What Makes Us Human?: Evolution of the Human Genome, Species-Specific Gene Regulation, and the Development of the Human Cerebral Cortex

Abstract

The human cerebral cortex differs in critical aspects from that of our closest primate ancestor, the chimpanzee. Traits that distinguish us as a species, including unique brain morphology, higher cognitive functions, and spoken language capabilities, all must have originated in evolutionary genetic changes. The link between human-specific DNA sequence alterations and our distinguishing brain traits, however, remains almost entirely unknown. In this thesis, I present our work studying the role of Human Accelerated Regions (HARs), the fastest-evolving elements of the human genome, during brain development. HARs are a set of 3171 genomic loci that are highly conserved throughout vertebrate evolution yet show rapid sequence changes between humans and chimpanzees. As the vast majority of HARs do not code for functional proteins, HARs are hypothesized to function as human-specific gene regulatory elements that coordinate precise spatiotemporal patterns of gene expression. Previous studies have cherry-picked HARs to assay in cell lines and mouse models, but no study to date has analyzed the gene regulatory activity of HARs in human primary tissue. We harnessed high-throughput, next generation sequencing methods to assess the regulatory potential of all 3171 HARs in the developing human brain and to prioritize those sequences most likely to contribute to human brain evolution. We found that many HARs function as active enhancers in the fetal cerebral cortex and that the majority of HARs exhibit different transcriptional activity in comparison to their chimpanzee orthologous sequence. Finally, I describe in more detail one example of an active neurodevelopmental enhancer, HAR2635. This HAR appears to regulate expression of PPP1R17 in the human developing cortex, a spatiotemporal pattern not observed in other mammals. We found PPP1R17 expression slows cell cycle progression in neural progenitor cells, which is a well-described feature of evolution and a mechanism which may contribute to human brain development. Overall, our systematic assessment of HARs provides evidence that HARs not only function as species- specific neurodevelopmental enhancers but that many of them regulate gene expression in specific cell types of the human fetal cortex.