Genetic studies of human–chimpanzee divergence using stem cell fusions

Abstract

Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human–chimpanzee divergence, we have generated human and chimpanzee autotetraploids and allotetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or autotetraploid iPSCs. Analysis of gene expression patterns in interspecific allotetraploid iPSCs shows that human–chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allotetraploid cells. We successfully generated derivative cells with nested deletions or interspecific recombination on the X chromosome. These studies confirm an important role for the X chromosome in trans regulation of expression differences between species and illustrate the potential of this system for more detailed cis and trans mapping of the molecular basis of human and chimpanzee evolution.

The genetic basis of novel trait gain in walking fish

“…Trimmed reads were aligned to a composite P. carolinus - P. evolans genome using STAR 2.7.9a 43 . Differential gene expression (DGE) between individual species and allele-specific expression (ASE) within hybrids was determined as described previously 45 . For each tissue and stage (e.g.…”

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

“…Recent studies have used allotetraploid cells to identify candidate cis -regulatory changes in iPSCs, neural crest cells and neural lineage cells, revealing candidate cell types, such as astrocytes with an enrichment of cis -regulatory changes, and candidate genes, such as EVC2 , that may influence craniofacial development 216 , 255 , 256 . Importantly, isolating trans -regulatory changes will still require consistent patterning and differentiation of human and chimpanzee contributor lines, including human–human and chimpanzee–chimpanzee autotetraploid cells, to fates similar to those of fused autotetraploid cells.…”

Genomic structural variation: A complex but important driver of human evolution

“…Ongoing work optimizing protocols for cortical organoids promise to increase the scale and reproducibility necessary to globally test gene functions in neurodevelopment (Bray, 2019). In particular, great promise exists in understanding species differences by manipulating and directly comparing the development of chimpanzee and human‐induced Pluripotent Stem Cell (iPSC)‐derived organoids (Gallego Romero et al, 2015; Pollen et al, 2019; Song et al, 2021). Ideally, expansion of iPSC resources for additional nonhuman primates would allow for more comprehensive comparisons (Fernandes et al, 2021).…”