Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region Dagan Loisel,1 Matthew V. Rockman,2 Gregory A. Wray,3 and Susan C. Alberts1 1Department of  Biology, Duke University, 2Lewis-Sigler Institute for Integrative Genomics, Princeton University, 3Institute for Genome Sciences and Policy, Duke University Abstract Precise regulation of major histocompatibility complex (MHC) gene expression is critical to vertebrate immune surveillance and response. Polymorphisms in the 5' proximal promoter region of the human class II gene, HLA-DQA1, have been shown to influence transcriptional regulation of the gene and may contribute to the pathogenesis of autoimmune diseases.  We investigated the evolutionary history of this cis-regulatory region by sequencing the DQA1 5' proximal promoter in eight non-human primate species. We identified multiple signatures of balancing selection in the patterns of sequence diversity in this region.  Specifically, the substantial sequence variation observed in the DQA1 promoter was characterized by abundant shared (or trans-species) polymorphism and a pronounced lack of fixed differences between species.  The majority of transcription factor binding sites in the promoter region were polymorphic within species, and these binding site polymorphisms were commonly shared among multiple species.  In addition, we experimentally determined the functional consequences of intra-specific promoter polymorphism.  We detected significant differences among baboon DQA1 promoter alleles, identified in a wild Kenyan population, in their ability to drive transcription in a reporter assay.  The functional differentiation of baboon promoter alleles, together with the significant deviations from neutral sequence evolution, suggests a role for balancing selection in the evolution of DQA1 transcriptional regulation in primates.