A two-step process for epigenetic inheritance in Arabidopsis

Mol Cell. 2014 Apr 10;54(1):30-42. doi: 10.1016/j.molcel.2014.02.019. Epub 2014 Mar 20.


In Arabidopsis, multisubunit RNA polymerases IV and V orchestrate RNA-directed DNA methylation (RdDM) and transcriptional silencing, but what identifies the loci to be silenced is unclear. We show that heritable silent locus identity at a specific subset of RdDM targets requires HISTONE DEACETYLASE 6 (HDA6) acting upstream of Pol IV recruitment and siRNA biogenesis. At these loci, epigenetic memory conferring silent locus identity is erased in hda6 mutants such that restoration of HDA6 activity cannot restore siRNA biogenesis or silencing. Silent locus identity is similarly lost in mutants for the cytosine maintenance methyltransferase, MET1. By contrast, pol IV or pol V mutants disrupt silencing without erasing silent locus identity, allowing restoration of Pol IV or Pol V function to restore silencing. Collectively, these observations indicate that silent locus specification and silencing are separable steps that together account for epigenetic inheritance of the silenced state.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / enzymology
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Cytosine / metabolism
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • DNA Methylation
  • DNA Transposable Elements
  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Epigenesis, Genetic*
  • Gene Expression Regulation, Enzymologic*
  • Gene Expression Regulation, Plant*
  • Genetic Loci
  • Genotype
  • Heredity
  • Histone Deacetylases / genetics*
  • Histone Deacetylases / metabolism
  • Mutation
  • Phenotype
  • RNA Interference*
  • RNA, Small Interfering / biosynthesis


  • Arabidopsis Proteins
  • DNA Transposable Elements
  • RNA, Small Interfering
  • Cytosine
  • MET1 protein, Arabidopsis
  • DNA (Cytosine-5-)-Methyltransferases
  • RNA polymerase IV, Arabidopsis
  • RNA polymerase V, Arabidopsis
  • DNA-Directed RNA Polymerases
  • HDA6 protein, Arabidopsis
  • Histone Deacetylases