Skip to main content
eScholarship
Open Access Publications from the University of California

UC San Diego

UC San Diego Electronic Theses and Dissertations bannerUC San Diego

Studying human development by single-cell profiling of primary human tissues and genetic perturbations of novel developmental models

  • Author(s): Wu, Yan
  • Advisor(s): Zhang, Kun
  • Mali, Prashant
  • et al.
No data is associated with this publication.
Abstract

Understanding human development is critical to understanding human evolution, treating developmental disorders, and creating regenerative therapeutics. Single-cell methods have enabled the high-resolution profiling of developmental trajectories and novel organoid models have facilitated a greater understanding of difficult to access developmental periods, especially through the use of perturbation experiments. Here, we used a novel multi-lineage developmental model along with profiling of the developing human prefrontal cortex to better understand human development and evolution. First, we developed a novel visualization method, Similarity Weighted Nonnegative Embedding (SWNE), which both preserves the structure of single-cell datasets and enables key marker genes and relevant genesets to be embedded alongside the cells. We then leveraged a novel multi-lineage developmental model, the teratoma, to study the role of key developmental genes. We conducted a pooled CRISPR knockout screen of those regulators in the teratoma with a single cell RNA-seq readout, enabling us to better understand the function of these genes across all major human lineages. Finally, we used both single-cell RNA-seq and single-cell chromatin accessibility profiling to study the role of human accelerated regions (HARs), genomic regions thought to influence human-specific evolution, in human corticogenesis. The chromatin accessibility enabled us to assess the activity of HARs in specific developmental cell types and link those HARs to genes using co-accessibility of the HARs and gene promoters, while the RNA-seq enabled us to validate the expression of those HAR-linked genes.

Main Content

This item is under embargo until April 3, 2022.