Figure 3. Mechanisms of siRNA Silencing.
During canonical RNAi (lower right), siRISC recognizes a perfectly complementary mRNA, leading to Ago-catalyzed mRNA cleavage at a single site within the duplex. After cleavage, functional siRISC is regenerated, whereas the mRNA fragments are further degraded. siRNAs are also capable of recognizing targets with imperfect complementarity (upper right). In some cases, they can silence targets by miRNA-like mechanisms involving translational repression and exonucleolytic degradation, though the frequency with which natural siRNAs use these pathways is not clear. Finally, siRISC can direct heterochromatin formation (left) by associating with nascent transcripts and RNA polymerases (RNA Pol II in S. pombe and RNA Pol IV/V in A. thaliana). In plants, target engagement leads to the association or activation of a DNA methyltransferase (DMT) that methylates the DNA (lower left), leading to heterochromatin formation. In S. pombe and probably in animals (upper left), the pathway involves a histone methyltransferase (HMT) that methylates Lys9 of histone H3 (data not shown), thereby inducing heterochromatinization. In most eukaryotes other than insects and mammals, target recognition by siRISC induces the synthesis of secondary dsRNAs and siRNAs by RdRP enzymes (lower middle). The secondary dsRNAs are processed by Dicer into siRNAs, which add to the pool of siRISC. In nematodes, many of the secondary siRNAs arise as single-stranded, unprimed transcripts with 5′-triphosphates and do not require Dicer processing.