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Pinpointing a puzzling polymerase

Nature Structural & Molecular Biology volume 19, pages 865–866 (2012)Cite this article

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One of the surprising discoveries in the genomic age was the presence in plant genomes of two noncanonical DNA-dependent RNA polymerases involved in small RNA–mediated gene silencing. Two recent studies map the binding sites of RNA polymerase V, uncovering new mysteries concerning the targeting and function of this enigmatic enzyme.

RNA polymerase IV (Pol IV) and RNA polymerase V (Pol V) are required for RNA-directed DNA methylation (RdDM) in plants1. Pol IV initiates the production of 24-nucleotide (nt) short interfering RNAs (p4-siRNAs) that guide Argonaute effectors to nascent transcripts produced by Pol V. In turn, Pol V transcripts nucleate the assembly of a silencing complex that includes an Argonaute protein and the de novo DNA methyltransferase DRM2. Methylation generated by DRM2 represses transposable elements and regulates the expression of some protein-coding genes2. Pol IV and Pol V activity is inferred at loci producing p4-siRNAs, but Pol V transcription has been detected at only a handful of sites. Using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), two research groups recently described the binding sites of Pol V genome wide, providing the first comprehensive maps of transcription by a noncanonical RNA polymerase3,4.

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Figure 1: Pol V binding sites.

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  1. Rebecca A. Mosher is at the School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.,

    Rebecca A Mosher

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  1. Rebecca A Mosher
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Correspondence to Rebecca A Mosher.

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Mosher, R. Pinpointing a puzzling polymerase. Nat Struct Mol Biol 19, 865–866 (2012). https://doi.org/10.1038/nsmb.2374

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