The research goal of this project is to uncover the fundamental mechanisms through which interactions between chromosomes and the periphery of the cell nucleus regulate gene expression. The function of a cell, including gene expression, is determined not only by the letters of the DNA code, but also by how the DNA (contained in the chromosomes) is packaged tightly and intricately inside the tiny volume of the cell nucleus. This complex nuclear architecture - organization of the genome in 3D - has a profound effect on how the genes work and how the cell functions. However, the effects of chromosome attachments to the nuclear periphery on 3D genome organization and key cell functions are largely unknown. This project will employ a tight integration between computation and experiment: computational models can explore vast amounts of spatial chromosomal configurations and many relevant parameter values to identify a small subset of the most promising ones, which will be tested experimentally. The research will establish a set of general principles that translate the 'language' of 3D chromosome organization into the 'language' of gene expression, which if of fundamental importance to biology. The project also integrates research and education with emphasis on outreach among middle-school students and mentoring undergraduate and graduate students. Specifically, the research team will host a hands-on exhibit of 3D interactive models of chromosomes at Kids' Tech University (KTU), which is a semester-long enrichment program. Virginia Tech undergraduate and graduate students will have an opportunity to investigate chromosomes in a Multi-Screen Immersive 3D Display where researchers can be virtually present inside the cell nucleus. In addition, the project will provide the broad scientific and educational communities with a unique approach for visualizing the complex hierarchy of chromosome structure and interactions in 3D, based on versatile and powerful, freely available, visualization software already well-established in the structural biology community.
The project will study nuclear organization in fruit fly giant polytene chromosomes using confocal microscopy and regular interphase chromosomes using the powerful Hi-C technique. Experimental analyses of nuclear architecture will be complemented and guided by computer simulation. Specifically, the project will develop computational models of chromosome organization in Drosophila nuclei for polytene and regular (non-polytene) interphase chromosomes, including information-rich visualization tools. It will also explore by simulation, and test experimentally, the hypothesis that chromosome-nuclear envelope attachments in Drosophila nuclei affect the frequency of long-range intra-/inter- chromosomal contacts. Finally, the research will provide a direct connection to cell physiology by exploring the effects of chromosome-nuclear envelope detachments on gene expression via re-patterning of long-range intra-/inter-chromosomal contacts. Successful completion of this highly interdisciplinary work will reveal the extent and mechanism of how the functional organization of the genome in the nuclear space is regulated by chromosome-nuclear envelope interactions - a common dynamic feature of living cells whose effect on the nuclear architecture is unclear.
