We propose to dissect the genetic control and immunological function of ERAP2, a gene previously shown to play a role in antigen processing. Two haplotypes at the ERAP2 locus have been maintained by natural selection in humans where the more frequent haplotype (Haplotype B) is associated with risk for Crohn's disease, ankylosing spondylitis, preeclampsia and HIV susceptibility. Enigmatically, while Haplotype A encodes a full-length enzyme that cleaves viral peptides for antigen presentation, Haplotype B encodes a transcript efficiently degraded by nonsense-mediated decay. Why would natural selection have maintained a seemingly loss-of-function version of the gene and by what mechanism would it cause disease? We found a possible explanation by studying the antiviral response of monocyte-derived dendritic cells in 250 healthy individuals. In response to in vitro stimulations, influenza infection induced the transcription of two unannotated short isoforms from Haplotype B that are not observed in resting or interferon-beta stimulated cells. This observation, combined with previous immunological results and evidence of natural selection, leads us to hypothesize that the two ERAP2 haplotypes encode distinct gene products that play divergent roles in viral antigen processing and presentation. In this proposal, we will apply state-of-the-art molecular and immunological tools to test this hypothesis. In Aim 1, we will use functional genomic techniques (long-read RNA-seq, ribosomal footprinting and proteomics) to characterize the transcriptional and translational properties of ERAP2 in response to a spectrum of viral challenges. In Aim 2, we will map the cis-genetic control of ERAP2 using reporter assays and CRISPR/Cas9-mediated genome editing. In Aim 3, we will measure how different ERAP2 isoforms affect antigen presentation and T cell function. Our findings will shed new light on the regulation and function of the ERAP2 haplotypes and contribute to the understanding of how genetic variants under natural selection could cause autoimmune disease.