4D Nucleome-Guided Cellular Reprogramming

Abstract

The 4D Nucleome (4DN) refers to the dynamical relationship between chromatin architecture and gene expression in the nucleus that gives rise to cellular phenotype. Our ability to steer cellular phenotype hinges on our ability to understand and precisely characterize a dynamic cellular state. The 4DN framework can be instrumental in helping to realize such reprogramming potential. In this dissertation, I demonstrate how 4DN data can be used to evaluate the impact of perturbations to a cell, examining how TF silencing sensitizes colorectal cancer cells to treatment and assessing how altering genome structure could be a viable therapeutic strategy harnessed for directly modulating in vivo disease processes. I then showcase how recent experimental innovations have allowed us to refine the 4DN framework. Profiling spatially-resolved gene expression in tissue, I characterize the disruption of adult adipose tissue morphogenesis during obesity progression. Finally, I offer a computational framework to analyze multi-way chromatin interactions and reveal organization principles of the genome that govern how transcription factors regulate the formation of transcription clusters. The culmination of this work has allowed us to move beyond the traditional scope of 4DN and consider insights from spatial networks and complex higher-order genome organization. Together, these advances can enable us to develop reprogramming regimes that reach target states with higher fidelity through exploring endogenous nucleome modifications, considering the anatomical context of cells, and ensuring recapitulation of a target cell’s conformational state.