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Atypical RNA polymerase subunits required for RNA-directed DNA methylation

Nature Genetics volume 37, pages 761765 (2005) | Download Citation

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Abstract

RNA-directed DNA methylation, one of several RNA interference–mediated pathways in the nucleus1, has been documented in plants2,3 and in human cells4,5. Despite progress in identifying the DNA methyltransferases, histone-modifying enzymes and RNA interference proteins needed for RNA-directed DNA methylation1, the mechanism remains incompletely understood. We screened for mutants defective in RNA-directed DNA methylation and silencing of a transgene promoter in Arabidopsis thaliana and identified three drd complementation groups6. DRD1 is a SNF2-like protein6 required for RNA-directed de novo methylation. We report here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants. DRD3 is a functionally diversified homolog of NRPD1a or SDE4, identified in a separate screen for mutants defective in post-transcriptional gene silencing7,8. The identical DNA methylation patterns observed in all three drd mutants suggest that DRD proteins cooperate to create a substrate for RNA-directed de novo methylation.

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Acknowledgements

We thank C. Pikaard, A. Herr and D. Baulcombe for discussions and preprints and the Monsanto Company for marker information. This work was supported by funds from the Austrian Fonds zur Förderung der wissenschaftlichen Forschung.

Author information

Author notes

    • M Florian Mette

    Present address: IPK Gatersleben, Correnstrasse 3, D-06466 Gatersleben, Germany.

Affiliations

  1. Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, UZA2, Pharmazie Zentrum, Althanstrasse 14/2D-541, A-1090 Vienna, Austria.

    • Tatsuo Kanno
    • , Bruno Huettel
    • , M Florian Mette
    • , Werner Aufsatz
    • , Estelle Jaligot
    • , Lucia Daxinger
    • , Marjori Matzke
    •  & Antonius J M Matzke
  2. WWTF Vienna Science Chair of Bioinformatics, Department of Biotechnology c/o IAM, Muthgasse 18, A-1190 Vienna, Austria.

    • David P Kreil

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Marjori Matzke.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Bisulfite sequencing.

  2. 2.

    Supplementary Fig. 2

    Sequence comparisons.

  3. 3.

    Supplementary Fig. 3

    DRD protein-dependent RNA-directed de novo methylation.

  4. 4.

    Supplementary Fig. 4

    AtSN1 methylation analysis.

  5. 5.

    Supplementary Table 1

    Oligonucleotides and small RNA probes.

  6. 6.

    Supplementary Methods

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DOI

https://doi.org/10.1038/ng1580

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