Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase

Abstract

Gene silencing in eukaryotes is associated with the formation of heterochromatin, a complex of proteins and DNA that block transcription. Heterochromatin is characterized by the methylation of cytosine nucleotides of the DNA, the methylation of histone H3 at lysine 9 (H3 Lys 9), and the specific binding of heterochromatin protein 1 (HP1) to methylated H3 Lys 9 (refs 17). Although the relationship between these chromatin modifications is generally unknown, in the fungus Neurospora crassa, DNA methylation acts genetically downstream of H3 Lys 9 methylation8. Here we report the isolation of KRYPTONITE, a methyltransferase gene specific to H3 Lys 9, identified in a mutant screen for suppressors of gene silencing at the Arabidopsis thaliana SUPERMAN (SUP) locus. Loss-of-function kryptonite alleles resemble mutants in the DNA methyltransferase gene CHROMOMETHYLASE3 (CMT3)9, showing loss of cytosine methylation at sites of CpNpG trinucleotides (where N is A, C, G or T) and reactivation of endogenous retrotransposon sequences. We show that CMT3 interacts with an Arabidopsis homologue of HP1, which in turn interacts with methylated histones. These data suggest that CpNpG DNA methylation is controlled by histone H3 Lys 9 methylation, through interaction of CMT3 with methylated chromatin.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: KRYPTONITE mutants.
Figure 2: Methyltransferase activity of KRYPTONITE.
Figure 3: Effect of kryptonite on DNA methylation and retrotransposon activation.
Figure 4: Interaction of CMT3 with histones and LHP1.

References

  1. 1

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

    ADS  CAS  Article  Google Scholar 

  2. 2

    Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D. & Grewal, S. I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113 (2001)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001)

    CAS  Article  PubMed  Google Scholar 

  5. 5

    Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001)

    ADS  CAS  Article  Google Scholar 

  6. 6

    Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001)

    ADS  CAS  Article  Google Scholar 

  7. 7

    Jacobs, S. A. et al. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J. 20, 5232–5241 (2001)

    CAS  Article  PubMed  Google Scholar 

  8. 8

    Tamaru, H. & Selker, E. U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414, 277–283 (2001)

    ADS  CAS  Article  PubMed  Google Scholar 

  9. 9

    Lindroth, A. M. et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077–2080 (2001)

    CAS  Article  Google Scholar 

  10. 10

    Tschiersch, B. et al. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 13, 3822–3831 (1994)

    CAS  Article  PubMed  Google Scholar 

  11. 11

    Allshire, R. C., Nimmo, E. R., Ekwall, K., Javerzat, J. P. & Cranston, G. Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9, 218–233 (1995)

    CAS  Article  PubMed  Google Scholar 

  12. 12

    Ivanova, A. V., Bonaduce, M. J., Ivanov, S. V. & Klar, A. J. The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nature Genet. 19, 192–195 (1998)

    CAS  Article  PubMed  Google Scholar 

  13. 13

    Peters, A. H. et al. Loss of the suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323–337 (2001)

    CAS  Article  PubMed  Google Scholar 

  14. 14

    Jacobsen, S. E. & Meyerowitz, E. M. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277, 1100–1103 (1997)

    CAS  Article  PubMed  Google Scholar 

  15. 15

    Bartee, L., Malagnac, F. & Bender, J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 15, 1753–1758 (2001)

    CAS  Article  PubMed  Google Scholar 

  16. 16

    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  PubMed  Google Scholar 

  17. 17

    Tachibana, M., Sugimoto, K., Fukushima, T. & Shinkai, Y. Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J. Biol. Chem. 276, 25309–25317 (2001)

    CAS  Article  PubMed  Google Scholar 

  18. 18

    Finnegan, E. J., Peacock, W. J. & Dennis, E. S. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl Acad. Sci. USA 93, 8449–8454 (1996)

    ADS  CAS  Article  PubMed  Google Scholar 

  19. 19

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

    ADS  CAS  Article  PubMed  Google Scholar 

  20. 20

    Kishimoto, N. et al. Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Mol. Biol. 46, 171–183 (2001)

    CAS  Article  Google Scholar 

  21. 21

    Soppe, W. J. et al. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 6, 791–802 (2000)

    CAS  Article  Google Scholar 

  22. 22

    Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993)

    ADS  CAS  Article  Google Scholar 

  23. 23

    Steimer, A. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12, 1165–1178 (2000)

    CAS  Article  PubMed  Google Scholar 

  24. 24

    Henikoff, S. & Comai, L. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics 149, 307–318 (1998)

    CAS  PubMed Central  PubMed  Google Scholar 

  25. 25

    Akhtar, A., Zink, D. & Becker, P. B. Chromodomains are protein–RNA interaction modules. Nature 407, 405–409 (2000)

    ADS  CAS  Article  Google Scholar 

  26. 26

    Gaudin, V. et al. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 128, 4847–4858 (2001)

    CAS  Google Scholar 

  27. 27

    Peters, A. H. F. M. et al. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nature Genet. 30, 77–80 (2002)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank T. Jenuwein for the GST–Suv constructs and H3 N-terminal peptides, Y. Shinkai for the H3 N-terminal GST fusion constructs, A. Kouzarides for an HP1 construct, and S. Peyvandi for technical assistance. This work was supported by grants from the National Institutes of Health, the Beckman Young Investigator programme, and the Searle Scholars Foundation to S.E.J. J.P.J. was supported by an NIH training grant and A.M.L. by a post-doctoral fellowship from the Damon Runyon Walter Winchel Foundation.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Steven E. Jacobsen.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Jackson, J., Lindroth, A., Cao, X. et al. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002). https://doi.org/10.1038/nature731

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Sign up for the Nature Briefing newsletter for a daily update on COVID-19 science.
Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing