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Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1

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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Figure 1: The crystal structure of the Tudor domain of PHF1 in complex with the H3K36me3 peptide.
Figure 2: The PHF1 Tudor domain recognizes H3K36me3.
Figure 3: Interaction of the PHF1 Tudor domain with H3K36me3 is specific.
Figure 4: Recognition of H3K36me3 by PHF1 inhibits PRC2 methyltransferase activity.
Figure 5: Binding of PHF1 to H3K36me3 decreases PRC2-mediated deposition of H3K27me3.
Figure 6: Tudor-dependent accumulation and retention of PHF1 at laser-irradiated sites of DSBs.

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References

  1. Margueron, R. & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011).

    Article  CAS  Google Scholar 

  2. Varambally, S. et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419, 624–629 (2002).

    Article  CAS  Google Scholar 

  3. Morin, R.D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181–185 (2010).

    Article  CAS  Google Scholar 

  4. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).

    Article  CAS  Google Scholar 

  5. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

    Article  CAS  Google Scholar 

  6. Czermin, B. et al. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185–196 (2002).

    Article  CAS  Google Scholar 

  7. Müller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197–208 (2002).

    Article  Google Scholar 

  8. Cao, R. et al. Role of hPHF1 in H3K27 methylation and Hox gene silencing. Mol. Cell Biol. 28, 1862–1872 (2008).

    Article  CAS  Google Scholar 

  9. Sarma, K., Margueron, R., Ivanov, A., Pirrotta, V. & Reinberg, D. Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. Mol. Cell Biol. 28, 2718–2731 (2008).

    Article  CAS  Google Scholar 

  10. Nekrasov, M. et al. Pcl-PRC2 is needed to generate high levels of H3–K27 trimethylation at Polycomb target genes. EMBO J. 26, 4078–4088 (2007).

    Article  CAS  Google Scholar 

  11. Hong, Z. et al. A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell. Nucleic Acids Res. 36, 2939–2947 (2008).

    Article  CAS  Google Scholar 

  12. O'Connell, S. et al. Polycomblike PHD fingers mediate conserved interaction with enhancer of zeste protein. J. Biol. Chem. 276, 43065–43073 (2001).

    Article  CAS  Google Scholar 

  13. Botuyan, M.V. et al. Structural basis for the methylation state-specific recognition of histone H4–K20 by 53BP1 and Crb2 in DNA repair. Cell 127, 1361–1373 (2006).

    Article  CAS  Google Scholar 

  14. Huang, Y., Fang, J., Bedford, M.T., Zhang, Y. & Xu, R.M. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science 312, 748–751 (2006).

    Article  CAS  Google Scholar 

  15. Lee, J., Thompson, J.R., Botuyan, M.V. & Mer, G. Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-Tudor. Nat. Struct. Mol. Biol. 15, 109–111 (2008).

    Article  CAS  Google Scholar 

  16. Roy, S. et al. Structural insight into p53 recognition by the 53BP1 tandem Tudor domain. J. Mol. Biol. 398, 489–496 (2010).

    Article  CAS  Google Scholar 

  17. Tripsianes, K. et al. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nat. Struct. Mol. Biol. 18, 1414–1420 (2011).

    Article  CAS  Google Scholar 

  18. Yang, Y. et al. TDRD3 is an effector molecule for arginine-methylated histone marks. Mol. Cell 40, 1016–1023 (2010).

    Article  CAS  Google Scholar 

  19. Wagner, E.J. & Carpenter, P.B. Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell Biol. 13, 115–126 (2012).

    Article  CAS  Google Scholar 

  20. Krogan, N.J. et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell Biol. 23, 4207–4218 (2003).

    Article  CAS  Google Scholar 

  21. Morris, S.A. et al. Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot. Cell 4, 1446–1454 (2005).

    Article  CAS  Google Scholar 

  22. Vezzoli, A. et al. Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat. Struct. Mol. Biol. 17, 617–619 (2010).

    Article  CAS  Google Scholar 

  23. Xu, C., Cui, G., Botuyan, M.V. & Mer, G. Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S. Structure 16, 1740–1750 (2008).

