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There are some puzzling genetic phenomena in nature that have kept geneticists busily searching for clues for decades. Among genetics' X-files are cases in which alleles of the same gene have the same sequence but very different functional states. Gene behaviors of this sort fall under the heading of “epigenetic phenomena.” Traits attributable to epigenetically altered alleles (epialleles) are often not transmitted between generations as independent, immutable characters, according to the rules that Mendel worked out with his garden peas. Instead, there are cases where alleles can change state if and when they find themselves in the same nucleus as epialleles that are locked into a different functional state. This is the case in paramutation, which describes the situation whereby a silent, paramutagenic allele can influence the expression of an active, paramutable allele of the same gene when the two alleles are exposed to one another within the same genome [1]. The silent allele, which is defined as being paramutagenic, somehow transfers its silent state to the other allele, causing that previously active allele to become silenced, too. Most interestingly, the previously active allele is now stably altered in such a way that it can retain the silenced state through meiosis and future generations. Moreover, the newly silenced allele is paramutagenic itself and will silence compatible paramutable alleles. All of this happens without any changes in the nucleotide sequence at the affected locus. This unusual allelic behavior is the genic analogue of the shape-shifting that occurs among proteins that can convert to a prion state and then cause other proteins of identical amino acid sequence to acquire the altered conformation [2],[3]. How alleles can influence one another to acquire or maintain a paramutated or paramutagenic state is not yet known. However, in this issue of PLoS Genetics, two interesting papers from the Hollick (Stonaker et al. [4]) and Chandler (Sidorenko et al. [5]) laboratories provide further evidence that paramutation in maize has an RNA basis. Specifically, the studies suggest that multiple alternative subunits of the plant-specific multi-subunit RNA polymerases, Pol IV and Pol V, first discovered in Arabidopsis [6],[7], might assemble into Pol IV or Pol V sub-types that have different roles in paramutation and gene silencing.

RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?