Folding, Misfolding, and Unfolding: How human 3D genome structure resists, adapts, or succumbs to physical stresses in health and disease - Project Summary/Abstract: The 3D folding of human chromosomes inside the nucleus affects critical biological processes, including gene regulation and DNA repair, while also influencing the physical properties of the nucleus. To make progress toward our overarching goal of understanding the principles of chromosome folding and their importance in health and disease, my research program investigates the responses of 3D genome structure to physical perturbations. We examine alterations of chromosome structure in the context of DNA damage, nucleus structure disruption by lamin mutation, cell migration through narrow constrictions, and externally applied forces. Our recent work has revealed a striking robustness of chromosome structure to many transient perturbations, but has shown stable alterations in the 3D genome and cell phenotype can result from chronic or repeated stresses. By comparing complementary systems, we have identified different levels of the chromosome structure hierarchy that respond to different stresses: DNA damage results in strengthening of the local loop and topologically associating domain (TAD) structure while physical deformations of the nucleus associated with altered spatial segregation of heterochromatin and euchromatin. New research in a variety of systems is revealing the important role of nucleus mechanosensation in cell fate decisions. We are now well- positioned to connect cellular and imaging observations of such phenomena with the 3D genome changes that accompany them. In this next funding period, our research will examine what molecular mechanisms contribute to stable 3D genome and phenotype changes after cancer cells pass through multiple rounds of constricted migration. We will contrast this constricted migration system with responses elicited by externally applied forces on the cell. We will examine how disruption of nucleus architecture by a lamin mutation affects genome structure reprogramming during differentiation and contributes to the patient phenotypes of the premature aging disease Progeria. As many of these stressors also induce DNA damage, we will finally investigate the effects of chromosome structure alterations after DNA damage on DNA repair, gene regulation, and cellular response to subsequent stresses. Observations across our experimental systems combined with computational analysis and modeling will clarify the relationship between changes in chromosome structure and gene expression and reveal how microscopically observed alterations in chromosome conformation relate to changes in contact patterns detected by chromosome conformation capture (Hi-C) family techniques. Our previous innovations in single cell genomic data analysis and integration position us to investigate how average shifts in cell population behavior connect to the heterogeneity and dynamics of chromosome structure and gene expression at a single cell level. Defining connections between physical perturbations, genome architecture, and cell fate will inform future diagnostics and treatments for diseases such as cancer, premature aging, cardiomyopathies, and any condition where the physical state of the cell influences cell function.
