An Ancient Neural Enhancer that has Rapidly Evolved in the Human Lineage

University Of California, San Diego, La Jolla CA

Investigators

Abstract

The distinctive features of humanity—our intelligence, creativity, language, as well as our ecological and demographic success—are thought to be the result of evolutionary changes elicited by several non-mutually exclusive genetic mechanisms. One means by which this may be achieved is through the action of ancient DNA sequence that have undergone rapid evolution specifically in the human lineage. These sequences—called human accelerated regions (HARs)—have since been shown to be almost exclusively non-coding sequences. Of HARs that have been evaluated functionally, 30 to 50% are transcriptional enhancers. It has been hypothesized that rapid evolution of these HAR enhancers in the human lineage has driven changes in gene expression that ultimately yielded useful human-specific traits. In support, a handful of HAR enhancers have been shown to regulate neighboring genes in a temporal and/or spatial-specific manner. However, to date, none of the identified >3000 HARs have been definitively shown to confer human-specific traits. This application is focused on one particular HAR—called “HAR123”—that has characteristics that we believe make it a strong candidate to confer human-specific traits. HAR123 is a neural enhancer highly conserved in mammals and marsupials, but has undergone rapid evolution specifically in the human lineage. HAR123 strongly promotes the generation of human neural progenitor cells (NPCs). In support of human HAR123 having human-specific functions, we found—through single-cell RNA-sequencing (scRNAseq) analysis—that human HAR123 drives cellular and molecular events that differ from those elicited by chimpanzee HAR123. To examine its function in vivo, we deleted HAR123 in mice and found that this causes a specific defect in cognitive flexibility, as determined by two independent behavioral tests. Together, these data lead to our central hypothesis that HAR123 is an ancient neural enhancer that has acquired new properties in the human lineage, leading to changes in gene expression that impact NPC generation and, ultimately, cognitive flexibility. In this application, we propose to address this central hypothesis. Towards this goal, we will elucidate the cellular and molecular functions of mouse, chimpanzee, and human HAR123. Aim 1: to decipher the roles of HAR123 in human neural cells, including NPCs, with a focus on how HAR123 acts as an enhancer. We will investigate how human HAR123 differs—at both the cellular and molecular level—from chimpanzee HAR123 in its impact on NPC genesis and neural development. Our planned studies are designed to elucidate the selective forces that have acted on HAR123 during primate evolution. Aim 2: to elucidate the neural roles of HAR123 in vivo. In this Aim, we will investigate the cellular and molecular mechanisms underlying the intriguing cognitive flexibility defect we have defined in HAR123-KO mice. Through behavioral, cellular, and molecular analyses of human and chimp HAR123 knock-in mice, we will elucidate the evolving functions of HAR123 in an in vivo context. The proposed research addresses a fundamental question that is currently a black box in the field.