Epigenetic mechanism of rRNA gene silencing: temporal order of NoRC-mediated histone modification, chromatin remodeling, and DNA methylation

Mol Cell Biol. 2005 Apr;25(7):2539-46. doi: 10.1128/MCB.25.7.2539-2546.2005.


Epigenetic control mechanisms silence about half of the rRNA genes in eukaryotes. Previous studies have demonstrated that recruitment of NoRC, a SNF2h-containing remodeling complex, silences rRNA gene transcription. NoRC mediates histone H4 deacetylation, histone H3-Lys9 dimethylation, and de novo DNA methylation, thus establishing heterochromatic features at the rRNA gene promoter. Here we show that inhibition of any of these activities alleviates NoRC-dependent silencing, indicating that these processes are intimately linked. We have studied the temporal order of epigenetic events at the rRNA gene promoter during gene silencing and demonstrate that recruitment of NoRC by TTF-I is a prerequisite for the deacetylation of histone H4 and the dimethylation of histone H3-Lys9. Inhibition of histone deacetylation prevents DNA methylation, while inhibition of DNA methylation does not affect histone modification. Importantly, ATP-dependent chromatin remodeling is required for methylation of a specific CpG dinucleotide within the upstream control element of the rRNA gene promoter, and this modification impairs preinitiation complex formation. The results of this study reveal a clear hierarchy of epigenetic events that control de novo DNA methylation and lead to silencing of RNA genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Adenosine Triphosphate / pharmacology
  • Animals
  • Cell Line
  • Chromatin Assembly and Disassembly*
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • CpG Islands / genetics
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Gene Silencing*
  • Histones / metabolism*
  • Humans
  • Iron-Binding Proteins / metabolism
  • Mice
  • Multiprotein Complexes / metabolism*
  • Nucleosomes / metabolism
  • Promoter Regions, Genetic / genetics
  • RNA, Ribosomal / genetics*
  • Transcription, Genetic / genetics


  • BAZ2A protein, human
  • Baz2a protein, mouse
  • Chromosomal Proteins, Non-Histone
  • Histones
  • Iron-Binding Proteins
  • Multiprotein Complexes
  • Nucleosomes
  • RNA, Ribosomal
  • Adenosine Triphosphate