Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation

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Modifications on histones control important biological processes through their effects on chromatin structure1,2,3. Methylation at lysine 4 on histone H3 (H3K4) is found at the 5′ end of active genes and contributes to transcriptional activation by recruiting chromatin-remodelling enzymes4,5. An adjacent arginine residue (H3R2) is also known to be asymmetrically dimethylated (H3R2me2a) in mammalian cells6, but its location within genes and its function in transcription are unknown. Here we show that H3R2 is also methylated in budding yeast (Saccharomyces cerevisiae), and by using an antibody specific for H3R2me2a in a chromatin immunoprecipitation-on-chip analysis we determine the distribution of this modification on the entire yeast genome. We find that H3R2me2a is enriched throughout all heterochromatic loci and inactive euchromatic genes and is present at the 3′ end of moderately transcribed genes. In all cases the pattern of H3R2 methylation is mutually exclusive with the trimethyl form of H3K4 (H3K4me3). We show that methylation at H3R2 abrogates the trimethylation of H3K4 by the Set1 methyltransferase. The specific effect on H3K4me3 results from the occlusion of Spp1, a Set1 methyltransferase subunit necessary for trimethylation. Thus, the inability of Spp1 to recognize H3 methylated at R2 prevents Set1 from trimethylating H3K4. These results provide the first mechanistic insight into the function of arginine methylation on chromatin.

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Figure 1: H3R2me2a associates with heterochromatin.
Figure 2: H3R2me2a enrichment at euchromatic genes is mutually exclusive with H3K4me3.
Figure 3: H3R2me2a regulates the activity of the Set1 complex towards H3K4.
Figure 4: H3R2me2a blocks the binding of Spp1 to methylated H3K4.


  1. 1

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

  2. 2

    Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nature Rev. Mol. Cell Biol. 6, 838–849 (2005)

  3. 3

    Wysocka, J., Allis, C. D. & Coonrod, S. Histone arginine methylation and its dynamic regulation. Front. Biosci. 11, 344–355 (2006)

  4. 4

    Ruthenburg, A. J., Allis, C. D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15–30 (2007)

  5. 5

    Sims, R. J. & Reinberg, D. Histone H3 Lys 4 methylation: caught in a bind? Genes Dev. 20, 2779–2786 (2006)

  6. 6

    Torres-Padilla, M. E., Parfitt, D. E., Kouzarides, T. & Zernicka-Goetz, M. Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature 445, 214–218 (2007)

  7. 7

    Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96–99 (2006)

  8. 8

    Wysocka, J. et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442, 86–90 (2006)

  9. 9

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

  10. 10

    Schneider, J. et al. Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol. Cell 19, 849–856 (2005)

  11. 11

    Steward, M. M. et al. Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes. Nature Struct. Mol. Biol. 13, 852–854 (2006)

  12. 12

    Schurter, B. T. et al. Methylation of histone H3 by coactivator-associated arginine methyltransferase 1. Biochemistry 40, 5747–5756 (2001)

  13. 13

    Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998)

  14. 14

    Liu, C. L. et al. Single-nucleosome mapping of histone modifications in S. cerevisiae . PLoS Biol. 3, e328 (2005)

  15. 15

    Pokholok, D. K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005)

  16. 16

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

  17. 17

    Shi, X. et al. Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J. Biol. Chem. 282, 2450–2455 (2007)

  18. 18

    Guccione, E. et al. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature doi: 10.1038/nature06166 (this issue)

  19. 19

    Wood, A. et al. Ctk complex-mediated regulation of histone methylation by COMPASS. Mol. Cell. Biol. 27, 709–720 (2007)

  20. 20

    Liang, G., Klose, R. J., Gardner, K. E. & Zhang, Y. Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase. Nature Struct. Mol. Biol. 14, 243–245 (2007)

  21. 21

    Seward, D. J. et al. Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nature Struct. Mol. Biol. 14, 240–242 (2007)

  22. 22

    Li, H. et al. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442, 91–95 (2006)

  23. 23

    Pena, P. V. et al. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442, 100–103 (2006)

  24. 24

    Morillon, A., O’Sullivan, J., Azad, A., Proudfoot, N. & Mellor, J. Regulation of elongating RNA polymerase II by forkhead transcription factors in yeast. Science 300, 492–495 (2003)

  25. 25

    Perez-Burgos, L. et al. Generation and characterization of methyl-lysine histone antibodies. Methods Enzymol. 376, 234–254 (2004)

  26. 26

    Slater, G. S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005)

  27. 27

    David, L. et al. A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA 103, 5320–5325 (2006)

  28. 28

    Santos-Rosa, H. et al. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol. Cell 12, 1325–1332 (2003)

  29. 29

    Nelson, C. J., Santos-Rosa, H. & Kouzarides, T. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell 126, 905–916 (2006)

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We thank C. Nelson, A. Bannister and M. Christophorou for critical reading of the manuscript; S. Marguerat for helpful discussions; L. Packman and M. Weldon for assistance with protein sequencing; N. Jiang and R. Selzer for assistance with microarray analyses; and M. Gilchrist for help with displaying genomic data. This work was supported by postdoctoral fellowship grants to A.K. from the European Molecular Biology Organization (EMBO) and Marie Curie. The T.K. laboratory is funded by grants from Cancer Research UK (CRUK) and the 6th Research Framework Programme of the European Union (Epitron and Heroic). The microarray data sets are available from GEO (Gene Expression Omnibus) under accession number GSE8626, and from

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Correspondence to Tony Kouzarides.

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Competing interests: T.K. is a director of Abcam PLC; R.D.G. and M.A.S. are employees of NimbleGen Systems, Inc.

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Kirmizis, A., Santos-Rosa, H., Penkett, C. et al. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449, 928–932 (2007) doi:10.1038/nature06160

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