# Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans

## TL;DR

This study explores how DNA from ancient hominins like Neanderthals and Denisovans affects gene regulation in modern Papuans, particularly in immune-related genes.

## Contribution

The study experimentally validates regulatory activity of thousands of archaic variants in Papuans using a novel functional genomic approach.

## Key findings

- Approximately 8-9% of Denisovan and Neanderthal introgressed SNPs showed regulatory activity in immune cells.
- Differentially active archaic alleles were linked to immune genes like IFIH1 and TNFAIP3.
- Higher frequency Denisovan alleles were less likely to show differential activity, suggesting selective constraints.

## Abstract

Interbreeding between anatomically modern humans and archaic hominins has contributed to the genomes of present-day human populations. However, our understanding of the specific gene regulatory consequences of Neanderthal, and particularly, Denisovan introgression is limited. Here, we used a massively parallel reporter assay to investigate the regulatory effects of 25,869 high-confidence introgressed SNPs segregating in present-day individuals of Papuan genetic ancestry in immune cell types. Overall, 8.22% of Denisovan and 8.58% of Neanderthal sequences showed active regulatory activity, and 9.22% of these displayed differential activity between archaic and modern alleles. We found no association between introgressed allele frequency on activity regardless of introgression source, but introgressed Denisovan alleles at higher frequencies were less likely to be differentially active than expected, suggesting introgression is under some degree of selective constraint. Both activity and differentially activity were associated with distance to the nearest transcription start site, while differential activity was additionally associated with differential transcription factor binding. Genes predicted to be regulated by differentially active sequences included IFIH1 and TNFAIP3, key immune genes and known examples of archaic introgression. Overall, this work provides experimental validation of regulatory activity for thousands of archaic variants in populations with the highest levels of Denisovan ancestry worldwide, revealing how human evolutionary history actively shapes present-day genetic diversity and immune function.

Modern humans carry DNA inherited from extinct archaic hominins, the Neanderthals and Denisovans. Archaic DNA influences present-day traits, including immunity, but our understanding of the mechanisms of this process are limited. Here, we characterise the gene regulatory potential of Neanderthal and Denisovan variants present in Papuans, who have the highest levels of Denisovan ancestry globally. We identify variants capable of modulating gene expression, many of which are predicted to impact immune-related genes. Our data supports a role of Neanderthal and Denisovan DNA in the immune response of modern-day Papuans and provides examples of how human evolutionary history shapes present-day diversity. By applying a novel technology to answer evolutionary questions, we highlight how functional genomic approaches will be useful in driving our understanding of global genetic variation.