An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation

Small interfering RNAs (siRNAs) are important regulators of gene expression in the plant model Arabidopsis, and intriguingly the vast majority of the small RNAs involved are generated from methylated regions of the genome. A previously unknown protein termed RdDM (for regulator of RNA-directed DNA methylation) has now been identified in Arabidopsis, throwing more light on the interactions of epigenetics, DNA methylation and small RNAs in plants. RDM1 is a novel methyl DNA-binding protein that binds to single-stranded methylated DNA: the many methyl DNA-binding proteins known previously in plants and animals bind only to double-stranded methylated DNA. RDM1 interacts with complexes of the effector protein Argonaute 4 (AGO4) with siRNAs to direct de novo DNA methylation and gene silencing.