Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection

Cell. 1992 May 29;69(5):769-80. doi: 10.1016/0092-8674(92)90289-o.


Integration of retroviral DNA can serve as a paradigm for cellular functions that are affected by the packaging of DNA into chromatin. We have used a novel polymerase chain reaction-based assay to survey DNA and chromatin for the precise distribution of many integration sites. Integration into naked DNA targets is non-uniform, implying a nucleotide sequence bias. In chromatin, integration occurs preferentially at positions where the major groove is on the exposed face of the nucleosomal DNA helix, generating a 10 bp periodic spacing of preferred sites. Chromatin assembly enhances the reactivity of many sites, so that integration occurs most frequently at sites in nucleosomal, rather than nucleosome-free, regions of minichromosomes. In contrast, integration is prevented in a region occupied by a site-specific DNA-binding protein. Comparisons of integration events mediated by viral nucleoprotein complexes or by two different retroviral integrases show that the integration machinery also affects target site selection.

Publication types

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

MeSH terms

  • Base Sequence
  • DNA, Viral / metabolism*
  • DNA-Binding Proteins / metabolism
  • Leukemia Virus, Murine / metabolism*
  • Molecular Sequence Data
  • Nucleosomes / metabolism*
  • Oligodeoxyribonucleotides / genetics
  • Polymerase Chain Reaction
  • Virus Integration / genetics*


  • DNA, Viral
  • DNA-Binding Proteins
  • Nucleosomes
  • Oligodeoxyribonucleotides