Investigation of the Gene Expression Dynamics of Early Mammalian Germ Layer Differentiation

Abstract

The mechanisms regulating the timing of developmental processes are poorly understood. To systematically investigate the timing of development and its underlying mechanisms, the dynamics of development must first be characterized. Although the dynamics of developmental growth and morphogenesis have been well characterized for many species, the continuous dynamics of cell differentiation that leads to the diversity of cell types that arise during development is lacking. In this dissertation supervised by Sharad Ramanathan, I, along with Sandeep Choubey and Leon Furchtgott, characterize the continuous gene expression dynamics of early mouse germ layer differentiation, inferred from single-cell RNA-seq data. We further validate our results by using the inferred gene expression dynamics to model and experimentally test a gene regulatory network. Working with Adele Doyle, we also develop a method for extracting intact RNA from fixed, immunostained and sorted mammalian cells, which was adapted by Thomsen et al. to characterize human radial glial cells, a rare subpopulation of the developing brain. Finally, I discuss some preliminary findings that suggest programmed cell death may be a key factor in the temporal coordination of growth and early differentiation.