Article | Published:

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

Nature Structural & Molecular Biology volume 19, pages 12571265 (2012) | Download Citation

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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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.

Author information

Author notes

    • Cecilia Ballaré
    • , Martin Lange
    •  & Audrone Lapinaite

    These authors contributed equally to this work.

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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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Luciano Di Croce.

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7, Supplementary Table 3 and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 1

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

  2. 2.

    Supplementary Table 2

    Summary table of microarray data

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DOI

https://doi.org/10.1038/nsmb.2434

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