Fig. 4

The plant heterochromatic and trans-acting siRNA biogenesis pathways. Heterochromatic siRNAs: Pol IV transcribes the genomic DNA into ssRNA [55, 58]. The ssRNA is made into long dsRNA by RNA-dependent RNA polymerase 2 (RDR2) [46]. The long dsRNA is processed by DCL3 to yield siRNA duplexes that are 3′ methylated by HEN1 (as with miRNAs). One strand from the siRNA duplex is incorporated into the RNAi-induced transcriptional silencing (RITS) complex with the aid of AGO4 and the other strand is degraded [60]. Twenty-four-nucleotide heterochromatic siRNAs associated with the RITS complex facilitate chromatin modification and transcriptional silencing. Trans-acting siRNAs: The trans-acting siRNA (TAS) precursor is transcribed by Pol II. AGO1 facilitates miRNA directed cleavage of the TAS precursor. The 5′ cleavage product or 3′ cleavage product is used by RNA-dependent RNA polymerase 6 (RDR6) and suppressor of gene silencing 3 (SGS3) as a template to produce dsRNA [6, 9, 10, 59]. The dsRNA is cleaved in a phased pattern every 21 nt by DCL4 [6, 7, 10, 11]. An interaction between DCL4 and dsRNA binding protein 4 (DRB4) is involved in the processing of the 21 nt ta-siRNAs [11, 85]. The ta-siRNAs are methylated at the 3′ ends by HEN1 and then guided by an AGO protein (AGO1 and possibly another AGO protein) to their targets for cleavage [20, 86]. The cleavage products may be degraded or may serve as a resource for additional ta-siRNAs [87, 88].