ULTRASTRUCTURAL ALLELIC VARIATION IN HLA-DQB1 PROMOTER ELEMENTS

Sequence variation among HLA class II promoter elements may contribute to functional differences in transcriptional regulation of different class II alleles, In addition to influencing the binding sites for nuc lear transcription factors, promoter polymorphism may also alter intri nsic structural properties of the DNA strands, such as conformation an d curvature, which influence the formation of stable transcription com plexes. We used SSCP analysis of PCR-amplified promoter regions from t he DQB1 locus to evaluate conformational polymorphism within DQ allele s. Distinct electrophoretic migration patterns of the SSCP products we re detected for six DQB1 alleles; analysis of the DQB10302 promoter, known to be associated with type 1 diabetes, showed no SSCP difference s between IDDM patients and normal controls. Using computer modeling b ased on a ''nearest-neighbor'' energy of predicted curvature theory, w e examined the effect of allelic promoter region sequence polymorphism on the predicted curvature of double-stranded DNA, and found distinct allelic differences in predicted DNA curvature, both in transcription al consensus binding sites and in regions located between binding site s. These data are consistent with a model in which intrinsic sequence variation in the promoter region results in ultrastructural difference s which may influence DNA bending and interactions with multimeric DNA -protein transcription complexes.