UCSF

The coding regions of the human and chimpanzee genomes are 99% identical, which implies changes to the noncoding genome are likely responsible for the divergent phenotypes between these species. A large body of research has focused on noncoding regions in an attempt to decode their function and implications on phenotypes and disease. In this work, I examined noncoding regulatory sequences unique to modern humans and identified candidate regulatory sequences that may have contributed to modern human speciation. First, I tested the regulatory potential of all fixed or nearly fixed single nucleotide changes in the modern human lineage as compared to Neanderthal and Denisovan using Massively Parallel Reporter Assays (MPRA). We found that a subset of these sequences are potentially active regulatory elements, and an additional subset were differentially active between the archaic and modern sequence versions. The differentially active sequences were linked to genes involved in brain development, vocal tract function, and other phenotypes. Additionally, we annotated changes in CTCF binding sites between humans, great apes, and archaic humans. CTCF is an architectural protein that helps facilitate genome looping and enhancer-promoter interactions. We identified CTCF binding sites that were uniquely gained or lost in the human genome, as compared to great apes (human specific), and separately compared to Neanderthal and Denisovan (recent human specific). We identified 2,230 human specific gained CTCF sites and 24 human specific lost CTCF sites, as compared to great apes. As compared to Neanderthal and Denisovan, we found 24 recent human specific gained sites. We observed an enrichment of human gained sites at TAD boundaries, but no enrichment for the human lost CTCF sites. Additionally, we found that human specific gained CTCF sites were enriched near genes involved in cognitive function and recent human specific CTCF sites were enriched near genes related to chondrocyte differentiation. Finally, I created a stable human iPSC line in which I deleted one human specific gained CTCF site. I differentiated these cells into neurons for further characterization but found that this deletion had no effect on gene expression in the region. My work provides a list of single nucleotide changes and CTCF sites that are interesting targets for future research in determining the effects of noncoding sequence changes on modern human evolution