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Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining

Abstract

DNA double-strand break (DSB) repair occurs within chromatin and can be modulated by chromatin-modifying enzymes. Here we identify the related human histone deacetylases HDAC1 and HDAC2 as two participants in the DNA-damage response. We show that acetylation of histone H3 Lys56 (H3K56) was regulated by HDAC1 and HDAC2 and that HDAC1 and HDAC2 were rapidly recruited to DNA-damage sites to promote hypoacetylation of H3K56. Furthermore, HDAC1- and 2-depleted cells were hypersensitive to DNA-damaging agents and showed sustained DNA-damage signaling, phenotypes that reflect defective DSB repair, particularly by nonhomologous end-joining (NHEJ). Collectively, these results show that HDAC1 and HDAC2 function in the DNA-damage response by promoting DSB repair and thus provide important insights into the radio-sensitizing effects of HDAC inhibitors that are being developed as cancer therapies.

Figure 1: HDAC1 and HDAC2 localize to, and H3K56Ac is reduced at, sites of DNA damage.
Figure 2: H3K56Ac decreases during oncogene-induced and replicative senescence and H4K16Ac is a DNA damage–responsive histone mark.
Figure 3: HDAC1 and HDAC2 coregulate H3K56Ac and H4K16Ac.
Figure 4: HDAC1 and HDAC2 specifically and directly target H3K56 and H4K16.
Figure 5: Cells depleted of HDAC1 and HDAC2 show defective DNA-damage responses.
Figure 6: HDAC1 and HDAC2 promote efficient DNA repair, particularly through NHEJ.
Figure 7: Inhibition of HDAC results in NHEJ factor persistence at sites of DNA damage.
Figure 8: Model for the role of HDAC1 and HDAC2, as well as the inhibitory effects of class I/II HDAC inhibitors, in the DDR.

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Acknowledgements

We thank all members of the Jackson laboratory for help and support, P. Huertas, A. Kaidi and B. Xhemalce for reading of the manuscript, B. Xhemalce for assistance with ChIP, F. d'Adda di Fagagna for OIS cells, A. Meier for replicative senescent BJ cells, P. Frit for GFP-KU70 and NEB Biolabs for AsiSI genomic DNA. K.M.M. is funded by a Wellcome Trust project grant (086861/Z/08/Z). J.V.T. is supported by a Biotechnology and Biological Sciences Research Council Cooperative Award in Science and Engineering studentship with KuDOS Pharmaceuticals. G.L.'s research is funded by grants from Association pour la Recherche sur le Cancer, the Centre National de la Recherche Scientifique and PRES-University of Toulouse. S.E.P. is funded by the Human Frontier Science Program Organization. S.B. is funded by Cancer Research UK and an EMBO Long-Term Fellowship. Research in the S.P.J. laboratory is also supported by the European Community (EU Projects DNA Repair (LSHG-CT-2005-512113) and GENICA) and by core infrastructure provided by Cancer Research UK and the Wellcome Trust. We thank F. d'Adda di Fagagna (IFOM-IEO) for providing OIS cells, A. Meier for replicative senescent BJ cells and P. Frit (CNRS) for GFP-Ku70.

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K.M.M., J.V.T., and J.C. performed experiments; G.L. provided the AsiSI-expressing cell line; S.E.P. provided initial observation of HDAC1 localization; S.B. created and assisted with cell lines expressing NHEJ-tagged factors; K.M.M., J.V.T. and S.P.J. designed and analyzed the experiments; K.M.M. and S.P.J. wrote the manuscript.

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Correspondence to Stephen P Jackson.

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Miller, K., Tjeertes, J., Coates, J. et al. Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining. Nat Struct Mol Biol 17, 1144–1151 (2010). https://doi.org/10.1038/nsmb.1899

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