Fig. 1

A simple model describes the biosynthesis and assembly of small RNAs. ① MIR genes are transcribed by RNA Polymerase II (RNA Pol II) into primary miRNAs (pri-miRNAs). Pri-miRNAs form an imperfect fold-back structure and then are processed into a stem-loop-structured precursor miRNAs (pre-miRNAs). The pre-miRNAs are further processed into 21- or 24-nt miRNA duplexes by the complex that mainly includes DCL1 or DCL3, HYPONASTICLEAVES1(HYL1) and SERRATE (SE). The overhang ends of miRNA duplex are methylated by HUA ENHANCER 1 (HEN1) to increase stability and then one strand of the miRNA duplex is loaded into AGO proteins to form RNA-induced gene silencing complex (RISC) in the cytoplasm or the nucleus. The 21-nt miRNAs exploit two pathways to incorporate into AGO1 protein. One, the miRNA duplex is exported to the cytoplasm via HASTY channel, then one strand of the duplex is loaded into AGO1 to form RISC. Two, some 21-nt miRNAs could be directly loaded into AGO1 to form RISC in the nucleus and the RISC is exported to the cytoplasm. Then, the RISCs repress gene expression via mRNA cleavage, or translational inhibition. Besides, 24-nt miRNAs are loaded into AGO4 in the cytoplasm and reenter into the nucleus to mediate DNA methylation by recruiting DOMAINS REARRANGED METHYLTRANSFERASE (DRM). ② The transposons or repetitive elements are transcribed by an unknown RNA Polymerase (RNA Pol?), then these transcripts are used as templates by RDR2 to synthesize double stranded RNAs (dsRNAs). Later, the dsRNAs are processed into 24-nt repeat-associated siRNAs (ra-siRNAs) by DCL3 and are methylated by HEN1 at 3′-terminal. Then one strand of ra-siRNAs is loaded into AGO4 to form RISC to mediate DNA methylation of target gene by recruiting the methyltransferases DRM1 and DRM2. ③ The specific intergenic regions are transcribed by RNA Pol II to generate the TAS precursors. The TAS precursors are targeted by some specific miRNA-AGO1 complex (such as miR390-AGO1 or miR173-AGO1) and are cleaved into fragments, then the 5′ or 3′ fragments of TAS precursors are exploited by RDR6 and SGS3 as the templates to synthesize the dsRNAs. The dsRNAs are imported into the nucleus and processed by DCL4 and DRB4 into 21-nt phased, trans-acting siRNAs (ta-siRNAs). After the methylation of ta-siRNAs at 3′-terminal, ta-siRNAs are exported into the cytoplasm and one strand of the ta-siRNAs is loaded into AGO1 or AGO7 to form RISC to suppress gene expression