Investigating human cis-regulatory evolution with hybrid iPS cells

Project Summary Despite a great deal of research, we have discovered surprisingly little about the genetic basis of uniquely human traits—largely due to the ethical and practical considerations that severely limit comparisons between humans and other primates. To advance this field, we have integrated two effective approaches for studying evolution: induced pluripotent stem (iPS) cells, and interspecific hybrids. iPS cells can be differentiated into a wide range of cell types in vitro, circumventing many limitations of primate research, while measurement of allele-specific gene expression in hybrids allows cis-regulatory divergence and gene expression adaptations to be mapped genome-wide. To combine these approaches, we have recently generated human/chimpanzee hybrid iPS cells. We propose to characterize this powerful resource with RNA-seq and cellular phenotyping in diverse cell types, including cardiomyocytes, motor neurons, hepatocytes, pancreatic progenitors, skeletal muscle, retinal pigmented epithelium, and skin organoids that include dermis/epidermis, adipose, cartilage, hair follicles, and more. Our goal is to discover and experimentally validate genes and genetic variants that have contributed to the evolutionary origin of our species.