The role of DNA methylation in gene silencing has long been established, but the relationship between DNA methylation and histone methylation was only finally unravelled last year, when it was shown in Neurospora that mutations in a widely conserved Su(var)-like methyl transferase and in lysine 9 (lys9) of histone H3 could abolish all DNA methylation, indicating that DNA methylation is downstream of histone methylation. But is this just a fungus-specific phenomenon? By identifying and characterizing the Arabidopsis Su(var) homologue, KRYPTONITE (KYP), Jackson et al. now extend the previous findings by showing that this relationship is also conserved in plants.

The study started with a genetic screen for suppressors of a hypermethylated allele of SUPERMAN (SUP), which causes disrupted flower morphology. As well as identifying mutations in CHROMOMETHYLASE3 (CMT3), a known DNA methyltransferase, the screen yielded alleles of another gene, which the authors called KYP. KYP contains a SET domain that is characteristic of Su(var)9-3 proteins, which are known to be involved in histone H3 methylation and, as expected, it specifically methylates lys9 of histone H3. Sequence analysis showed that the activity of the SET domain is either reduced or eliminated in kyp mutants, indicating that this domain is necessary for its function.

Given the dependence of DNA methylation on histone methylation in Neurospora, the authors decided to investigate the effects of loss-of-function mutations in KYP on DNA methylation. They used methylation-sensitive restriction enzymes and bisulphite sequencing to compare the methylation status of several loci, including SUP, which is predominantly methylated at CpNpG sites, and FLOWERING LOCUS WA , which is mostly methylated at CpG sites. The authors found that, as in the cmt3 mutants, in kyp mutants DNA methylation was affected specifically at CpNpG sites in all of the sequences tested.

So how is the histone methylation that is brought about by KYP 'translated' into DNA methylation? The fact that CMT3 has a chromodomain made the authors wonder whether CMT3 could bind directly to lys9 of histone H3, as does HP1, which binds to methylated, heterochromatic regions. Their in vitro studies and binding assays of tagged CMT3 and histone H3 in Escherichia coli gave negative results — instead, CMT3 turned out to bind directly to the Arabidopsis HP1.

On the basis of their findings, the authors propose the following model. HP1 is attracted to lys9 of histone H3, once it has been methylated by KYP. HP1 then binds to CMT3, thus bringing it to the site of histone methylation. It is then up to CMT3 to methylate the DNA. Although this model awaits an in vivo validation, it suggests the existence of a eukaryote-wide mechanism for attracting DNA methyltransferases to the chromatin, in which HP1 has a central role.