Molecular mechanisms of the RNA polymerases in plant RNA-directed DNA methylation.

RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation pathway that relies on the atypical RNA polymerases Pol IV-RDR2 complex and Pol V to produce the siRNA precursor and lncRNA, respectively. Both Pol IV and Pol V have evolved from Pol II, but adopt unique biochemical features relevant for their functions in siRNA precursor (Pol IV) and scaffold lncRNA (Pol V) production. Recent structural studies suggest that the Pol IV and Pol V NRPD(E)2 subunit-induced enhanced backtracking plays an important role in their ncRNA production function. A dual measurement mechanism was proposed for the siRNA precursor production by Pol IV-RDR2 holoenzyme in RdDM. In plants, two atypical DNA-dependent RNA polymerases, RNA polymerase IV (Pol IV) and Pol V, and an RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) together produce noncoding RNAs (ncRNAs) to guide the plant-specific RNA-directed DNA methylation (RdDM). Although both Pol IV and Pol V have evolved from the canonical Pol II, they have adapted to different roles in RdDM. The mechanisms of their adaptation are key to understanding plant DNA methylation and the divergent evolution of polymerases. In this review, we summarize insights that have emerged from recent structural studies of Pol IV, Pol V, and RDR2 and discuss their structural features critical for efficient ncRNA production in RdDM. [ABSTRACT FROM AUTHOR]