The Role of the Nuclear Periphery in Chromosome 3D Structure

Jackson Laboratory, Bar Harbor ME

Investigators

Abstract

The overall goal of this study is to determine how structures at the periphery of the nucleus aid in the folding and organization of genetic information encoded in DNA. Within the cell, genomic DNA is packaged and folded several times to fit within a small organelle, the nucleus. This three-dimensional (3D) folding further influences gene activity. Genes can be positioned close to each other in the nucleus and "interact", even though they are far apart in the DNA sequence. Genes also can be in contact with different nuclear compartments, small regions within the nucleus with specific sets of proteins and specific activities. Though critical for genome function, the positions of most mammalian genes within the nucleus and the mechanisms that mediate their 3D organization are poorly understood. The PI has assembled state-of-the-art techniques to probe nuclear structures. These include fluorescent probes targeted to large regions of chromosomes, mouse genetic resources, and new high-resolution 3D microscopy to image the nucleus at an unprecedented level of detail. Using these tools, this study tests the roles of candidate structures found at the nuclear periphery in the 3D organization of mammalian DNA. One candidate structure is the nuclear lamina, a network of DNA-binding filaments. This study tests the hypothesis that the nuclear lamina plays a role in both DNA 3D folding and associations between specific genes. This project also tests the hypothesis that some genes cluster near nuclear pores, protein channels that span the nuclear membranes and act as "gene gates" to the cytoplasm. Finally, to complement these studies of nuclear structures, specific DNA sequences also are tested for roles in nuclear periphery targeting. Thus, this study advances fundamental concepts of genome architecture and has far-reaching implications for structure-function constraints shaping genome evolution. Broader Impacts: Studies of genome 3D structure in the nucleus require an interdisciplinary approach, where cell biology is combined with genomics, genetics, and biophysical methods to visualize structures in the nucleus that are smaller than one millionth of a meter. The PI is a founding member of the Institute for Molecular Biophysics (IMB), an interdisciplinary partnership that brings together the genetics and genomic resources of The Jackson Laboratory with the physics resources of the University of Maine. This study specifically applies the IMB's 4Pi confocal microscope to resolve structures in the nuclear membrane previously unresolvable with the light microscope. The PI's interdisciplinary research program offers a comprehensive approach to research and training. Her research is integrated into core curriculum modules in the Functional Genomics graduate program at the University of Maine. This graduate program provides education and training to Maine students in genetics, genomics, and biophysics to prepare them for the next frontier in biological systems research. Furthermore, this study integrates high school and college students in The Jackson Laboratory's Summer Student program, which successfully targets women and minority students and provides them with an outstanding first research experience. Further developing our understanding of genome structure and function also has broad-reaching societal impacts. The public sector has heavily invested in whole genome sequencing projects, and the proposed research program puts this investment into action by dissecting the molecular mechanisms that take the DNA sequence and form it into its active state in 3D within the cell. The knowledge gained from this study will become key building blocks of the systems biology of genomes on a large scale, providing a structural framework for how genes can physically associate together and interact within the nucleus. Because genomic primary sequence organization is similar in many organisms, findings uncovered here for 3D genome organization are likely to apply to many species.