Researchers at Kyoto University have identified millions of human-specific genetic changes, revealing that genes responsible for cartilage maintenance are markedly less active in humans than in great apes. Published in Nature, the findings offer new insight into the evolution of the human skeleton and potential susceptibility to osteoarthritis.
Mapping Millions of Human-Specific Genetic Changes
A Japanese research team at the Institute for the Advanced Study of Human Biology (ASHBi) at Kyoto University in Japan compared and analyzed human genes and great ape genomes on a large scale. By evaluating more than 15,000 humans alongside 139 great apes—including 10 bonobos, 59 chimpanzees, 43 gorillas, and 27 orangutans, all mapped to the human reference genome GRCh37—the team built a map tracking genetic changes related to the skeleton.
Depending on how it is calculated, the genomes of humans and chimpanzees are thought to differ by about 1–4%. Because the regions of the genome that encode proteins are analyzed to be almost identical, scientists focus on the possibility that differences between humans and great apes stem not from the genes themselves, but from changes in regulatory regions that determine when, where, and how strongly genes are expressed.
The team compared the genomes of more than 15,000 humans with those of 139 great apes. As a result, they identified about 5.7 million single-nucleotide variants that appear only in the human lineage, after excluding variants overlapping RepeatMasker repetitive regions and simple tandem repeats from Tandem Repeats Finder, as well as variants overlapping the ENCODE set of problematic genomic regions. Of these 5,731,772 variants, around 561,000 were located in gene regulatory regions known as promoters and enhancers, which control gene activity.
Functional Analysis in Chondrocytes and Stem Cells
To understand how these regulatory variants alter cell function, the researchers synthesized human-type and ancestral-type sequences for each of these regions and compared their gene activity in chondrocytes. Using the MPRA (massively parallel reporter assay) technique, which can measure the activity of hundreds of thousands of regulatory sequences at once, the team found that about 15,000 variants actually affected gene activity.
In the next step, the researchers fused human and gorilla induced pluripotent stem cells (iPS cells) to create interspecies hybrid cells containing chromosomes from both species in a single cell. The team then induced these interspecies hybrid cells to become progenitor cells capable of differentiating into bone and cartilage, and directly compared gene activity between human and gorilla chromosomes within the same cellular environment.
Glycosaminoglycans and Cartilage Maintenance
The most striking difference in gene activity appeared in pathways related to glycosaminoglycans (GAGs). GAGs are major components of the extracellular matrix surrounding cells and are involved in maintaining the shape, elasticity, and water content of cartilage. On human chromosomes, several GAG-related genes showed lower activity than on gorilla chromosomes.
The same trend was observed in actual joint tissue. When the team measured GAG content in elbow and knee tissues from humans and great apes, human GAG levels were only about one-quarter to one-third of those in great apes. Among great ape species, GAG content did not differ greatly.
By conducting large-scale functional analyses of gene regulatory variants found only in humans, we demonstrated how changes in gene regulation led to the evolution of the human skeleton.
Yan Yizhi, PhD candidate of Kyoto University
Evolutionary Trade-Offs and Susceptibility to Disease
The researchers suggest that, over the course of evolution, changes in enhancers regulating GAG-related gene activity reduced GAG levels in cartilage, and that these lower GAG levels may have contributed to the formation of the human-specific skeletal structure. They add that this could also offer clues to why osteoarthritis is more common in humans than in great apes. This study is significant in that it goes beyond a simple comparison of DNA sequences between humans and great apes and verifies how human-specific genetic variants actually alter gene function in cells.