Changes in gene regulation are key drivers of human evolution. Yet for the vast majority of these changes, we know neither which human traits they shaped nor how. Here, we used massively parallel reporter assays (MPRAs) in skeletal, neural, and skin cells to measure the regulatory effects of each of the 561,410 variants that arose along the human lineage after our divergence from other great apes, as well as the 71,443 variants that distinguish modern humans from Neanderthals and Denisovans. This catalog revealed thousands of variants that altered human regulatory activity. To link these variants to the genes they control in their native genomic context, we generated human–chimpanzee and human–gorilla hybrid cells, in which both parental genomes share a single nucleus, allowing us to distinguish true genetic effects from environmental and cellular confounders. Integrating the two approaches uncovered pervasive regulatory divergence in the human brain and skeleton. The most pronounced changes involved the extracellular matrix and resulted in a threefold reduction in glycosaminoglycan content in human joints. This human-specific shift bears strong signatures of selection and likely contributes to our exceptional susceptibility to degenerative skeletal disease. We then traced a neural regulatory variant from sequence to cellular phenotype: an archaic-derived variant in an enhancer of PPM1E, which we ‘Neanderthalized’ in modern human cells using CRISPR–Cas9. Introducing the archaic allele increased PPM1E expression, delayed neuronal maturation, and reduced the formation of mature synapses. Together, these results provide a functional map of regulatory changes across both recent and deep human evolution, and link specific sequence changes to central human adaptations and to the diseases that came with them.

 

1. Yan, Y., Mishol, N., et al. The gene-regulatory evolution of the human skeleton. Nature 658, 698–706. (2026) https://doi.org/10.1038/s41586-026-11053-x

2. Gokhman, D., et al. Human-chimp hybrid cells reveal gene regulatory evolution underlying skeletal divergence. Nature Genetics 53, 467–476. (2021) https://doi.org/10.1038/s41588-021-00804-3

3. Weiss, C. V., Harshman, L., et al. The cis-regulatory effects of modern human-specific variants. Elife 10. (2021) https://doi.org/10.7554/eLife.63713

 

東京大学大学院理学系研究科・生物科学専攻・ゲノム人類学研究室