Evolution of plant-specific Snf2 proteins and RNA polymerases and their function in maintaining paramutations in Zea mays

Paramutation describes an interaction between specific alleles which results in heritable epigenetic changes in gene expression. To study the mechanisms underlying paramutation, genetic screens were performed to identify factors required to maintain repression (rmr) of paramutant states. For my thesis research I mapped and identified rmr1 as encoding a novel, plant-specific Rad54-like Snf2 protein. Additionally, I have participated in the identification of rmr6 as encoding RPD1, the largest subunit of the plant specific RNA polymerase IV (Pol IV), and rmr7 as encoding RPD2a, the second largest subunit of either Pol IV and / or an additional plant-specific RNA polymerase, Pol V. Pol IV and Pol V, along with RMR1 and related Snf2 proteins, have evolved exclusively in plants to mediate RNA-based epigenetic repression. While the epigenetic changes mediated by rmr1, rmr6, and rmr7 appear to indirectly affect the paramutation mechanism, the identification of these factors has facilitated cross-species comparisons of the RNA-based repression mechanisms and provided new evidence for the role of these types of regulatory mechanisms in plant development and evolution