Fig. 3. Biogenesis of siRNAs and hcRNAs. (A) Biogenesis of different classes of siRNA (see text for more details). Endogenous siRNAs are transcribed in the nucleus, whereas exogenous siRNAs are either chemically synthesized or virally derived. siRNAs are further processed by RNase III enzymes, such as Dicer. tasiRNAs are specific to plants and, after initial cleavage by specific miRNAs (red) and complementary strand synthesis by the RNA-dependent RNA polymerase (RdRp) RDR6, are processed by the Dicer DCL4. They are then phosphorylated (P) and subsequently methylated (me) by the RNA methyltransferase HEN1. In C. elegans and plants, secondary siRNAs participate in a signal amplification loop. In plants, the cleaved mRNA is converted into dsRNA by a RdRP, and is further processed by Dicer (the RNase III in green). In C. elegans, secondary siRNAs have a 5' di- or triphosphate group and associate with Class 3 Ago/Piwi protein members, Sago-1/Sago-2, leading to target mRNA (black) cleavage. (B) Biogenesis of hcRNAs (see also text for more details). In the yeast S. pombe and in plants, hcRNAs are processed by RNase III enzymes. In S. pombe, hcRNAs associate with Ago1 and form the RNA-induced transcriptional gene silencing (RITS) complex, which participates in RNA-directed RNA polymerase complex (RDRC) formation and histone (gray circles) methylation. In plants, hcRNAs form a complex with AGO4, which participates in DNA methylation. Chp1, chromodomain protein 1; Clr4, cryptic loci regulator 4; Cid12, caffeine induced death protein; DRD1, defective in RNA-directed DNA methylation 1 (an SNF2-like chromatin remodeling protein); DRM2, domain rearranged methyltransferase 2; Hrr1, a helicase required for RNAi-mediated heterochromatin assembly; Rdp1, RNA-directed RNA polymerase 1; Tas3, targeting complex subunit 3.