RNA-directed DNA methylation (RdDM) is an epigenetic process first elucidated in plants whereby small double-stranded RNAs (dsRNA's) are processed to guide methylation to complementary DNA loci. In the model plant organism Arabidopsis thaliana, these small dsRNA's may be generated from three sources:
These dsRNAs are then processed to direct histone 3 lysine 9 (H3K9) methylation via Ago4 and the SUVH (Suppressor of Variegation Homolog) histone methyltransferase family. This H3K9 dimethylation is then putatively bound by the cytosine methyltransferase CMT3, which methylates cytosines in a non-CG context.
These marks, H3K9 dimethylation and cytosine methylation, are canonical marks of gene silencing. Thus small double stranded RNAs generated in diverse contexts bring about transcriptional silencing at specific loci.