We used a transgene system to study spreading of RNAdirected DNA methylation (RdDM) during transcriptional gene silencing in Arabidopsis thaliana. Forward and reverse genetics approaches using this system delineated a stepwise pathway for the biogenesis of secondary siRNAs and unidirectional spreading of methylation from an upstream enhancer element into downstream sequences. Trans-acting, hairpin-derived primary siRNAs induce primary RdDM, independently of an enhancer-associated 'nascent' RNA, at the target enhancer region. Primary RdDM is a key step in the pathway because it attracts the secondary siRNA-generating machinery, including RNA polymerase IV, RNA-dependent RNA polymerase2 and Dicer-like3 (DCL3). These factors act in a turnover pathway involving a nascent RNA, which normally accumulates stably in non-silenced plants, to produce cis-acting secondary siRNAs that induce methylation in the downstream region. The identification of DCL3 in a forward genetic screen for silencing-defective mutants demonstrated a strict requirement for 24-nt siRNAs to direct methylation. A similar stepwise process for spreading of DNA methylation may occur in mammalian genomes, which are extensively transcribed in upstream regulatory regions.

RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery comprising two RNA polymerase II-related RNA polymerases, called Pol IV and Pol V, as well as chromatin remodelers, transcription factors, and other novel proteins whose roles in the RdDM mechanism remain poorly understood. We have identified a new component of the RdDM machinery, DMS11 (defective in meristem silencing 11), which has a GHKL (gyrase, Hsp90, histidine kinase, MutL) ATPase domain. siRNAs accumulate in the dms11 mutant, and repressive epigenetic modifications undergo only modest reductions at target sequences. DMS11 interacts physically with another RdDM component, DMS3, an unusual structural maintenance of chromosomes (SMC) hinge domain-containing protein that lacks the ATPase motifs of authentic SMC proteins. The hinge region of DMS3 resembles that of the mammalian epigenetic factor SMCHD1, which also has a GHKL-type ATPase. In vitro, DMS11 has ATPase activity that is stimulated by DMS3. We suggest that DMS11 provides the missing ATPase function for DMS3 and that these proteins cooperate in the RdDM pathway to promote transcriptional repression. GHKL ATPases are thus emerging as new players in epigenetic regulation in plants and mammals.

RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points.