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Evolutionary genomics of the vitamin D pathway in humans - Resubmission 01

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A large body of evidence supports the notion that variation at cis regulatory elements is the major contributor to phenotypic diversity and to genetic adaptations. Within this framework, a long-standing hypothesis posits that cis regulatory variants are more likely to be targets of positive natural selection than those acting in trans, because the latter may have deleterious pleiotropic effects. Under this scenario, one might hypothesize that evolution would occur through polygenic adaptation, involving relatively subtle allele frequency shifts at multiple cis regulatory variants, rather than by large changes in allele frequency at few trans acting variants, as predicted by a standard selective sweep model. The transcriptional response to vitamin D is an ideal case study to test the above hypotheses. It is now well established that vitamin D influences many biological functions, including the immune response. Vitamin D acts by binding to the vitamin D receptor (VDR), which allows the VDR to heterodimerize with the retinoic X receptor (RXR) and to act as a transcription factor. Importantly, this pathway was exposed to different selective pressures during human evolution due to changes in UVB exposure, in diet and pathogen pressures. Despite this, the population genetics of the transcriptional response to vitamin D is poorly understood. Here, we propose to identify the VDR target genes and their cis regulatory variants in primary peripheral blood mononuclear cells of African and European ancestry. Two complementary genomics approaches will be used. In Aim 1, we will map the genetic variation influencing target gene expression in response to treatment with vitamin D. In Aim 2, we will generate a genome-wide map of VDR and RXR binding sites and then we will test for inter-individual and inter-population differences in VDR binding. Finally, in Aim 3, we will use the catalog of cis regulatory variants identified in the previous aims to investigate the impact of natural selection on this class of variants and to determine whether adaptations occurred mainly by small allele frequency shifts at many loci or by large allele frequency changes at a few key loci. The results of this study wil allow testing fundamental hypotheses about molecular adaptations as they apply to a pathway playing a crucial role in health and disease. Additionally, we will generate a large and comprehensive catalog of candidate susceptibility variants for vitamin D-related diseases that may be leveraged in future genome-wide association studies of diseases of the immune response.
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