The length of eukaryotic chromosomes is many times longer than the nucleus diameter in most cells; thus, their confinement depends on adopting highly folded configurations. Remarkably, these configurations are non-random and may be important for gene expression and regulation. Thus, genome sequences must be understood in the context of their 3D organization which critically influences the flow of information. The effort to understand this added complexity now encompasses an entire field of chromosome biology and is reshaping the traditional concept of the central dogma. Although little is known about the principles which govern chromosome folding and influence gene regulation, the nuclear envelope is expected to play a significant role since it serves as the physical boundary preventing chromosome from freely diffusing in the cell cytosol. Moreover, experiments suggest that the nuclear envelope engages chromosomes actively by anchoring specific loci and limiting their range of motion. The broad goal of the research presented in this dissertation is to advance our understanding of 3D genome organization with an emphasis on determining the role of the nuclear envelope. / Ph. D.