Retrovirus silencing, variegation, extinction, and memory are controlled by a dynamic interplay of multiple epigenetic modifications

Mol Ther. 2004 Jul;10(1):27-36. doi: 10.1016/j.ymthe.2004.04.007.


Retrovirus silencing in stem cells produces silent or variegated provirus. Additional memory and extinction mechanisms act during differentiation. Here we show that retrovirus is silent or variegated in mouse embryonic stem (ES) cells that are de novo methyltransferase (dnmt3a and dnmt3b) null. Memory is maintained during differentiation, and extinction occurs on variegated retrovirus, indicating that DNA methylation is dispensable for all forms of retrovirus silencing. Silent and variegated provirus are marked by hypoacetylated histone H3 and bound H1. In wild-type ES cells, silent and variegated proviruses are methylated and bound by hypoacetylated H3, MeCP2, and less H1. Silencing, variegation, and extinction are partially reactivated by 5-AzaC in this context. Lentivirus vectors are also silent or variegated, marked by silent chromatin, and exhibit memory and extinction. We conclude that the universal epigenetic mark of retrovirus silencing is silent chromatin established via the dynamic interplay of multiple epigenetic modifications that include but do not require DNA methylation. A molecular mechanism of competitive H1 and MeCP2 binding may account for this epigenetic interplay, and a model for variegation is discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Azacitidine / pharmacology
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • DNA / chemistry
  • DNA / metabolism
  • DNA Methylation / drug effects
  • DNA Restriction Enzymes / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Epigenesis, Genetic*
  • Gene Expression Regulation, Viral*
  • Gene Silencing*
  • Genetic Therapy / methods
  • Green Fluorescent Proteins / analysis
  • Green Fluorescent Proteins / genetics
  • Histones / genetics
  • Histones / metabolism
  • Methyl-CpG-Binding Protein 2
  • Mice
  • Phosphoglycerate Kinase / analysis
  • Phosphoglycerate Kinase / genetics
  • Phosphoglycerate Kinase / metabolism
  • Proviruses / genetics
  • Proviruses / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Retroviridae / genetics*
  • Retroviridae / metabolism
  • Stem Cells / metabolism
  • Stem Cells / virology


  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • Histones
  • Mecp2 protein, mouse
  • Methyl-CpG-Binding Protein 2
  • Repressor Proteins
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins
  • DNA
  • Phosphoglycerate Kinase
  • DNA Restriction Enzymes
  • McrBC endonuclease
  • Azacitidine