Abstract
The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here we show that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9-Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular mechanism of H3K36me3 recognition using NMR. Binding of PHF1 to H3K36me3 inhibits the ability of the Polycomb PRC2 complex to methylate Lys27 of histone H3 in vitro and in vivo. Laser microirradiation data show that PHF1 is transiently recruited to DNA double-strand breaks, and PHF1 mutants impaired in the H3K36me3 interaction exhibit reduced retention at double-strand break sites. Together, our findings suggest that PHF1 can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response.
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Acknowledgements
We thank B. Phillips, J. Gupta, D. Maranon and A. Morris for help with experiments. This research is supported by grants from the US National Institutes of Health (NIH; GM096863 and CA113472 to T.G.K.; GM084020 to J.N.) and the Canadian Institutes of Health Research (CIHR; MOP-64289 to J.C.). C.A.M. is supported by an NIH National Research Service Award postdoctoral fellowship (F32 HL096399).
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C.A.M. and T.G.K. designed the study. C.A.M., N.A., R.W., C.G.A., M.-E.L., S.R. and J.K.N. performed experiments and together with Z.H., C.A., J.N., C.A.K., A.Y., J.C and T.G.K. analyzed the data. T.G.K. and C.A.M. wrote the manuscript.
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Supplementary Text and Figures
Supplementary Figures 1–6 (PDF 2414 kb)
Supplementary Video 1
H3K36me-dependent recruitment of PHF1 to the sites of DSBs. Accumulation and dissociation of GFP-PHF1 wild type (a), GFP-PHF1 W41A (b) and GFPPHF1 Y47A (c) at laser-irradiated DSB sites within six minutes in U2OS cells. (MOV 10275 kb)
Supplementary Video 2
Inhibition of the GFP-PHF1 accumulation at DNA DSBs by inhibitors. Accumulation and dissociation of GFP-PHF1 wild type (top panel), GFP-PHF1 W41A (middle panel) and GFP-PHF1 Y47A (bottom panel) at laser-irradiated DSB sites within six minutes in U2OS cells either untreated (left panel), treated with the PARP1 inhibitor AZD2281 (middle panel) or an ATM/ATR kinase inhibitor (right panel). (MOV 19992 kb)
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Musselman, C., Avvakumov, N., Watanabe, R. et al. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1. Nat Struct Mol Biol 19, 1266–1272 (2012). https://doi.org/10.1038/nsmb.2435
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DOI: https://doi.org/10.1038/nsmb.2435
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