Evidence for methylation as a regulatory mechanism in HLA-DR alpha gene expression

We examined the possibility that one mechanism for controlling HLA-DR alpha gene expression occurs through DNA hypomethylation. We employed the restriction enzyme Hpa II, which recognizes the sequence 5'CCGG3' but not 5'CmCGG3', to study DNA methylation. We first compared a DR-positive B lymphoblastoid cell line (LCL) with an isogenic DR-negative T-LCL. Using a genomic probe for the DR alpha gene, we showed that an Hpa II digestion of DNA from the B-LCL resulted in bands of lower molecular weight than that of the T-LCL. This indicates that the B-LCL DR gene is hypomethylated relative to the T-LCL gene. Demethylation of the gene from the B-LCL is incomplete, suggesting that complete demethylation is not required for its expression. We also examined somatic cell hybrids of T-LCL and B-LCL since the DR alpha gene, which is inactive in the T-LCL, is expressed in the hybrids, providing a system to study DR alpha gene induction. We examined the hybrid line 174 X CEM.T1, which contains and expresses solely the DR alpha gene from the T-LCL parent since both copies of the DR alpha gene from the B-LCL parent, 174, are deleted. The expressed DR alpha gene from the hybrid was compared with the unexpressed gene from the T-LCL parental line, and again an association between DR alpha gene expression and DNA hypomethylation was observed. In contrast to the DR alpha gene from B-LCL, which is not completely demethylated, the DR alpha gene in this hybrid line is not methylated at either of the Msp I sites covered by our probe. This suggests that different regulatory mechanisms operating through DNA methylation may be involved in the expression of DR alpha genes from T-LCL and B-LCL. Examination of another hybrid line which has DR alpha genes from both parental lines supports this contention. The implications of these findings are discussed.