RNA-directed DNA methylation

RNA-DNA interactions can serve as a signal that triggers de novo DNA methyl ation in plants. As yet, this RNA-directed DNA methylation mechanism merely targets transgenes, but it appears likely that methylation of some endogen ous 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 sy mmetric and asymmetric sites are detectable on both DNA strands within thes e regions. Methylation progressively decreases in the sequences adjacent to the putative RNA-DNA duplex. The extreme sensitivity of RNA-directed DNA m ethylation was demonstrated by analysing a short 30 bp DNA region that was complementary to the targeting RNA. Association of RNA-directed DNA methyla tion with homology-dependent gene silencing indicated that the methylation- directing RNA molecules may be double-stranded or may contain double-strand ed regions. Whereas the function of DNA methylation in transcriptional gene silencing is nearly understood, its role in post-transcriptional gene sile ncing 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 ge ne regulation throughout eukaryotes.