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ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing

Abstract

Constitutive heterochromatin in Arabidopsis thaliana is marked by repressive chromatin modifications, including DNA methylation, histone H3 dimethylation at Lys9 (H3K9me2) and monomethylation at Lys27 (H3K27me1). The enzymes catalyzing DNA methylation and H3K9me2 have been identified; alterations in these proteins lead to reactivation of silenced heterochromatic elements. The enzymes responsible for heterochromatic H3K27me1, in contrast, remain unknown. Here we show that the divergent SET-domain proteins ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) and ATXR6 have H3K27 monomethyltransferase activity, and atxr5 atxr6 double mutants have reduced H3K27me1 in vivo and show partial heterochromatin decondensation. Mutations in atxr5 and atxr6 also lead to transcriptional activation of repressed heterochromatic elements. Notably, H3K9me2 and DNA methylation are unaffected in double mutants. These results indicate that ATXR5 and ATXR6 form a new class of H3K27 methyltransferases and that H3K27me1 represents a previously uncharacterized pathway required for transcriptional repression in Arabidopsis.

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Figure 1: ATXR5 and ATXR6 monomethylate H3K27.
Figure 2: ATXR5 and ATXR6 have redundant roles in leaf development.
Figure 3: atxr5 atxr6 (atxr5/6) mutations lead to disruption of constitutive heterochromatin, reduced H3K27 monomethylation and reactivation of silenced elements.
Figure 4: Di- and trimethylation of H3K27 are not altered in atxr5 atxr6 mutants.
Figure 5: Mutations in atxr5 and atxr6 do not affect H3K9 dimethylation or DNA methylation.

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Gene Expression Omnibus

References

  1. Li, B., Carey, M. & Workman, J.L. The role of chromatin during transcription. Cell 128, 707–719 (2007).

    CAS  Article  Google Scholar 

  2. Maluszynska, J. & Heslop-Harrison, J.S. Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J. 1, 159–166 (1991).

    Article  Google Scholar 

  3. Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).

    CAS  Article  Google Scholar 

  4. Johnson, L., Cao, X. & Jacobsen, S. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12, 1360–1367 (2002).

    CAS  Article  Google Scholar 

  5. Probst, A.V., Fransz, P.F., Paszkowski, J. & Mittelsten Scheid, O. Two means of transcriptional reactivation within heterochromatin. Plant J. 33, 743–749 (2003).

    CAS  Article  Google Scholar 

  6. Tariq, M. et al. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc. Natl. Acad. Sci. USA 100, 8823–8827 (2003).

    CAS  Article  Google Scholar 

  7. Zhang, X. et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, e129 (2007).

    Article  Google Scholar 

  8. Cao, X. & Jacobsen, S.E. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl. Acad. Sci. USA 99, S16491–S16498 (2002).

    Article  Google Scholar 

  9. Cao, X. & Jacobsen, S.E. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138–1144 (2002).

    CAS  Article  Google Scholar 

  10. Ronemus, M.J., Galbiati, M., Ticknor, C., Chen, J. & Dellaporta, S.L. Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273, 654–657 (1996).

    CAS  Article  Google Scholar 

  11. Jackson, J.P., Lindroth, A.M., Cao, X. & Jacobsen, S.E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002).

    CAS  Article  Google Scholar 

  12. Finnegan, E.J. & Dennis, E.S. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res. 21, 2383–2388 (1993).

    CAS  Article  Google Scholar 

  13. Ebbs, M.L., Bartee, L. & Bender, J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol. Cell. Biol. 25, 10507–10515 (2005).

    CAS  Article  Google Scholar 

  14. Ebbs, M.L. & Bender, J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18, 1166–1176 (2006).

    CAS  Article  Google Scholar 

  15. Naumann, K. et al. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J. 24, 1418–1429 (2005).

    CAS  Article  Google Scholar 

  16. Malagnac, F., Bartee, L. & Bender, J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J. 21, 6842–6852 (2002).

    CAS  Article  Google Scholar 

  17. Vaillant, I. & Paszkowski, J. Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 10, 528–533 (2007).

    CAS  Article  Google Scholar 

  18. Lindroth, A.M. et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4146–4155 (2004).

    Article  Google Scholar 

  19. Mathieu, O., Probst, A.V. & Paszkowski, J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 24, 2783–2791 (2005).

    CAS  Article  Google Scholar 

  20. Müller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197–208 (2002).

    Article  Google Scholar 

  21. Ketel, C.S. et al. Subunit contributions to histone methyltransferase activities of fly and worm Polycomb group complexes. Mol. Cell. Biol. 25, 6857–6868 (2005).

    CAS  Article  Google Scholar 

  22. Baumbusch, L.O. et al. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res. 29, 4319–4333 (2001).

    CAS  Article  Google Scholar 

  23. Chanvivattana, Y. et al. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131, 5263–5276 (2004).

    CAS  Article  Google Scholar 

  24. Grossniklaus, U., Vielle-Calzada, J.P., Hoeppner, M.A. & Gagliano, W.B. Maternal control of embryogenesis by MEDEA, a Polycomb group gene in Arabidopsis. Science 280, 446–450 (1998).

    CAS  Article  Google Scholar 

  25. Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).

    CAS  Article  Google Scholar 

  26. Springer, N.M. et al. Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132, 907–925 (2003).

    CAS  Article  Google Scholar 

  27. Johnson, L. et al. Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res. 32, 6511–6518 (2004).

    CAS  Article  Google Scholar 

  28. Zhang, K., Sridhar, V.V., Zhu, J., Kapoor, A. & Zhu, J.K. Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS One 2, e1210 (2007).

