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HDACs link the DNA damage response, processing of double-strand breaks and autophagy

Nature volume 471, pages 74–79 (2011)Cite this article

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Abstract

Protein acetylation is mediated by histone acetyltransferases (HATs) and deacetylases (HDACs), which influence chromatin dynamics, protein turnover and the DNA damage response. ATM and ATR mediate DNA damage checkpoints by sensing double-strand breaks and single-strand-DNA–RFA nucleofilaments, respectively. However, it is unclear how acetylation modulates the DNA damage response. Here we show that HDAC inhibition/ablation specifically counteracts yeast Mec1 (orthologue of human ATR) activation, double-strand-break processing and single-strand-DNA–RFA nucleofilament formation. Moreover, the recombination protein Sae2 (human CtIP) is acetylated and degraded after HDAC inhibition. Two HDACs, Hda1 and Rpd3, and one HAT, Gcn5, have key roles in these processes. We also find that HDAC inhibition triggers Sae2 degradation by promoting autophagy that affects the DNA damage sensitivity of hda1 and rpd3 mutants. Rapamycin, which stimulates autophagy by inhibiting Tor, also causes Sae2 degradation. We propose that Rpd3, Hda1 and Gcn5 control chromosome stability by coordinating the ATR checkpoint and double-strand-break processing with autophagy.

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Figure 1: VPA treatment counteracts DNA double-strand-break processing.
Figure 2: VPA affects Sae2 and Exo1 but not Mre11 protein levels.
Figure 3: GFP–Atg8 Cherry–Ape1 cellular distributions in VPA-treated cells.
Figure 4: Sae2 in VPA-treated cells.
Figure 5: Gcn5, Rpd3 and Hda1 influence Sae2 levels and cell survival in atg1 mutants in response to DNA damage.

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Acknowledgements

We thank S. Piatti, M. P. Longhese, M. Grunstein, J. K. Tyler, A. Pellicioli, M. Costanzo, R. Brost, M. Vogelauer, D. Klionsky, T. Roberts and C. Bertoli for reagents and technical suggestions, J. Barlow for DNA damage foci analysis, A. Sartori and S. Ferrari for communicating unpublished results, C. Lucca, D. Branzei, R. Bermejo and the members of our laboratories for comments. Work in M.F. laboratory was supported by grants from the Italian Association for Cancer Research and partially from Telethon, European Community (GENICA) and the Italian Ministry of Health. T.R. was supported by fellowships from FRM and EMBO and I.C. was supported by a short fellowship from HFSP and from FIRC. This work was also supported by GM50237 (to R.R.), GM67055 (to R.R.) and GM088413 (to K.B.).

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Author notes

  1. Thomas Robert, Fabio Vanoli and Irene Chiolo: These authors contributed equally to this work.

Authors and Affiliations

  1. Fondazione IFOM (Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus, via Adamello 16, Milan 20139, Italy,

    Thomas Robert, Fabio Vanoli, Irene Chiolo, Ghadeer Shubassi & Marco Foiani

  2. Department of Genome Biology, LBNL, Berkeley, 94710-2722, California, USA

    Irene Chiolo

  3. Department of Genetics and Development, Columbia University Medical Center, New York, 10032-2704, New York, USA

    Kara A. Bernstein & Rodney Rothstein

  4. European Institute of Oncology, IFOM-IEO campus, Milan 20139, Italy,

    Oronza A. Botrugno & Saverio Minucci

  5. Cogentech, Milan 20139, Italy,

    Dario Parazzoli & Amanda Oldani

  6. DSBB-Università degli Studi di Milano, Milan 20139, Italy,

    Saverio Minucci & Marco Foiani

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Contributions

T.R. and F.V. performed the experiments in Figs 1, 2, 4 and 5, T.R. performed those in Fig. 3 and Supplementary Fig. 3, F.V. and I.C. those in Supplementary Figs 1 and 2. I.C. contributed to Fig. 1, G.S. to Fig. 5, O.A.B. to Fig. 4. K.A.B., A.O. and D.P. provided advice and technical support for imaging. T.R., F.V., I.C. and M.F conceived the experiments. T.R., F.V., G.S., R.R., S.M. and M.F. analysed the results. T.R., F.V., G.S. and M.F. wrote the paper, S.M. and M.F. conceived the project.

Corresponding authors

Correspondence to Saverio Minucci or Marco Foiani.

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The authors declare no competing financial interests.

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Robert, T., Vanoli, F., Chiolo, I. et al. HDACs link the DNA damage response, processing of double-strand breaks and autophagy. Nature 471, 74–79 (2011). https://doi.org/10.1038/nature09803

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