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Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation

Nature Structural & Molecular Biology volume 19, pages 12731281 (2012) | Download Citation

Abstract

Polycomb group proteins are repressive chromatin modifiers with essential roles in metazoan development, cellular differentiation and cell fate maintenance. How Polycomb proteins access active chromatin to confer transcriptional silencing during lineage transitions remains unclear. Here we show that the Polycomb repressive complex 2 (PRC2) component PHF19 binds trimethylated histone H3 Lys36 (H3K36me3), a mark of active chromatin, via its Tudor domain. PHF19 associates with the H3K36me3 demethylase NO66, and it is required to recruit the PRC2 complex and NO66 to stem cell genes during differentiation, leading to PRC2-mediated trimethylation of histone H3 Lys27 (H3K27), loss of H3K36me3 and transcriptional silencing. We propose a model whereby PHF19 functions during mouse embryonic stem cell differentiation to transiently bind the H3K36me3 mark via its Tudor domain, forming essential contact points that allow recruitment of PRC2 and H3K36me3 demethylase activity to active gene loci during their transition to a Polycomb-repressed state.

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Acknowledgements

We are indebted to members of the Bracken laboratory for their valuable comments on the manuscript. We thank the Conway Mass Spectrometry Resource at University College Dublin. Work in the Bracken lab is supported by Science Foundation Ireland under the Principal Investigator Career Advancement Award (SFI PICA SFI/10/IN.1/B3002), the Health Research Board under the Health Research Awards 2010 (HRA_POR/2010/124) and the Irish Research Council for Science, Engineering and Technology (IRCSET).

Author information

Affiliations

  1. The Smurfit Institute of Genetics, Trinity College Dublin, Ireland.

    • Gerard L Brien
    • , Emilia Jerman
    • , Siobhán A Turner
    • , Chris M Egan
    • , Eiseart J Dunne
    •  & Adrian P Bracken
  2. Conway Institute, University College Dublin, Ireland.

    • Guillermo Gambero
    • , David J O'Connell
    • , Maike C Jurgens
    • , Kieran Wynne
    • , Amanda J Lohan
    • , Neil Ferguson
    • , Brendan J Loftus
    •  & Gerard Cagney
  3. Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

    • Lianhua Piao
    •  & Xiaobing Shi
  4. Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

    • Krishna M Sinha
  5. The Adelaide & Meath Hospital, including the National Children's Hospital, Dublin, Ireland.

    • Adrian P Bracken

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Contributions

G.L.B. and A.P.B. designed the research. G.L.B. performed most of the experiments. G.G., K.W. and G.C. prepared, performed and analyzed Flag-HA–PHF19 MS samples. D.J.O. performed all SPR analyses. E.J. contributed to immunoprecipitations of Flag-HA–PHF19. L.P. and X.P. performed the initial PHF19 binding assay. S.A.T., M.C.J. and N.J. helped with protein purification and initial SPR experiments. C.M.E. performed H&E staining of embryoid bodies and quantifications thereof. A.J.L. and B.J.L. sequenced ChIP-seq material and E.J.D. analyzed ChIP-seq data. K.M.S. contributed the NO66 antibody and advised on its use. G.L.B. and A.P.B. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Adrian P Bracken.

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    Mass spectrometry (MS) of FLAG–HA–PHF19 in human cells.

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DOI

https://doi.org/10.1038/nsmb.2449

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