Cell
Volume 163, Issue 2, 8 October 2015, Pages 445-455
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Article
A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

https://doi.org/10.1016/j.cell.2015.09.032Get rights and content
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Highlights

  • Pol IV transcribes 30 to 40 nucleotide short RNAs to initiate siRNA biogenesis

  • P4RNAs mirror siRNAs in distribution, abundance, strand bias and 5′-A preference

  • P4RNAs feature TSSs similar to Pol II products

  • P4RNAs carry 3′-misincorporation that preferentially occurs at methylated cytosines

Summary

RNA-directed DNA methylation in Arabidopsis thaliana is driven by the plant-specific RNA Polymerase IV (Pol IV). It has been assumed that a Pol IV transcript can give rise to multiple 24-nt small interfering RNAs (siRNAs) that target DNA methylation. Here, we demonstrate that Pol IV-dependent RNAs (P4RNAs) from wild-type Arabidopsis are surprisingly short in length (30 to 40 nt) and mirror 24-nt siRNAs in distribution, abundance, strand bias, and 5′-adenine preference. P4RNAs exhibit transcription start sites similar to Pol II products and are featured with 5′-monophosphates and 3′-misincorporated nucleotides. The 3′-misincorporation preferentially occurs at methylated cytosines on the template DNA strand, suggesting a co-transcriptional feedback to siRNA biogenesis by DNA methylation to reinforce silencing locally. These results highlight an unusual mechanism of Pol IV transcription and suggest a “one precursor, one siRNA” model for the biogenesis of 24-nt siRNAs in Arabidopsis.

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Present address: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK