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PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing

Nature Structural & Molecular Biology volume 16, pages 304–311 (2009)Cite this article

Abstract

Mammalian gene silencing is established through methylation of histones and DNA, although the order in which these modifications occur remains contentious. Using the human β-globin locus as a model, we demonstrate that symmetric methylation of histone H4 arginine 3 (H4R3me2s) by the protein arginine methyltransferase PRMT5 is required for subsequent DNA methylation. H4R3me2s serves as a direct binding target for the DNA methyltransferase DNMT3A, which interacts through the ADD domain containing the PHD motif. Loss of the H4R3me2s mark through short hairpin RNA–mediated knockdown of PRMT5 leads to reduced DNMT3A binding, loss of DNA methylation and gene activation. In primary erythroid progenitors from adult bone marrow, H4R3me2s marks the inactive methylated globin genes coincident with localization of PRMT5. Our findings define DNMT3A as both a reader and a writer of repressive epigenetic marks, thereby directly linking histone and DNA methylation in gene silencing.

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Figure 1: PRMT5 symmetrically dimethylates histone H4R3 on the gene encoding γ-globin.
Figure 2: PRMT5 mediates transcriptional silencing of the γ-gene.
Figure 3: PRMT5 and DNMT3A function cooperatively in gene silencing.
Figure 4: DNMT3A binds specifically to histone H4 carrying the R3me2s modification.
Figure 5: Role of PRMT5 in developmental globin gene silencing.
Figure 6: Model of PRMT5-induced silencing of gene expression.

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Acknowledgements

We thank S. Pestka (University of Medicine and Dentistry of New Jersey) for the PRMT5Δ plasmid, R. Gaynor (University of Texas Southwestern) for the PRMT5 plasmid and members of the Jane and Cunningham laboratories for helpful discussions. This work was supported by grants from The National Health and Medical Research Council of Australia, the US National Institutes of Health (PO1 HL53749-03 and RO1 HL69232-01) (S.M.J.), The Roche Foundation for anemia research (RoFAR) (S.M.J.), The Cooley's Anemia Foundation (Q.Z.), The Natural Science Foundation of China #30670422 (Q.Z.), Cancer Centre Support CORE Grant P30 CA 21765, the American Lebanese Syrian Associated Charities (ALSAC) and the Assisi Foundation of Memphis (J.M.C.).

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  1. Quan Zhao and Gerhard Rank: These authors contributed equally to this work.

Authors and Affiliations

  1. Rotary Bone Marrow Research Laboratories, Melbourne Health Research Directorate, c/o Royal Melbourne Hospital Post Office, Grattan Street, Parkville, 3050, VIC, Australia

    Quan Zhao, Gerhard Rank, Yuen T Tan, Loretta Cerruti, David J Curtis & Stephen M Jane

  2. Molecular Immunology and Cancer Research Center, The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 22 Hankou Road, Nanjing, 210093, China

    Quan Zhao

  3. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, 10021, New York, USA

    Haitao Li & Dinshaw J Patel

  4. Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research and Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, 3050, VIC, Australia

    Robert L Moritz & Richard J Simpson

  5. Laboratory of Chromatin Biology, The Rockefeller University, 1230 York Avenue, New York, 10021, New York, USA

    C David Allis

  6. Department of Pediatrics and Institute of Molecular Pediatric Sciences, University of Chicago, 5839 South Maryland Avenue, Chicago, 60637, Illinois, USA

    John M Cunningham

  7. Department of Medicine, University of Melbourne, Grattan Street, Parkville, VIC, 3050, Australia

    Stephen M Jane

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Contributions

Q.Z., G.R., L.C. and Y.T.T. performed the experiments; R.L.M. and R.J.S. performed and analyzed the mass spectrometry; Q.Z., G.R. and S.M.J. designed and analyzed the research; D.J.C., C.D.A., H.L., D.J.P. and J.M.C. provided ideas, reagents and discussion; Q.Z., G.R. and S.M.J. wrote the manuscript.

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Correspondence to Quan Zhao or Stephen M Jane.

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Zhao, Q., Rank, G., Tan, Y. et al. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 16, 304–311 (2009). https://doi.org/10.1038/nsmb.1568

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