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

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.

References

  1. 1

    Bird, A. W. et al. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419, 411–415 (2002)

    ADS  CAS  Article  Google Scholar 

  2. 2

    Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834–840 (2009)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Peterson, C. L. & Cote, J. Cellular machineries for chromosomal DNA repair. Genes Dev. 18, 602–616 (2004)

    CAS  Article  Google Scholar 

  4. 4

    Scott, K. L. & Plon, S. E. Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in checkpoint-deficient strains of Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 4522–4531 (2003)

    CAS  Article  Google Scholar 

  5. 5

    Yang, X. J. & Seto, E. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nature Rev. Mol. Cell Biol. 9, 206–218 (2008)

    CAS  Article  Google Scholar 

  6. 6

    Bolden, J. E., Peart, M. J. & Johnstone, R. W. Anticancer activities of histone deacetylase inhibitors. Nature Rev. Drug Discov. 5, 769–784 (2006)

    CAS  Article  Google Scholar 

  7. 7

    Gottlicher, M. et al. Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. EMBO J. 20, 6969–6978 (2001)

    CAS  Article  Google Scholar 

  8. 8

    Harrison, J. C. & Haber, J. E. Surviving the breakup: the DNA damage checkpoint. Annu. Rev. Genet. 40, 209–235 (2006)

    CAS  Article  Google Scholar 

  9. 9

    Paques, F. & Haber, J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63, 349–404 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10

    Ira, G. et al. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431, 1011–1017 (2004)

    ADS  CAS  Article  Google Scholar 

  11. 11

    Jeong, H. et al. Acetylation targets mutant huntingtin to autophagosomes for degradation. Cell 137, 60–72 (2009)

    CAS  Article  Google Scholar 

  12. 12

    Lamark, T. & Johansen, T. Autophagy: links with the proteasome. Curr. Opin. Cell Biol. 22, 192–198 (2009)

    Article  Google Scholar 

  13. 13

    Kirkin, V., McEwan, D. G., Novak, I. & Dikic, I. A role for ubiquitin in selective autophagy. Mol. Cell 34, 259–269 (2009)

    CAS  Article  Google Scholar 

  14. 14

    Mathew, R. et al. Autophagy suppresses tumor progression by limiting chromosomal instability. Genes Dev. 21, 1367–1381 (2007)

    CAS  Article  Google Scholar 

  15. 15

    Shao, Y., Gao, Z., Marks, P. A. & Jiang, X. Apoptotic and autophagic cell death induced by histone deacetylase inhibitors. Proc. Natl Acad. Sci. USA 101, 18030–18035 (2004)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Degenhardt, K. et al. Autophagy promotes tumor cell survival and restricts necrosis, inflammation, and tumorigenesis. Cancer Cell 10, 51–64 (2006)

    CAS  Article  Google Scholar 

  17. 17

    Vaze, M. B. et al. Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase. Mol. Cell 10, 373–385 (2002)

    CAS  Article  Google Scholar 

  18. 18

    Liberi, G. et al. Srs2 DNA helicase is involved in checkpoint response and its regulation requires a functional Mec1-dependent pathway and Cdk1 activity. EMBO J. 19, 5027–5038 (2000)

    CAS  Article  Google Scholar 

  19. 19

    Robert, T., Dervins, D., Fabre, F. & Gangloff, S. Mrc1 and Srs2 are major actors in the regulation of spontaneous crossover. EMBO J. 25, 2837–2846 (2006)

    CAS  Article  Google Scholar 

  20. 20

    Lisby, M., Barlow, J. H., Burgess, R. C. & Rothstein, R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118, 699–713 (2004)

    CAS  Article  Google Scholar 

  21. 21

    Huertas, P., Cortes-Ledesma, F., Sartori, A. A., Aguilera, A. & Jackson, S. P. CDK targets Sae2 to control DNA-end resection and homologous recombination. Nature 455, 689–692 (2008)

    ADS  CAS  Article  Google Scholar 

  22. 22

    Gravel, S., Chapman, J. R., Magill, C. & Jackson, S. P. DNA helicases Sgs1 and BLM promote DNA double-strand break resection. Genes Dev. 22, 2767–2772 (2008)

    CAS  Article  Google Scholar 

  23. 23

    Mimitou, E. P. & Symington, L. S. Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 455, 770–774 (2008)

    ADS  CAS  Article  Google Scholar 

  24. 24

    Zhu, Z., Chung, W. H., Shim, E. Y., Lee, S. E. & Ira, G. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134, 981–994 (2008)

    CAS  Article  Google Scholar 

  25. 25

    Bernstein, K. A. & Rothstein, R. At loose ends: resecting a double-strand break. Cell 137, 807–810 (2009)

    CAS  Article  Google Scholar 

  26. 26

    Fu, J., Shao, C. J., Chen, F. R., Ng, H. K. & Chen, Z. P. Autophagy induced by valproic acid is associated with oxidative stress in glioma cell lines. Neuro Oncol. 12, 328–340 (2010)

