Atypical RNA polymerase subunits required for RNA-directed DNA methylation

RNA- directed DNA methylation, one of several RNA interference - mediated pathways in the nucleus(1), has been documented in plants(2,3) and in human cells(4,5). Despite progress in identifying the DNA methyltransferases, histone-modifying enzymes and RNA interference proteins needed for RNA- directed DNA methylation(1), the mechanism remains incompletely understood. We screened for mutants defective in RNA- directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups(6). DRD1 is a SNF2- like protein(6) required for RNA- directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second- largest subunit and largest subunit, respectively, of a fourth class of DNA- dependent RNA polymerase ( polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post- transcriptional gene silencing(7,8). The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA- directed de novo methylation.