Date of Award
Spring 2024
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Genetics
First Advisor
Noonan, James
Abstract
The evolutionary emergence of the uniquely large and complex human brain isunderpinned by the alteration and expansion of the neural stem and progenitor cell (NSC) pool during development. These modifications are the manifestation of numerous regulatory and genetic changes, many of which have yet to be described. One salient set of candidates consists of ~1500 Human Accelerated Regions (HARs), which are noncoding regions of the genome that have been highly constrained throughout evolution until the human lineage, where a significant number of substitutions occur, indicating divergent functions. I designed a direct-capture Perturb-seq screen repressing 180 HARs with evidence of neurodevelopmental activity in human NSCs with single-cell readout. After profiling 188,000 cells, I identified a set of 13 HAR perturbations which converge on the downregulation of gene modules associated with apicobasal polarity and Rho-GTPase activity, as well as the activation of gene modules associated with cell migration and protein synthesis – all transcriptional markers of NSC delamination, a process known to expand the NSC pool during cortical development and observed to occur more frequently in humans than in chimpanzees. Further, I found within these perturbed cells consistent downregulation of SETD2, PCM1, and ABI2, important regulators of cell structure, polarity, and NSC expansion. Additionally, I identified significant enrichments for autism- and intellectual-disability-associated genes downstream of HAR perturbation. These results demonstrate the crucial and overlapping developmental roles HARs play in NSC biology and cortical development, and point to candidate regulatory regions which may have contributed to cortical expansion in evolution.
Recommended Citation
Noble, Mark Alan, "Single-Cell Perturbation of Human Accelerated Regions in Neural Stem Cells" (2024). Yale Graduate School of Arts and Sciences Dissertations. 1383.
https://elischolar.library.yale.edu/gsas_dissertations/1383
