Figure 1. The four best characterized endogenous RNA silencing pathways in Arabidopsis plants. The miRNA pathway depicted on the top is initiated with the processing of primary miRNA (pri-miRNA) in two sequential steps to generate mature miRNA. This process is catalysed by DCL1 with the help of HYL1, a DRB family protein. The miRNAs are then recruited by AGO1 to guide the cleavage of cognate RNAs. The tasiRNA pathway (middle, right) initiates with a TAS transcript that is cleaved at one or both ends by miRNA-guided slicing (shown as dotted arrow). This transcript then serves as template for RDR6 to produce dsRNA, which in turn is processed into mature tasiRNA by DCL4 with the help of DRB4. tasiRNAs can be recruited by AGO1 or AGO7 to direct target cleavage. The cis-siRNA pathway (bottom) regulates the gene expression through the modification of the homologous chromosomal DNA. In this pathway, NRPD, a DNA-dependent RNA polymerase unique to plants, is likely responsible for making the initial transcript from the repetitive DNA to be modified. This NRPD transcript is then copied by RDR2 into dsRNA, the later being processed by DCL3 into 24 nt cis-siRNAs. The nat-siRNA pathway (middle, left) is initiated only when both of the genes that are positioned tail-to-tail are actively transcribed, creating dsRNA at their 3¢ ends. After the initial processing by DCL2, the subsequent steps are similar to that of tasiRNA pathway.

Figure 2. VSRs from diverse viruses target different steps of the RNA silencing pathway. See main text for details.