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Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis


Most eukaryotes produce small RNA (sRNA) mediators of gene silencing that bind to Argonaute proteins and guide them, by base pairing, to an RNA target. MicroRNAs (miRNAs) that normally target messenger RNAs for degradation or translational arrest are the best-understood class of sRNAs. However, in Arabidopsis thaliana flowers, miRNAs account for only 5% of the sRNA mass and less than 0.1% of the sequence complexity. The remaining sRNAs form a complex population of more than 100,000 different small interfering RNAs (siRNAs) transcribed from thousands of loci1,2,3,4,5. The biogenesis of most of the siRNAs in Arabidopsis are dependent on RNA polymerase IV (PolIV), a homologue of DNA-dependent RNA polymerase II2,3,6. A subset of these PolIV-dependent (p4)-siRNAs are involved in stress responses, and others are associated with epigenetic modifications to DNA or chromatin; however, the biological role is not known for most of them. Here we show that the predominant phase of p4-siRNA accumulation is initiated in the maternal gametophyte and continues during seed development. Expression of p4-siRNAs in developing endosperm is specifically from maternal chromosomes. Our results provide the first evidence for a link between genomic imprinting and RNA silencing in plants.

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Figure 1: p4-siRNAs accumulate to high concentrations in seeds during early embryogenesis.
Figure 2: p4-siRNA expression in the zygote requires maternal NRPD1A.
Figure 3: p4-siRNA expression in developing seeds is uniparental genome-wide.
Figure 4: Uniparental expression of p4-siRNAs is specific to the seed.

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We thank I. Furner for met1-1 seed and A. Davis for photography. This work was supported by the Gatsby Charitable Foundation, the European Union Sixth Framework Programme Integrated Project SIROCCO (grant LSHG-CT-2006-037900), a postdoctoral fellowship from the National Science Foundation (to R.A.M.), and Commonwealth and NSERC Scholarships (to C.W.M.). D.C.B. is funded as a Royal Society Research Professor.

Author Contributions Experiments were designed by R.A.M. and D.C.B. and executed by R.A.M. with assistance from C.W.M. Bioinformatic and statistical analyses were performed by K.A.K., R.M.D. and D.J.S. The manuscript was prepared by R.A.M. and D.C.B.

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Correspondence to David C. Baulcombe.

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Deep sequencing libraries are deposited in NCBI GEO (GSE15348).

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This file contains Supplementary Notes, Supplementary Tables S1-S3, Supplementary Figures S1-S4 with Legends and Supplementary References. (PDF 960 kb)

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Mosher, R., Melnyk, C., Kelly, K. et al. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460, 283–286 (2009).

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