Methylation of the HLA-DR alpha gene is positively correlated with expression

We have evaluated the state of methylation of the HLA-DR alpha and HLA-DQ alpha genes in a set of melanoma cell lines which differ in their characteristic expression of these genes and a matching B-cell line. In contrast to the prevailing assumption that genes are methylated when their expression is repressed, we found that one particular site within the first intron of the DR alpha gene is methylated when the cells express HLA-DR or are inducible for its expression. In addition, the HLA-DQ alpha gene may be methylated when it is expressed in a given cell. These findings extend recent observations from other groups that show mixed negative and positive correlations between methylation and class II gene expression, because the cell lines we compared are all from the same individual and, except for the B-cell line, are clonally derived. We tested whether methylation at the identified site was required for expression of the gene by treating the cell lines with the demethylating agent, 5'-azacytidine. Unexpectedly, the treatment actually increases transcription of the DR alpha gene in cell lines already expressing HLA-DR. Possibly other genes that regulate class II expression are demethylated by the treatment and consequently mask any direct effects of the treatment on DR alpha expression. Thus, methylation of the DR alpha gene does not appear to be a simple mechanism for controlling expression. Although our data suggest that methylation of HLA class II genes is not required absolutely for transcription of the DR alpha gene, we believe that chromatin structure in the vicinity of the site may be altered by methylation and thereby exert control.