1Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation

In plants, RNA can induce de novo cytosine methylation of homologous DNA by a mechanism that is poorly understood. Cytosines in all sequence contexts become modified in response to RNA signals [1, 2]. Recent work has implicated the de novo DNA methyltransferases (DMTases), DRM1 DRM2, in establishing RNA-directed methylation of the constitutive nopaline synthase promoter [3] and the DMTase MET1 [4] and the putative histone deacetylase HDA6 [5] in maintaining or enhancing CpG methylation induced by RNA. Despite the identification of enzymes that catalyze epigenetic modifications in response to RNA signals, it is unclear how RNA targets DNA for methylation. A screen for mutants defective in RNA-directed DNA methylation identified a novel putative chromatin remodeling protein, DRD1. This protein belongs to a previously undefined, plant-specific subfamily of SWI2/SNF2-like proteins most similar to the RAD54/ATRX-subfamily. In drd1 mutants, RNA-induced non-CpG methylation is almost eliminated at a target promoter, resulting in reactivation, while methylation of centromeric and rDNA repeats is unaffected. Thus, unlike the SNF2-like proteins DDM1/Lsh1 [6, 7] and ATRX [8, 9], which regulate methylation of repetitiv