In eukaryotes with multiple small RNA pathways the mechanisms that channel RNAs within specific pathways are unclear. Here, we reveal the reactions that account for channeling in the siRNA biogenesis phase of the Arabidopsis RNA-directed DNA methylation pathway. The process begins with template DNA transcription by NUCLEAR RNA POLYMERASE IV (Pol IV) whose atypical termination mechanism, induced by nontemplate DNA basepairing, channels transcripts to the associated RNA-dependent RNA polymerase, RDR2. RDR2 converts Pol IV transcripts into double-stranded RNAs then typically adds an extra untemplated 3' terminal nucleotide to the second strands. The dicer endonuclease, DCL3 cuts resulting duplexes to generate 24 and 23nt siRNAs. The 23nt RNAs bear the untemplated terminal nucleotide of the RDR2 strand and are underrepresented among ARGONAUTE4-associated siRNAs.Collectively, our results provide mechanistic insights into Pol IV termination, Pol IV-RDR2 coupling and RNA channeling from template DNA transcription to siRNA guide strand/passenger strand discrimination.
KeywordsNuclear RNA Polymerase IV, noncoding RNA, RNA silencing, RNA-directed DNA methylation, transcription termination, dicing, ncRNA processing mismatched nucleotides and the short size of Pol IV transcripts (Zhai et al., 2015). However, RDR2 has terminal transferase activity that can add untemplated nucleotides to RNA 3' ends, suggesting an alternative hypothesis for the mismatched nucleotides (Blevins et al., 2015).Whether RDR2's terminal transferase activity might act on Pol IV transcripts, RDR2 transcripts, or both is unknown.Pol IV transcribes single-stranded (ss) DNA but lacks significant activity using sheared double-stranded (ds) DNA in vitro Onodera et al., 2005). Our current study provides an explanation, showing that when Pol IV is engaged in transcription of a ssDNA strand it terminates within 12-18 nt after encountering dsDNA. Importantly, Pol IV termination induced in this manner is key to channeling the transcript to RDR2, which converts the Pol IV transcript into dsRNA. We show that single-stranded M13 bacteriophage DNA can template siRNA biogenesis in vitro, with Pol IV synthesizing first strand transcripts, RDR2 synthesizing the second strands and DCL3 dicing the duplexes into both 24 bp and 23bp siRNAs, as in vivo.DNA-mismatched nucleotides are present at precursor and siRNA 3' ends, as in vivo, with sequencing showing these to be hallmarks of RDR2 transcripts, not Pol IV transcripts.Collectively, the reactions of Pol IV, RDR2 and DCL3 are necessary and sufficient for siRNA biogenesis and can account for the short length of P4R2 RNAs, the origin of untemplated 3' nucleotides, the mechanism of Pol IV-RDR2 coupling and the channeling of RNAs from DNA template transcription to siRNA strand discrimination.