DNA CpG methylation inhibits binding of NF-κB proteins to the HIV-1 long terminal repeat cognate DNA motifs

The regulation of cellular or viral gene expression is directly influenced by the pattern of methylated cytosine residues localized in the DNA of enhancer/promoter sequences. The mechanism of transcriptional silencing has been explained on the basis of either an indirect model, in which densely methylated DNA is recognized by proteins that may displace crucial transcription factors, or a direct model, in which binding of a single transcription protein is prevented by the presence of a methylated CpG dinucleotide localized in a sensitive region of a DNA motif. In this study, we have determined that methylation of the core CpG dinucleotide located within the NF-κB repeated motifs of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat can inhibit the binding of the NF-κB protein complex from crude nuclear extracts or from purified bovine spleen and specifically inhibit the binding of recombinant p50 protein. We have used the electrophoretic mobility shift assay (EMSA) and DNaseI footprinting analysis to demonstrate that binding of the NF-κB proteins to their cognate motifs can be inhibited via the direct model proposed for methylation-mediated inhibition of DNA-protein interaction.