Regulation of HLA class II transcription is complex, with both locus-s
pecific and allele-specific polymorphisms associated with consensus re
gulatory region promoter elements. In order to evaluate the potential
function of allele-specific elements, HLA-DQB1 transcripts and in vivo
footprinting of the DQB1 promoter were studied in human cell lines in
ducible for HLA class II expression. In the heterozygous melanoma cell
line Me9229/18, differential expression was observed for two DQB1 all
eles. This variation was reflected in both steady-state and inducible
transcripts, although methylation patterns of the promoter elements we
re similar for both alleles. This in vivo allelic difference expressio
n, which correlates with previous studies of in vitro reporter gene tr
anscription, indicates the potential for functionally important differ
ences in tissue-specific and inducible expression attributable to prom
oter region polymorphism in HLA genes.