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 1–7). 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.
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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.
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Supplementary information
41586_2002_BFnature731_MOESM1_ESM.pdf
Molecular nature of the kryptonite alleles, PCR primers and molecular markers used in this study and supplementary table 1 (PDF 9 kb)
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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
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DOI: https://doi.org/10.1038/nature731
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