Interbreeding between modern humans and archaic hominins has contributed to the genomes of present-day human populations. Introgressed archaic variants are not uniformly distributed throughout the genome, but are enriched in regulatory regions, particularly in enhancers active in immune cell types, suggesting they have the potential to contribute to gene regulation and organism-level traits. However, due to the lack of diversity in genomic databases, research on the impacts of archaic introgression has focused mainly on the Neanderthal variants present in European populations, to the detriment of our understanding of the Neanderthal and Denisovan variants present in the rest of the world.
Using a massively parallel reporter assay, we functionally characterise the regulatory activity of over 26,000 Neanderthal and Denisovan variants present in modern-day Papuan populations. To prioritise evolutionary and phenotypically relevant variants, we focused primarily on variants located within accessible, active chromatin in immune cell types and segregating at allele frequencies > 0.15, which together suggest they might have been targeted by positive selection . By quantifying the regulatory activity of these archaic variants, and their non-archaic counterparts, in three cell lines of different genetic background, we assess the contribution of archaic introgression in shaping modern human genetic diversity and demonstrate the value of massively parallel reporter assays as tools to study how gene regulatory changes have shaped phenotypes across human evolution. Overall, this project will give insight into the regulatory activity of archaic variants in Island Southeast Asia and contribute to ongoing efforts to increase human diversity in genomics studies.