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Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance

Nature Structural & Molecular Biology volume 19, pages 136–144 (2012)Cite this article

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Abstract

The asymmetric dimethylation of histone H3 arginine 2 (H3R2me2a) acts as a repressive mark that antagonizes trimethylation of H3 lysine 4. Here we report that H3R2 is also symmetrically dimethylated (H3R2me2s) by PRMT5 and PRMT7 and present in euchromatic regions. Profiling of H3-tail interactors by SILAC MS revealed that H3R2me2s excludes binding of RBBP7, a central component of co-repressor complexes Sin3a, NURD and PRC2. Conversely H3R2me2s enhances binding of WDR5, a common component of the coactivator complexes MLL, SET1A, SET1B, NLS1 and ATAC. The interaction of histone H3 with WDR5 distinguishes H3R2me2s from H3R2me2a, which impedes the recruitment of WDR5 to chromatin. The crystallographic structure of WDR5 and the H3R2me2s peptide elucidates the molecular determinants of this high affinity interaction. Our findings identify H3R2me2s as a previously unknown mark that keeps genes poised in euchromatin for transcriptional activation upon cell-cycle withdrawal and differentiation in human cells.

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Figure 1: H3R2me2s is a newly discovered histone modification associated with euchromatic sites.
Figure 2: H3R2me2s impedes co-repressor binding.
Figure 3: H3R2me2s is bound at high affinity by WDR5.
Figure 4: Crystal structure of WDR5 bound to the N terminus of histone H3 symmetrically dimethylated on arginine 2.
Figure 5: WDR5 is recruited by H3R2me2s to chromatin.
Figure 6: PRMT7 and PRMT5–WDR77 methylate H3R2me2s.

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Acknowledgements

We are grateful to C.L. Wei, H. Thoreau and Z.H. Yap for help with the Solexa high-throughput sequencing; to P. Rorth and X. Yang for the use of the Drosophila facility; to S. Choksi (Institute of Molecular and Cell Biology (IMCB)) for providing the zebrafish total protein extract; to V. Do Dang and X.Y. Fu (National University of Singapore) for sharing the PSuper vector targeting WDR77 and to N. Jennifer for technical help. We thank M. Walsh, P. Kaldis, X.Y. Fu and S. Choksi for discussions and P. Rorth, G. Gargiulo, M.M. Zhou and M. Walsh for critically reading the manuscript. This work was supported by the IMCB, A-STAR core funding to E.G.

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  1. Christian Bassi

    Present address: Current address: Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,

Authors and Affiliations

  1. Institute of Molecular and Cell Biology, Singapore

    Valentina Migliori, Julius Müller, Sameer Phalke, Diana Low, Marco Bezzi, Wei Chuen Mok, Sanjeeb Kumar Sahu, Jayantha Gunaratne, Walter Blackstock & Ernesto Guccione

  2. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

    Valentina Migliori, Marco Bezzi & Ernesto Guccione

  3. BioInformatic Institute, Singapore

    Diana Low & Vladimir Kuznetsov

  4. Cogentech, Protein Chemistry Unit, Milan, Italy

    Paola Capasso & Ario De Marco

  5. Department of Experimental Oncology, European Institute of Oncology, Milan, Italy

    Christian Bassi, Valentina Cecatiello, Bruno Amati & Marina Mapelli

  6. Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy

    Bruno Amati

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Contributions

V.M. and E.G. conceived the study and designed the experiments. V.M. conducted ChIP, ChIP-seq, SILAC sample preparation, analysis and experimental validation of SILAC results, methylation assay and biochemical experiments. E.G. supervised the project and wrote the manuscript, which was reviewed by V.M. and M.M. Figures were prepared by V.M., E.G., J.M., D.L. and M.M. J.M., D.L. and V.K. conducted the bioinformatic analysis of ChIP data. S.P. did the polytene staining. J.G. and W.B. generated the MS results and primary analysis, and P.C. and A.D.M. generated the BIACORE datasets. C.B. and B.A. carried out the initial peptide pull-down analysis. V.C. and M.M. obtained crystals, and collected and analyzed X-ray data. M.B., W.C.M. and S.K.S. contributed technical help.

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Correspondence to Ernesto Guccione.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 and Supplementary Methods (PDF 4820 kb)

Supplementary Data 1

Genomic coordinates and PSCR primers (XLS 272 kb)

Supplementary Data 2

Sheet1 (SILAC): Quantification of the interaction of all the components of the WDR5 complex with H3, H3R2me2a and H3R2me2s as revealed by SILAC screening. Sheet2 (BIACORE) Quantification of the interaction of WDR5 with differentially methylated pepides using BIACORE assays. The dissociation constant (KD) is indicated. (XLS 47 kb)

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Migliori, V., Müller, J., Phalke, S. et al. Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat Struct Mol Biol 19, 136–144 (2012). https://doi.org/10.1038/nsmb.2209

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