Expression of the H2-Ea gene is modulated by a polymorphic transcriptional enhancer

In all vertebrates the major histocompatibility complex (MHC) class II genes are polymorphic in their coding regions as well as in their promoter control elements. This polymorphism correlates with a variability in peptide binding and a variability in transcriptional activities. There is, however, one exception to this rule, which is the mouse H2-Ea gene or the corresponding human DRA gene. So far and for unkown reasons no polymorphism has been observed in these loci. We sequenced the distal transcriptional control elements of the H2-Ea, H2-Eb, and H2-Ab genes from the mouse haplotypes H2d, H2k, H2q, and H2z, and in contrast to the promoter and coding regions a sequence polymorphism can be detected which is limited to the H2-Ea gene. In transfection experiments this polymorphism can be seen to influence haplotype-specifically the transcriptional activities in B cells. This finding strongly suggests an evolutionary pressure towards a haplotype-specific expression pattern in all four MHC class II genes. The genetic differences in control elements of MHC class II genes may well contribute to differential immune reactivities and to immune disorders like allergies or autoimmune diseases.