and M.B.S. designed and performed experiments and analysed the data. P.Y.O. and M.B.S. performed the mass spectrometry experiments. F.M.B.O. performed the chromatin immunoprecipitation analysis and generated the slx4 mutants. Y.L. and P.Y.O. performed co-immunoprecipitations between Dpb11 and Rad9. Y.L. performed pull-down experiments with the BRCT domains of Dpb11. C.J.M. performed the Rtt107–H2A binding assay and the experiments with the Rtt107 BRCT domains. P.Y.O. and M.B.S. performed experiments involving the overexpression of Slx4. P.Y.O. and M.B.S. wrote the paper.

Corresponding author

Correspondence to Marcus B. Smolka.

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The authors declare no competing financial interests.

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Ohouo, P., Bastos de Oliveira, F., Liu, Y. et al. DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9. Nature 493, 120–124 (2013). https://doi.org/10.1038/nature11658

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