The gene-regulatory evolution of the human skeleton

Abstract Skeletal modifications were central to human evolution, enabling adaptations for bipedalism, large cranial vaults and childbirth 1 . Despite their importance, the genetic changes that gave rise to the unique human form remain mostly unknown 2 . Here we systematically map the gene-regulatory changes that shaped human skeletal evolution. Using massively parallel reporter assays (MPRAs) in chondrocytes, we assayed 561,410 human-derived substitutions in promoters and enhancers, identifying 15,077 loci with human-specific regulatory activity. We then generated human–ape hybrid cells and differentiated them into osteochondral progenitors. Integrating the hybrid cells with MPRA measurements produced genome-wide atlases of human-specific changes in cis -regulatory expression, and the sequence variants that drive them. These atlases reveal an extensive rewiring of the extracellular matrix (ECM), including a marked suppression of glycosaminoglycan (GAG) biosynthesis, leading to an approximately three-to-fourfold reduction in joint GAG content in humans compared with non-human apes. We find that this human-specific shift bears signatures of selection, and is likely to be a key contributor to the exceptional susceptibility of humans to degenerative skeletal diseases 3–5 . Together, our results reveal a coordinated evolutionary remodelling of the human skeletal ECM, and establish a comprehensive framework for dissecting the genetic basis of human skeletal biology.