    Article  Google Scholar 

  29. van Leeuwen, F., Gafken, P.R. & Gottschling, D.E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109, 745–756 (2002).

    CAS  Article  Google Scholar 

  30. Ng, H.H. et al. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 16, 1518–1527 (2002).

    CAS  Article  Google Scholar 

  31. Lacoste, N., Utley, R.T., Hunter, J.M., Poirier, G.G. & Cote, J. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J. Biol. Chem. 277, 30421–30424 (2002).

    CAS  Article  Google Scholar 

  32. Feng, Q. et al. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12, 1052–1058 (2002).

    CAS  Article  Google Scholar 

  33. Garcia, B.A. et al. Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 282, 7641–7655 (2007).

    CAS  Article  Google Scholar 

  34. Alonso, J.M. et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301, 653–657 (2003).

    Article  Google Scholar 

  35. Soppe, W.J. et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549–6559 (2002).

    CAS  Article  Google Scholar 

  36. Woo, H.R., Pontes, O., Pikaard, C.S. & Richards, E.J. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev. 21, 267–277 (2007).

    CAS  Article  Google Scholar 

  37. Henderson, I.R. & Jacobsen, S.E. Epigenetic inheritance in plants. Nature 447, 418–424 (2007).

    CAS  Article  Google Scholar 

  38. Peters, A.H. et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12, 1577–1589 (2003).

    CAS  Article  Google Scholar 

  39. Makarevich, G. et al. Different Polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep. 7, 947–952 (2006).

    CAS  Article  Google Scholar 

  40. Schönrock, N. et al. Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway. Genes Dev. 20, 1667–1678 (2006).

    Article  Google Scholar 

  41. Schubert, D. et al. Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J. 25, 4638–4649 (2006).

    CAS  Article  Google Scholar 

  42. Köhler, C. & Grossniklaus, U. Epigenetic inheritance of expression states in plant development: the role of Polycomb group proteins. Curr. Opin. Cell Biol. 14, 773–779 (2002).

    Article  Google Scholar 

  43. De Lucia, F., Crevillen, P., Jones, A.M., Greb, T. & Dean, C. A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc. Natl. Acad. Sci. USA 105, 16831–16836 (2008).

    CAS  Article  Google Scholar 

  44. Wood, C.C. et al. The Arabidopsis thaliana vernalization response requires a Polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc. Natl. Acad. Sci. USA 103, 14631–14636 (2006).

    Article  Google Scholar 

  45. Reyes, J.C. & Grossniklaus, U. Diverse functions of Polycomb group proteins during plant development. Semin. Cell Dev. Biol. 14, 77–84 (2003).

    CAS  Article  Google Scholar 

  46. Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).

    CAS  Article  Google Scholar 

  47. Vakoc, C.R., Sachdeva, M.M., Wang, H. & Blobel, G.A. Profile of histone lysine methylation across transcribed mammalian chromatin. Mol. Cell. Biol. 26, 9185–9195 (2006).

    CAS  Article  Google Scholar 

  48. Fuchs, J., Jovtchev, G. & Schubert, I. The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosome Res. 16, 891–898 (2008).

    CAS  Article  Google Scholar 

  49. Raynaud, C. et al. Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis. Plant J. 47, 395–407 (2006).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  52. Estève, P.O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006).

    Article  Google Scholar 

  53. Sarraf, S.A. & Stancheva, I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol. Cell 15, 595–605 (2004).

    CAS  Article  Google Scholar 

  54. Michaels, S.D., Bezerra, I.C. & Amasino, R.M. FRIGIDA-related genes are required for the winter-annual habit in Arabidopsis. Proc. Natl. Acad. Sci. USA 101, 3281–3285 (2004).

    CAS  Article  Google Scholar 

  55. Kizer, K.O., Xiao, T. & Strahl, B.D. Accelerated nuclei preparation and methods for analysis of histone modifications in yeast. Methods 40, 296–302 (2006).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank C.E. Walczak for assistance with microscopy. This work was supported by grants to S.D.M. from the National Science Foundation (IOB-0447583) and National Institutes of Health (GM075060); to Y.J. from the Fonds québécois de recherche sur la nature et les technologies; and to Y.V.B. from the US Public Health Service (National Research Service award GM07104). Research in the laboratory of S.E.J. was supported by National Institutes of Health grant GM60398. S.E.J. is an investigator of the Howard Hughes Medical Institute.

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Authors

Contributions

Y.J. carried out the genetic and biochemical characterization of ATXR5 and ATXR6. Y.J. and C.A.L. generated the gene expression and ChIP data. S.F. generated and sequenced the BS-Seq libraries. Y.V.B. conducted the locus-specific bisulfite sequencing analyses. H.S. validated the ChIP and RT-PCR results. C.A.L., Y.V.B. and L.M.J. conducted the immunofluorescence studies. S.C., M.P., S.F. and S.E.J. analyzed the BS-Seq data. S.D.M., M.P. and S.E.J. participated in the design of experiments.

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Correspondence to Scott D Michaels.

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Supplementary Figures 1–3, Supplementary Table 1 and Supplementary Methods (PDF 660 kb)

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Jacob, Y., Feng, S., LeBlanc, C. et al. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16, 763–768 (2009). https://doi.org/10.1038/nsmb.1611

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