Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects
DNA replication, transcription and the repair of DNA damage. Thus, a thorough
understanding of nuclear architecture is fundamental to the study of nuclear processes in
eukaryotic cells. Recent years have seen rapid proliferation of technologies to investigate
genome organization and function. Here, we review experimental and computational …

Gene expression in mammals is regulated by complex networks involving higher order
chromatin organization, transcription factor binding, histone and DNA biochemical
modifications, as well as other mechanisms. Our understanding of the functional relationship
between 3D chromosome architecture and gene regulation has been limited by the
technologies to map 3D chromatin looping and the breadth of cell or tissue types analyzed.
During my Ph. D. I have addressed technological shortcomings in the field by developing a …