Atypical RNA polymerase subunits required for RNA-directed DNA methylation

Nat Genet. 2005 Jul;37(7):761-5. doi: 10.1038/ng1580. Epub 2005 May 29.


RNA-directed DNA methylation, one of several RNA interference-mediated pathways in the nucleus, has been documented in plants and in human cells. Despite progress in identifying the DNA methyltransferases, histone-modifying enzymes and RNA interference proteins needed for RNA-directed DNA methylation, 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 groups. DRD1 is a SNF2-like protein 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 silencing. 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / enzymology*
  • Arabidopsis / genetics
  • DNA Methylation*
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism*
  • Gene Silencing*
  • Molecular Sequence Data
  • Mutation
  • Plants, Genetically Modified
  • Promoter Regions, Genetic
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • RNA, Plant / genetics
  • RNA, Plant / metabolism*


  • Protein Subunits
  • RNA, Plant
  • RNA polymerase IV, Arabidopsis
  • DNA-Directed RNA Polymerases

Associated data

  • GENBANK/AY927744