RNA-DNA interactions can serve as a signal that triggers de novo DNA methylation in plants. As yet, this RNA-directed DNA methylation mechanism merely targets transgenes, but it appears likely that methylation of some endogenous sequences is also directed by RNA. RNA-directed methylation of cytosine residues specifically occurs along the DNA regions that are complementary to the directing RNA pointing to the formation of a putative RNA-DNA duplex. Dense methylation patterns and the methylation of cytosine residues at symmetric and asymmetric sites are detectable on both DNA strands within these regions. Methylation progressively decreases in the sequences adjacent to the putative RNA-DNA duplex. The extreme sensitivity of RNA-directed DNA methylation was demonstrated by analysing a short 30 bp DNA region that was complementary to the targeting RNA. Association of RNA-directed DNA methylation with homology-dependent gene silencing indicated that the methylation-directing RNA molecules may be double-stranded or may contain double-stranded regions. Whereas the function of DNA methylation in transcriptional gene silencing is nearly understood, its role in post-transcriptional gene silencing is still under discussion. In mammals, X-chromosome inactivation and genomic imprinting are associated with DNA methylation but how methylation is initiated is unclear. The observation of a correlation between specific antisense RNAs and transcriptional and post-transcriptional gene silencing may indicate that RNA-directed DNA methylation is involved in epigenetic gene regulation throughout eukaryotes.