Eukaryotic genomes encode genetic information in their linear sequence, but appropriate expression of their genes requires chromosomes to fold into complex and spatially distinct three-dimensional structures. Recent advances in genomic-based approaches have uncovered a hierarchy of DNA interactions, from small chromatin loops that connect genes and enhancers to larger chromosomal domains and nuclear compartments. However, despite the remarkable conservation of these organizational features and their impact on gene function, we have a very limited understanding of how chromosomes are spatially partitioned, functionally packaged, and relatively positioned in the nucleus. Technical limitations have also hindered our ability to ask questions regarding cell-to-cell variability and the relationship between chromatin folding, positioning, and function at single cell resolution. Our previous studies involved the development of two technologies that use fluorescent in situ hybridization (FISH) to interrogate chromosome positioning at single-cell resolution. Our goal is to build on this work and use these tools to elucidate how chromosomal segments find each other and then form stable interactions within cells. I can envision three immediate stages for our work. The first is developing a rapid and precise method for identifying candidates involved in chromosome interactions. The second is establishing a battery of in situ-based assays that can be used to characterize the candidates, and the third is translating our findings from model organisms to humans. Collectively, the studies proposed here will uncover novel molecular mechanisms underlying nuclear organization, providing a new avenue to study how chromatin folding and positioning is established and inherited, and how dysfunctional organization contributes to disease.
The issue of chromosome interactions is clearly relevant to public health, as these can lead to dramatic changes in transcription and may, therefore, directly contribute to disease. Indeed, aberrant interactions may also increase mitotic recombination, aneuploidy, and the formation of translocations, all of which have long been known to be underlying causes for many diseases, including cancer. As the mechanisms of chromosome interactions have not yet been systematically explored, this study has the potential to reveal new therapeutic targets for the treatment and prevention of chromatin-based diseases.
