Article | Published:

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

Nature Structural & Molecular Biology volume 19, pages 136144 (2012) | Download Citation

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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. 1.

    Chromatin modifications and their function. Cell 128, 693–705 (2007).

  2. 2.

    et al. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449, 928–932 (2007).

  3. 3.

    et al. Methylation of histone H4 at arginine 3 occurs in vivo and is mediated by the nuclear receptor coactivator PRMT1. Curr. Biol. 11, 996–1000 (2001).

  4. 4.

    et al. Active genes are tri-methylated at K4 of histone H3. Nature 419, 407–411 (2002).

  5. 5.

    et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

  6. 6.

    , , & Arginine/lysine-methyl/methyl switches: biochemical role of histone arginine methylation in transcriptional regulation. Epigenomics 2, 119–137 (2010).

  7. 7.

    & The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6, 838–849 (2005).

  8. 8.

    , , , & How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007).

  9. 9.

    et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1, 286–298 (2007).

  10. 10.

    , , & The genomic landscape of histone modifications in human T cells. Proc. Natl. Acad. Sci. USA 103, 15782–15787 (2006).

  11. 11.

    et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181 (2005).

  12. 12.

    et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).

  13. 13.

    & WDR5, a complexed protein. Nat. Struct. Mol. Biol. 16, 678–680 (2009).

  14. 14.

    et al. Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol. Cell. Biol. 24, 5639–5649 (2004).

  15. 15.

    et al. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 449, 933–937 (2007).

  16. 16.

    et al. PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation. Genes Dev. 21, 3369–3380 (2007).

  17. 17.

    et al. Arginine methylation of the histone H3 tail impedes effector binding. J. Biol. Chem. 283, 3006–3010 (2008).

  18. 18.

    et al. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep. 10, 1235–1241 (2009).

  19. 19.

    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).

  20. 20.

    , , , & Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks. Mol. Cell 33, 181–191 (2009).

  21. 21.

    , , , & Transcriptional initiation is controlled by upstream GC-box interactions in a TATAA-less promoter. Mol. Cell. Biol. 10, 6632–6641 (1990).

  22. 22.

    et al. The histone-like NF-Y is a bifunctional transcription factor. Mol. Cell. Biol. 28, 2047–2058 (2008).

  23. 23.

    et al. The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J. 15, 2227–2235 (1996).

  24. 24.

    , , , & LEDGF binds to heat shock and stress-related element to activate the expression of stress-related genes. Biochem. Biophys. Res. Commun. 283, 943–955 (2001).

  25. 25.

    et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58–69 (2007).

  26. 26.

    et al. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13, 1924–1935 (1999).

  27. 27.

    , , , & Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

  28. 28.

    et al. A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature 418, 994–998 (2002).

  29. 29.

    , , & Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87, 95–104 (1996).

  30. 30.

    et al. Analysis of interaction partners of H4 histone by a new proteomics approach. Proteomics 9, 4934–4943 (2009).

  31. 31.

    et al. Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46. Structure 16, 1077–1085 (2008).

  32. 32.

    et al. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat. Struct. Mol. Biol. 13, 713–719 (2006).

  33. 33.

    & WDR5 interacts with mixed lineage leukemia (MLL) protein via the histone H3-binding pocket. J. Biol. Chem. 283, 35258–35264 (2008).

  34. 34.

    , , & A conserved arginine-containing motif crucial for the assembly and enzymatic activity of the mixed lineage leukemia protein-1 core complex. J. Biol. Chem. 283, 32162–32175 (2008).

  35. 35.

    , & Structure of WDR5 bound to mixed lineage leukemia protein-1 peptide. J. Biol. Chem. 283, 32158–32161 (2008).

  36. 36.

    , , & On the mechanism of multiple lysine methylation by the human mixed lineage leukemia protein-1 (MLL1) core complex. J. Biol. Chem. 284, 24242–24256 (2009).

  37. 37.

    et al. Structural basis for molecular recognition and presentation of histone H3 by WDR5. EMBO J. 25, 4245–4252 (2006).

  38. 38.

    et al. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat. Struct. Mol. Biol. 13, 704–712 (2006).

  39. 39.

    , & Molecular recognition of histone H3 by the WD40 protein WDR5. Nat. Struct. Mol. Biol. 13, 698–703 (2006).

  40. 40.

    et al. Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol. Cell 22, 137–144 (2006).

  41. 41.

    et al. Control of cell growth by c-Myc in the absence of cell division. Curr. Biol. 9, 1255–1258 (1999).

  42. 42.

    & Differentiation of promyelocytic (HL-60) cells into mature granulocytes: mitochondrial-specific rhodamine 123 fluorescence. J. Cell Biol. 96, 94–99 (1983).

  43. 43.

    & Methods and tips for the purification of human histone methyltransferases. Methods 31, 49–58 (2003).

  44. 44.

    et al. An Ash2L/RbBP5 heterodimer stimulates the MLL1 methyltransferase activity through coordinated substrate interactions with the MLL1 SET domain. PLoS ONE 5, e14102 (2010).

  45. 45.

    et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183–197 (2011).

  46. 46.

    , , , & Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein. J. Biol. Chem. 283, 33808–33815 (2008).

  47. 47.

    et al. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J. Biol. Chem. 285, 4268–4272 (2010).

  48. 48.

    et al. Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2. Nat. Genet. 41, 696–702 (2009).

  49. 49.

    , , , & In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856–2860 (2006).

  50. 50.

    & MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

  51. 51.

    & Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

  52. 52.

    , & Simple algorithm for a maximum-likelihood SAD function. Acta Crystallogr. D Biol. Crystallogr. 60, 1220–1228 (2004).

  53. 53.

    & Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

  54. 54.

    et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).

Download references

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.

Author information

Author notes

    • Christian Bassi

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

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

Authors

  1. Search for Valentina Migliori in:

  2. Search for Julius Müller in:

  3. Search for Sameer Phalke in:

  4. Search for Diana Low in:

  5. Search for Marco Bezzi in:

  6. Search for Wei Chuen Mok in:

  7. Search for Sanjeeb Kumar Sahu in:

  8. Search for Jayantha Gunaratne in:

  9. Search for Paola Capasso in:

  10. Search for Christian Bassi in:

  11. Search for Valentina Cecatiello in:

  12. Search for Ario De Marco in:

  13. Search for Walter Blackstock in:

  14. Search for Vladimir Kuznetsov in:

  15. Search for Bruno Amati in:

  16. Search for Marina Mapelli in:

  17. Search for Ernesto Guccione in:

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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ernesto Guccione.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Methods

Excel files

  1. 1.

    Supplementary Data 1

    Genomic coordinates and PSCR primers

  2. 2.

    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.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nsmb.2209

Further reading