    CAS  Article  Google Scholar 

  27. 27

    Shintani, T. & Reggiori, F. Fluorescence microscopy-based assays for monitoring yeast Atg protein trafficking. Methods Enzymol. 451, 43–56 (2008)

    CAS  Article  Google Scholar 

  28. 28

    Noda, T. & Klionsky, D. J. The quantitative Pho8Δ60 assay of nonspecific autophagy. Methods Enzymol. 451, 33–42 (2008)

    CAS  Article  Google Scholar 

  29. 29

    Cheong, H. & Klionsky, D. J. Biochemical methods to monitor autophagy-related processes in yeast. Methods Enzymol. 451, 1–26 (2008)

    CAS  Article  Google Scholar 

  30. 30

    Nakatogawa, H., Suzuki, K., Kamada, Y. & Ohsumi, Y. Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nature Rev. Mol. Cell Biol. 10, 458–467 (2009)

    CAS  Article  Google Scholar 

  31. 31

    Xie, Z. & Klionsky, D. J. Autophagosome formation: core machinery and adaptations. Nature Cell Biol. 9, 1102–1109 (2007)

    CAS  Article  Google Scholar 

  32. 32

    Kim, H. S. et al. Functional interactions between Sae2 and the Mre11 complex. Genetics 178, 711–723 (2008)

    CAS  Article  Google Scholar 

  33. 33

    Lee, D. H. & Goldberg, A. L. Selective inhibitors of the proteasome-dependent and vacuolar pathways of protein degradation in Saccharomyces cerevisiae. J. Biol. Chem. 271, 27280–27284 (1996)

    CAS  Article  Google Scholar 

  34. 34

    Kamada, Y., Sekito, T. & Ohsumi, Y. Autophagy in yeast: a TOR-mediated response to nutrient starvation. Curr. Top. Microbiol. Immunol. 279, 73–84 (2004)

    CAS  PubMed  Google Scholar 

  35. 35

    Robyr, D. et al. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109, 437–446 (2002)

    CAS  Article  Google Scholar 

  36. 36

    Grant, P. A. et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11, 1640–1650 (1997)

    CAS  Article  Google Scholar 

  37. 37

    Clerici, M., Mantiero, D., Lucchini, G. & Longhese, M. P. The Saccharomyces cerevisiae Sae2 protein negatively regulates DNA damage checkpoint signalling. EMBO Rep. 7, 212–218 (2006)

    CAS  Article  Google Scholar 

  38. 38

    Neecke, H., Lucchini, G. & Longhese, M. P. Cell cycle progression in the presence of irreparable DNA damage is controlled by a Mec1- and Rad53-dependent checkpoint in budding yeast. EMBO J. 18, 4485–4497 (1999)

    CAS  Article  Google Scholar 

  39. 39

    Sun, Y., Jiang, X., Chen, S., Fernandes, N. & Price, B. D. A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. Proc. Natl Acad. Sci. USA 102, 13182–13187 (2005)

    ADS  CAS  Article  Google Scholar 

  40. 40

    Fiorentino, D. F. & Crabtree, G. R. Characterization of Saccharomyces cerevisiae dna2 mutants suggests a role for the helicase late in S phase. Mol. Biol. Cell 8, 2519–2537 (1997)

    CAS  Article  Google Scholar 

  41. 41

    Nagai, S. et al. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 322, 597–602 (2008)

    ADS  CAS  Article  Google Scholar 

  42. 42

    Branzei, D. & Foiani, M. The checkpoint response to replication stress. DNA Repair 8, 1038–1046 (2009)

    CAS  Article  Google Scholar 

  43. 43

    Yu, X., Fu, S., Lai, M., Baer, R. & Chen, J. BRCA1 ubiquitinates its phosphorylation-dependent binding partner CtIP. Genes Dev. 20, 1721–1726 (2006)

    CAS  Article  Google Scholar 

  44. 44

    Pellicioli, A. et al. Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase. EMBO J. 18, 6561–6572 (1999)

    CAS  Article  Google Scholar 

  45. 45

    Fiorani, S., Mimun, G., Caleca, L., Piccini, D. & Pellicioli, A. Characterization of the activation domain of the Rad53 checkpoint kinase. Cell Cycle 7, 493–499 (2008)

    CAS  Article  Google Scholar 

  46. 46

    Lucca, C. et al. Checkpoint-mediated control of replisome-fork association and signalling in response to replication pausing. Oncogene 23, 1206–1213 (2004)

    CAS  Article  Google Scholar 

  47. 47

    Wang, X. & Haber, J. E. Role of Saccharomyces single-stranded DNA-binding protein RPA in the strand invasion step of double-strand break repair. PLoS Biol. 2, 104–112 (2004)

    CAS  Article  Google Scholar 

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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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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.

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Correspondence to Saverio Minucci or Marco Foiani.

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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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