Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans

EMBO Rep. 2010 Jan;11(1):52-8. doi: 10.1038/embor.2009.254. Epub 2009 Dec 4.


Epigenetic silencing of a fraction of ribosomal DNA (rDNA) requires association of the nucleolar chromatin-remodelling complex NoRC to 150-250 nucleotide RNAs (pRNA) that originate from an RNA polymerase I promoter located in the intergenic spacer separating rDNA repeats. Here, we show that NoRC-associated pRNA is transcribed from a sub-fraction of hypomethylated rRNA genes during mid S phase, acting in trans to inherit DNA methylation and transcriptional repression of late-replicating silent rDNA copies. The results reveal variability between individual rDNA clusters with distinct functional consequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Assembly and Disassembly / genetics
  • Chromatin Assembly and Disassembly / physiology
  • DNA Methylation / genetics
  • DNA Methylation / physiology
  • DNA, Intergenic / genetics*
  • DNA, Ribosomal / genetics*
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Epigenesis, Genetic / genetics*
  • Gene Silencing*
  • Mice
  • NIH 3T3 Cells
  • Promoter Regions, Genetic
  • RNA, Ribosomal / genetics*
  • RNA, Untranslated / genetics
  • RNA, Untranslated / metabolism
  • Repetitive Sequences, Nucleic Acid / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • S Phase
  • Transcription, Genetic*


  • DNA, Intergenic
  • DNA, Ribosomal
  • RNA, Ribosomal
  • RNA, Untranslated
  • DNA-Directed RNA Polymerases