Investigating the genetic basis of human evolution

The basis of the morphological and behavioral differences between humans and other animals have been studied since antiquity. However, the genetic basis for these human-specific traits remains poorly understood. Recent computational screens to identify different classes of promising genomic regions have highlighted regions that are selectively deleted in humans, regions that experience accelerated substitution rates in humans, and regions that are unique to humans. Although reporter assays suggest that some of these genomic regions may act as enhancers, little is known about how specific genomic changes affect cellular or organismal phenotypes. In my dissertation research, I have attempted to identify and understand genomic regions that underlie human evolution using two different approaches: (1) interrogating the function of specific genomic regions that were identified in prior computational screens; and (2) developing an experimental model system that would allow for the genetic dissection of human and chimpanzee differences within the same cell. I have focused much of my doctoral research on one particular human-specific insertion, a tandem repeat located intronic to CACNA1C, which encodes the pore-forming alpha subunit of the L-type voltage-gated calcium channel CaV1.2. We find that this human-specific tandem repeat is much larger than the size annotated in the human reference genome, is closely linked to SNPs associated with bipolar disorder and schizophrenia, and acts as an enhancer in vitro. Strikingly, different human alleles linked to either the protective-associated or risk-associated psychiatric disease SNPs display differential enhancer activity. We observe that this mirrors differences seen in CACNA1C expression in previous studies, suggesting that this human-specific insertion may play a critical role in both human evolution and human disease. To further investigate its function, we are now modeling this human-specific tandem repeat in mice and in brain organoids. In ongoing work, we have identified striking transcriptomic and calcium signaling changes in these models. I have also investigated a human-specific deletion that is located in the intergenic region between MET and CAV1. In initial experiments, we have examined lacZ reporter expression at E18.5 in the mouse and performed RNA sequencing at E14.5 and P28 in different brain regions in mice where this human-specific deletion has been recapitulated. Additional work is needed to follow-up on these preliminary results. Lastly, I have worked to develop a model system that would allow for unbiased experimental screens for genomic regions that underlie human evolution. We have fused human and chimpanzee iPSC lines to generate tetraploid lines that contain both the human and the chimpanzee diploid genomes (allo-tetraploids). We have also generated auto-tetraploids (same-species) and shown that these auto-tetraploid iPSC lines are very similar to diploid iPSC lines at the transcriptional level, suggesting that the tetraploid iPSC system may be suitable to uncover genetic differences between humans and chimpanzees. Using RNA sequencing, we have identified genes whose expression is controlled in cis or trans between humans and chimpanzees in iPSCs. We have also explored methods to induce mitotic recombination between human and chimpanzee chromosomes within tetraploid iPSC lines using small molecules and CRISPR, respectively. Future work to fully establish mitotic recombination workflows will allow us to map traits that differ between human and chimp cell lines to specific genomic regions

Keywords: Genetics.
Advisor: Kingsley David M. (David Mark) 
Gitler Aaron D. 
Sherlock Gavin 
Urban Alexander E.