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A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation

Nature Genetics volume 40, pages 670–675 (2008)Cite this article

Abstract

RNA-directed DNA methylation (RdDM) is a process in which dicer-generated small RNAs guide de novo cytosine methylation at the homologous DNA region1,2. To identify components of the RdDM machinery important for Arabidopsis thaliana development, we targeted an enhancer active in meristems for methylation, which resulted in silencing of a downstream GFP reporter gene. This silencing system also features secondary siRNAs, which trigger methylation that spreads beyond the targeted enhancer region. A screen for mutants defective in meristem silencing and enhancer methylation retrieved six dms complementation groups, which included the known factors DRD1 (ref. 3; a SNF2-like chromatin-remodeling protein) and Pol IVb subunits4,5. Additionally, we identified a previously unknown gene DMS3 (At3g49250), encoding a protein similar to the hinge-domain region of structural maintenance of chromosomes (SMC) proteins. This finding implicates a putative chromosome architectural protein that can potentially link nucleic acids6 in facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA methylation.

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Figure 1: Transgene constructs and silenced phenotype.
Figure 2: Bisulfite sequence analysis of DNA methylation.
Figure 3: RNA analysis.
Figure 4: Hypothetical model for production of secondary siRNAs.
Figure 5: Domain structure of DMS3 (At3g49250).
Figure 6: Loss of methylation and derepression of RdDM targets in a dms3 mutant.

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Acknowledgements

This work is supported by the European Science Foundation (ESF) under the EUROCORES Programme EuroDyna, through contract no. ERAS-CT-2003-980409 of the European Commission, DG Research, FP6, and the Austrian Fonds zur Förderung der wissenschaftlichen Forschung (FWF) (grant I26-B03), and the European Union (contract HPRN-CT-2002-00257). D.P.K. acknowledges support by the Vienna Science and Technology Fund (WWTF), Austrian Center of Biopharmaceutical Technology (ACBT), Austrian Research Center Seibersdorf and Baxter AG.

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Author notes

  1. Etienne Bucher

    Present address: Present address: Laboratory of Plant Genetics, University of Geneva, CH-1211 Geneva 4, Switzerland.,

  2. Tatsuo Kanno and Etienne Bucher: These authors contributed equally to this work.

Authors and Affiliations

  1. Gregor Mendel Institute for Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohrgasse 3, Vienna, A-1030, Austria

    Tatsuo Kanno, Etienne Bucher, Lucia Daxinger, Bruno Huettel, Gudrun Böhmdorfer, Marjori Matzke & Antonius J M Matzke

  2. Department of Science, Research Group of Molecular Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, A-1210, Austria

    Wolfgang Gregor

  3. Department of Bioinformatics, Boku University Vienna, Muthgasse 18, Vienna, A-1190, Austria

    David P Kreil

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Contributions

M.M. and A.J.M.M. designed and supervised the study. A.J.M.M. made the constructs and silenced Arabidopsis line. E.B. carried out the mutant screen, bisulfite sequencing and preliminary mapping of dms1–dms5 mutations. T.K. identified and sequenced the dms1, dms2, dms3 and dms5 mutant alleles and analyzed nascent RNAs. L.D. analyzed small RNAs. B.H. analyzed reactivation of target sequences in the dms3 mutant. D.P.K. performed the bioinformatics analysis. M.M. wrote the paper with contributions by all coauthors.

Note: Supplementary information is available on the Nature Genetics website.

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Correspondence to Marjori Matzke.

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Supplementary Figures 1–7 and Supplementary Table 1 (PDF 812 kb)

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Kanno, T., Bucher, E., Daxinger, L. et al. A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation. Nat Genet 40, 670–675 (2008). https://doi.org/10.1038/ng.119

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