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Biology 2013, 2(4), 1210-1223;

Pol IV-Dependent siRNA Production is Reduced in Brassica rapa

School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
Author to whom correspondence should be addressed.
Received: 27 August 2013 / Revised: 24 September 2013 / Accepted: 25 September 2013 / Published: 30 September 2013
(This article belongs to the Special Issue Insights from Plant Genomes)
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Plants produce a diverse array of small RNA molecules capable of gene regulation, including Pol IV-dependent short interfering (p4-si)RNAs that trigger transcriptional gene silencing. Small RNA transcriptomes are available for many plant species, but mutations affecting the synthesis of Pol IV-dependent siRNAs are characterized only in Arabidopsis and maize, leading to assumptions regarding nature of p4-siRNAs in all other species. We have identified a mutation in the largest subunit of Pol IV, NRPD1, that impacts Pol IV activity in Brassica rapa, an agriculturally important relative of the reference plant Arabidopsis. Using this mutation we characterized the Pol IV-dependent and Pol IV-independent small RNA populations in B. rapa. In addition, our analysis demonstrates reduced production of p4-siRNAs in B. rapa relative to Arabidopsis. B. rapa genomic regions are less likely to generate p4-siRNAs than Arabidopsis but more likely to generate Pol IV-independent siRNAs, including 24 nt RNAs mapping to transposable elements. These observations underscore the diversity of small RNAs produced by plants and highlight the importance of genetic studies during small RNA analysis. View Full-Text
Keywords: Brassica rapa; RNA Polymerase IV; RNA-directed DNA methylation; siRNA Brassica rapa; RNA Polymerase IV; RNA-directed DNA methylation; siRNA

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Huang, Y.; Kendall, T.; Mosher, R.A. Pol IV-Dependent siRNA Production is Reduced in Brassica rapa. Biology 2013, 2, 1210-1223.

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