Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells

Nat Struct Mol Biol. 2004 Nov;11(11):1068-75. doi: 10.1038/nsmb840. Epub 2004 Oct 3.


Transcriptional silencing in mammals is often associated with promoter methylation. However, a considerable number of genomic methylated CpGs exist in transposable elements, which are frequently found in intronic regions. To determine whether intragenic methylation influences transcription efficiency, we used the Cre/loxP-based system, RMCE, to introduce a transgene, methylated exclusively in a region downstream of the promoter, into a specific genomic site. This methylation pattern was maintained in vivo, and yielded a clear decrease in transgene expression relative to an unmethylated control. Notably, RNA polymerase II (Pol II) was depleted exclusively in the methylated region, as was histone H3 di- and trimethylated on Lys4 and acetylated on Lys9 and Lys14. As the methylated region adopts a closed chromatin structure in vivo, we propose that dense intragenic DNA methylation in mammalian cells initiates formation of a chromatin structure that reduces the efficiency of Pol II elongation.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Blotting, Southern
  • Cell Nucleus / metabolism
  • Chromatin / chemistry*
  • Chromatin Immunoprecipitation
  • DNA Methylation*
  • Exons
  • Flow Cytometry
  • Gene Silencing
  • Genes, Reporter
  • Green Fluorescent Proteins / metabolism
  • Histones / chemistry
  • Humans
  • Introns
  • Lysine / chemistry
  • Models, Genetic
  • Plasmids / metabolism
  • Promoter Regions, Genetic
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sulfites / pharmacology
  • Transcription, Genetic
  • Transgenes


  • Chromatin
  • Histones
  • Sulfites
  • Green Fluorescent Proteins
  • Lysine
  • sodium bisulfite