Folding, Misfolding, and Unfolding: How human 3D genome structure resists, adapts, or succumbs to physical stresses in health and disease

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Project Summary/Abstract: The 3D folding of human chromosomes inside the nucleus affects numerous fundamental biological processes, including gene regulation, DNA repair and replication, and even the physical properties of the nucleus. Recent research is beginning to define the key molecular factors that build the genome structure, but little is known about how this structure responds to physical stresses experienced by cells and nuclei. The 3D genome structure in healthy cells must withstand or respond to perturbations such as physical forces, nuclear shape changes, and DNA damaging insults, like radiation. Disruptions in genome structure and nuclear architecture can lead to diseases such as cancer or premature aging, so it is important that we determine the characteristics, causes, and effects of 3D genome changes. Often, disease-related changes in 3D genome organization are considered in isolation, i.e. “this change occurs in cancer,” but this perspective may miss common underlying mechanisms that govern the 3D genome across many biological situations. My research program seeks to develop an integrative view of the changes that chromosomes experience in response to physical disruptions through a complementary set of projects. Our overarching goals are to understand how different levels of 3D genome structure change in response to nuclear shape changes and DNA damaging radiation and how the network of 3D contacts in the genome can accomplish both gene regulatory functions and contribute to necessary physical properties of the nucleus. To this end, we will integrate microscopy, cutting edge sequencing-based techniques such as chromosome conformation capture (Hi-C), and computational approaches to investigate 3D genome disruptions in several systems, including: 1) cells exposed to DNA damaging X-ray irradiation, 2) the initial states and adaptations of the 3D genome necessary for cell nuclei to squeeze through tight spaces during confined migration, and 3) the aspects of genome structure that are disrupted and maintained during cellular aging in a lamin-mutant progeria cell. Our research program has yielded preliminary evidence that motivates further study of these systems: we have determined that the cell actively protects its 3D genome structure after X-ray damage and that the 3D genome folding state influences whether cancer cell nuclei can squeeze through tight spaces during metastatic migration. These results show that a comprehensive understanding of genome structure changes is necessary to better understand disease initiation and progression. Analyzing genome structure changes across systems will provide a unique, integrated view of what types of genomic regions or structures are the most robust or fragile and the degree of dependence between genome structures at different length scales. All these results will help us build a framework in which we can understand, and eventually predict, the impact of certain treatments or conditions on human cell types, depending on their initial genome folding state. This framework will open avenues for future chromosome structure-based disease diagnosis and treatment.