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A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

Zhai, Jixian, Bischof, Sylvain, Wang, Haifeng, Feng, Suhua, Lee, Tzuu-fen, Teng, Chong, Chen, Xinyuan, Park, Soo Young, Liu, Linshan, Gallego-Bartolome, Javier, Liu, Wanlu, Henderson, Ian R., Meyers, Blake C., Ausin, Israel, Jacobsen, Steven E.
Cell 2015 v.163 pp. 445-455
Arabidopsis thaliana, DNA, DNA methylation, DNA-directed RNA polymerase, biogenesis, models, nucleotides, small interfering RNA
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.