A Vicious Cycle: RNA Silencing and DNA Methylation in Plants

Several new studies have stimulated intense interest in understanding the mechanism and evolutionary significance of RNA silencing, the targeted degradation of RNA. RNA silencing is typically triggered by double-stranded RNA (dsRNA). The dsRNA trigger is diced into very small species of 21-25 nt (siRNAs), which then guide sequence-specific cleavage of other homologous RNAs, such as messenger RNAs. Thus, both the trigger and target RNAs are ultimately destroyed. This mechanism occurs in eukaryotic organisms as diverse as the laboratory plant Arabidopsis thaliana, nematode worms, and mice. It is speculated that RNA silencing exists as a defense against invasive dsRNA species such as RNA viruses. In fact, plants can recover from infection by RNA viruses via RNA silencing. RNA silencing might also have a role in developmental regulation. Furthermore, RNA silencing induced by injected dsRNA or dsRNA expressed from a transgene provides a powerful tool for reverse genetics in animals and plants. Plant RNA silencing displays certain unique features beyond this common framework. For example, some plant transgene constructs that would not obviously produce dsRNA nonetheless produce siRNAs and trigger RNA silencing. For this reason, it is thought that in plants, other "aberrant" RNAs exist that can be processed into siRNAs. In addition, plant RNA silencing is frequently accompanied by DNA cytosine methylation of the silenced gene. The general observation from plant transgene RNA silencing systems is that affected DNA sequences can become methylated over the regions that are homologous to the aberrant RNA silencing trigger. Methylation is usually diagnostic of heterochromatin formation-that is, the modification and remodeling of DNA-associated proteins into a condensed chromatin complex. When methylation occurs in the promoters of genes, transcription initiation is blocked. However, when methylation occurs in the coding sequences of genes, such as plant transgenes undergoing RNA silencing, transcription is not obviously impaired-at least not at the level of initiation. Why then are DNA methylation and presumably underlying chromatin changes involved in an RNA-based silencing mechanism? An intriguing explanation is that RNA-directed DNA methylation provides a means of amplifying the proportion of aberrant RNA generated during transcription to reinforce the RNA silencing process. In fact, there is evidence from a fungal system that methylation within the transcribed reg