Figure 1: Polymerase IV (Pol IV) initiates the RNA-directed DNA methylation (RdDM) pathway (1), generating transcripts that are then copied into double-stranded RNA (dsRNA) by RNA-DEPENDENT POLYMERASE 2 (RDR2) (2). The putative chromatin remodeler and/or helicase CLSY1 assists in one or more of these steps. DICER-LIKE 3 (DCL3) cleaves the dsRNA into 24-nucleotide small interfering RNA (siRNA) duplexes (3) that are methylated by HEN1 (4). A single strand of the siRNA duplex associates with AGO4 to form an RNA-induced silencing complex (RISC) (5).
Independent of siRNA biogenesis, Pol V transcription is assisted by the DDR complex (DRD1, DMS3, and RDM1) and DMS4 (6). AGO4 binds Pol V transcripts via base-pairing with the siRNA and is stabilized by AGO4 interaction with the NRPE1 carboxyl-terminal domain (CTD) and KTF1, which also binds RNA (7). IDN2 may stabilize Pol V transcriptsiRNA pairing (8). The RDM1 protein of the DDR complex binds AGO4 and the de novo cytosine methyltransferase DRM2, bringing them to Pol Vtranscribed regions (9). Histone modifications resulting from the RdDM pathway include the removal of activating marks (acetylation) and the establishment of repressive marks (deacetylation), facilitating transcriptional silencing (10).
See also Haag, J.R., and http://www.ncbi.nlm.nih.gov/pubmed?term=%22Pikaard%20CS%22%5BAuthor%5D"Pikaard, C.S. 2011. Nature Reviews Molecular Cell Biology 12:483492.