Maps and mechanisms of three-dimensional genome organization

Abstract

The three-dimensional organization of the genome inside the nucleus both impacts and is influenced by its functions, including transcription and DNA replication. Recent technological advances, particularly the high-throughput sequencing adaptation of the chromosome conformation capture assay called Hi-C, have improved the genomic coverage and resolution of maps of 3D genome organization. However, it remains challenging to resolve the two homologous copies of the genome that exist in most eukaryotic cells. Furthermore, for many chromosomal structures, the mechanisms driving their formation remains unknown, in part due to the difficulty of testing many perturbations for effects on these structures. In my thesis work, I first utilized the Hi-C method on diverged hybrids to map the conformations of homologous chromosomes, using Saccharomyces yeasts as a model system. I then developed a pooled mutational scanning method for studying chromosome conformation, and applied it to dissect the mechanisms underlying a novel inducible homolog pairing contact. This work both sheds light on the poorly understood process of mitotic homologous chromosome pairing and provides a powerful new approach for mechanistic studies of chromosome conformation.