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Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity

Nature Structural & Molecular Biology volume 19, pages 1257–1265 (2012)Cite this article

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Abstract

Polycomb-group proteins are transcriptional repressors with essential roles in embryonic development. Polycomb repressive complex 2 (PRC2) contains the methyltransferase activity for Lys27. However, the role of other histone modifications in regulating PRC2 activity is just beginning to be understood. Here we show that direct recognition of methylated histone H3 Lys36 (H3K36me), a mark associated with activation, by the PRC2 subunit Phf19 is required for the full enzymatic activity of the PRC2 complex. Using NMR spectroscopy, we provide structural evidence for this interaction. Furthermore, we show that Phf19 binds to a subset of PRC2 targets in mouse embryonic stem cells and that this is required for their repression and for H3K27me3 deposition. These findings show that the interaction of Phf19 with H3K36me2 and H3K36me3 is essential for PRC2 complex activity and for proper regulation of gene repression in embryonic stem cells.

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Figure 1: Phf19 is a component of the PRC2 complex.
Figure 2: Binding of Phf19-Tudor to methylated H3K36.
Figure 3: NMR-based structural analysis of the complex between Phf19-Tudor and an H3 peptide methylated at Lys36.
Figure 4: Phf19 is in integral part of the PRC2 complex in mES cells.
Figure 5: Phf19 is required for PRC2 binding to target genes.
Figure 6: Role of Phf19 in pluripotency.
Figure 7: Molecular mechanism of Phf19-mediated gene repression.

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Acknowledgements

We thank V.A. Raker for help in manuscript preparation, D. Patel, G. Castellano, A. Ladurner and members of the Di Croce laboratory for discussions, and the Centre for Genomic Regulation (CRG) Genomic, Bioinformatic and Proteomic Units. Peptides for NMR studies were supplied by R. Pipkorn, DKFZ (German Cancer Research Center). This work was supported by grants from the Spanish 'Ministerio de Educación y Ciencia' (BFU2010-18692), from AGAUR (Agency for Administration of University and Research Grants), from the European Commission's 7th Framework Program 4DCellFate grant number 277899 to L.D.C. and from the US National Institutes of Health (NCI118487 and GM071004) to Y.S. M.L. was supported by a Juan de la Cierva fellowship, R.L. was supported by a research fellowship from the German research foundation (DFG, LI 2057/1-1), and L.M. was supported by a postdoctoral CRG-Novartis fellowship. T.C., B.S. and A.L. were supported by the European Molecular Biology Laboratory.

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Author notes

  1. Cecilia Ballaré, Martin Lange and Audrone Lapinaite: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Gene Regulation and Stem Cells, Centre for Genomic Regulation (CRG), Barcelona, Spain

    Cecilia Ballaré, Martin Lange, Lluis Morey, Gloria Pascual, Salvador Aznar Benitah & Luciano Di Croce

  2. Universitat Pompeu Fabra, Barcelona, Spain

    Cecilia Ballaré, Martin Lange, Lluis Morey, Gloria Pascual, Salvador Aznar Benitah & Luciano Di Croce

  3. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Audrone Lapinaite, Bernd Simon & Teresa Carlomagno

  4. Department of Biological Sciences, Stanford University, Stanford, California, USA

    Gloria Mas Martin & Or Gozani

  5. Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Robert Liefke & Yang Shi

  6. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA

    Robert Liefke & Yang Shi

  7. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

    Salvador Aznar Benitah & Luciano Di Croce

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  1. Cecilia Ballaré
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Contributions

C.B., M.L., A.L., G.M.M., L.M., G.P., R.L., B.S., Y.S., O.G., T.C., S.A.B. and L.D.C. designed, executed and analyzed the experiments. C.B., M.L., O.G., T.C., S.A.B. and L.D.C. wrote the manuscript.

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Correspondence to Luciano Di Croce.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Table 3 and Supplementary Note (PDF 6534 kb)

Supplementary Table 1

Summary table of ChIP-seq data: Phf19 binding sites (ChIP-seq peaks) and target genes (XLSX 957 kb)

Supplementary Table 2

Summary table of microarray data (XLSX 395 kb)

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Ballaré, C., Lange, M., Lapinaite, A. et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 19, 1257–1265 (2012). https://doi.org/10.1038/nsmb.2434

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