Posttranscriptional regulation of HLA-A protein expression by alternative polyadenylation signals involving the RNA-binding protein syncrip

Genomic variation in the untranslated region (UTR) has been shown to influence HLA class I expression level and associate with disease outcomes. Sequencing of the 39UTR of common HLA-A alleles indicated the presence of two polyadenylation signals (PAS). The proximal PAS is conserved, whereas the distal PAS is disrupted within certain alleles by sequence variants. Using 39RACE, we confirmed expression of two distinct forms of the HLA-A 39UTR based on use of either the proximal or the distal PAS, which differ in length by 100 bp. Specific HLA-A alleles varied in the usage of the proximal versus distal PAS, with some alleles using only the proximal PAS, and others using both the proximal and distal PAS to differing degrees. We show that the short and the long 39UTR produced similar mRNA expression levels. However, the long 39UTR conferred lower luciferase activity as compared with the short form, indicating translation inhibition of the long 39UTR. RNA affinity pull-down followed by mass spectrometry analysis as well as RNA coimmunoprecipitation indicated differential binding of Syncrip to the long versus short 39UTR. Depletion of Syncrip by small interfering RNA increased surface expression of an HLA-A allotype that uses primarily the long 39UTR, whereas an allotype expressing only the short form was unaffected. Furthermore, specific blocking of the proximal 39UTR reduced surface expression without decreasing mRNA expression. These data demonstrate HLA-A allele-specific variation in PAS usage, which modulates their cell surface expression posttranscriptionally.