    Article  CAS  Google Scholar 

  24. Schmitges, F.W. et al. Histone methylation by PRC2 is inhibited by active chromatin marks. Mol. Cell 42, 330–341 (2011).

    Article  CAS  Google Scholar 

  25. Yuan, W. et al. H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J. Biol. Chem. 286, 7983–7989 (2011).

    Article  CAS  Google Scholar 

  26. Voigt, P. et al. Asymmetrically modified nucleosomes. Cell 151, 181–192 (2012).

    Article  CAS  Google Scholar 

  27. Taverna, S.D., Li, H., Ruthenburg, A.J., Allis, C.D. & Patel, D.J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007).

    Article  CAS  Google Scholar 

  28. Kutateladze, T.G. SnapShot: Histone readers. Cell 146, 842–842 e1 (2011).

    Article  CAS  Google Scholar 

  29. Friberg, A., Oddone, A., Klymenko, T., Muller, J. & Sattler, M. Structure of an atypical Tudor domain in the Drosophila Polycomblike protein. Protein Sci. 19, 1906–1916 (2010).

    Article  CAS  Google Scholar 

  30. Pokholok, D.K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005).

    Article  CAS  Google Scholar 

  31. Kizer, K.O. et al. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol. Cell Biol. 25, 3305–3316 (2005).

    Article  CAS  Google Scholar 

  32. Kirmizis, A. et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18, 1592–1605 (2004).

    Article  CAS  Google Scholar 

  33. Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

    Article  CAS  Google Scholar 

  34. Fnu, S. et al. Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining. Proc. Natl. Acad. Sci. USA 108, 540–545 (2011).

    Article  CAS  Google Scholar 

  35. Peng, J.C. et al. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139, 1290–1302 (2009).

    Article  Google Scholar 

  36. Shen, X. et al. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell 139, 1303–1314 (2009).

    Article  Google Scholar 

  37. Pasini, D. et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 464, 306–310 (2010).

    Article  CAS  Google Scholar 

  38. Li, G. et al. Jarid2 and PRC2, partners in regulating gene expression. Genes Dev. 24, 368–380 (2010).

    Article  Google Scholar 

  39. Margueron, R. et al. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762–767 (2009).

    Article  CAS  Google Scholar 

  40. Xu, C. et al. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc. Natl. Acad. Sci. USA 107, 19266–19271 (2010).

    Article  CAS  Google Scholar 

  41. Hansen, K.H. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10, 1291–1300 (2008).

    Article  CAS  Google Scholar 

  42. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).

    Article  CAS  Google Scholar 

  43. Chou, D.M. et al. A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc. Natl. Acad. Sci. USA 107, 18475–18480 (2010).

    Article  CAS  Google Scholar 

  44. Gieni, R.S., Ismail, I.H., Campbell, S. & Hendzel, M.J. Polycomb group proteins in the DNA damage response: a link between radiation resistance and “stemness”. Cell Cycle 10, 883–894 (2011).

    Article  CAS  Google Scholar 

  45. Pflugrath, J.W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D Biol. Crystallogr. 55, 1718–1725 (1999).

    Article  CAS  Google Scholar 

  46. McCoy, A.J., Storoni, L.C. & Read, R.J. Simple algorithm for a maximum-likelihood SAD function. Acta Crystallogr. D Biol. Crystallogr. 60, 1220–1228 (2004).

    Article  Google Scholar 

  47. Adams, P.D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954 (2002).

    Article  Google Scholar 

  48. Altaf, M. et al. Interplay of chromatin modifiers on a short basic patch of histone H4 tail defines the boundary of telomeric heterochromatin. Mol. Cell 28, 1002–1014 (2007).

    Article  CAS  Google Scholar 

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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.

Corresponding author

Correspondence to Tatiana G Kutateladze.

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Supplementary information

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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