Methylation patterns of HLA-DR alpha genes in six mononuclear cell lines

The relationship between DNA methylation and HLA-DR alpha gene expression was investigated in six mononuclear cell lines. RPMI-4265 (B cell) and HUT-78 (T cell) constitutively express HLA-DR. HL-60 (myelomonocyte) and U-937 (monocyte) can be induced to express HLA-DR. Jurkat and Molt-4 (T cells) do not and cannot be induced to express HLA-DR. Based on the known nucleotide sequence of the HLA-DR alpha gene, methylation-sensitive restriction endonucleases Msp I, Hpa II, Hha I, Ava I, Hae II, and Sma I were used to detect the CpG methylation in three regions of the HLA-DR alpha gene: the 5'flanking region, the exon 1 region, and the coding region containing exons 2, 3, 4, and 5. This precise mapping of CpG methylation yielded no correlation between DNA hypomethylation and HLA-DR alpha gene expression. In all cell lines, exon 1 region is hypomethylated, whereas 5' and coding regions are hypermethylated. Whereas hypermethylation of the coding region does not block transcription, hypomethylation of the exon 1 region may be essential but is clearly not sufficient for HLA-DR alpha gene transcription. This exon 1 region demethylation may result in an open (deoxyribonuclease I hypersensitive) chromatin conformation around the promoter where trans-acting regulatory factors presumably bind and initiate HLA-DR alpha transcription. In the course of this study, a novel Msp I polymorphism in the intron 1 of the HLA-DR alpha gene was found.