Maddy Comerford, Davide M. Vespasiani, Navya Shukla, Laura E. Cook, Danat Yermakovich et al.
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.
Maddy Comerford, Davide M. Vespasiani, Navya Shukla, Laura E. Cook, Danat Yermakovich, Michael Dannemann, Matthew Leavesley, Christopher Kinipi, François-Xavier Ricaut, Nicolas Brucato, Murray P. Cox, Irene Gallego Romero. Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans. 2026-03-24. https://doi.org/10.1371/journal.pgen.1012067
One condition of the study's transient episomal MPRA. The 61,812-oligo library of Papuan Denisovan/Neanderthal introgressed variants, haplotype-like combinations, positive controls and random negative controls was assayed in GM12878 human lymphoblastoid cells across two usable biological replicates; matched cDNA and plasmid DNA barcode counts were summarized at the oligo level.
One condition of the study's transient episomal MPRA. The 61,812-oligo library of Papuan Denisovan/Neanderthal introgressed variants, haplotype-like combinations, positive controls and random negative controls was assayed in the PNG22 Papuan human lymphoblastoid cell line across two usable biological replicates; matched cDNA and plasmid DNA barcode counts were summarized at the oligo level.
One condition of the study's transient episomal MPRA. The 61,812-oligo library of Papuan Denisovan/Neanderthal introgressed variants, haplotype-like combinations, positive controls and random negative controls was assayed in the PNG8 Papuan human lymphoblastoid cell line; PNG8 Rep1 lacked sufficient cDNA and was omitted by the authors, so this table contains the single usable PNG8 biological replicate.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 9 files (ZIP)README.txtS1_file_all_MPRA_library_sequences.xlsxS2_file_activity_single_variant.xlsxS3_file_differential_activity_single_variant.xlsxS4_file_haplotype_allele_counts.xlsxS5_file_haplotype_differential_activity_anova.xlsxS7_file_MPRA_primers.xlsxS8_file_barcode_oligo_associations.xlsxS9_file_MPRAcount_normalized_log2.zip