UC San Diego

A detailed understanding of higher order chromatin structure is critical to understand the mechanisms used by regulatory elements to affect expression of their target genes. Yet, until recently, most methods used to study higher order chromatin structure were laborious and low- throughput. Recent advancements in the methods used to study chromatin structure have allowed for the first time the identification of genome wide patterns of higher-order chromatin interactions. During my Ph.D, I have used the Hi -C technique to study genome wide patterns of chromatin interactions. I have observed that chromosomes appear to fold into megabase-sized self-interacting structures that we have termed "topological domains." These domains are stable between cell types and conserved in evolution. These domains appear to be separated from each other by boundary elements in the genome, and appear to contain clusters of co-regulated cis-acting elements. The structure of the domains is dependent on the DNA-binding factor CTCF and the Cohesin complex. Notably, Cohesin and CTCF appear to have unique roles in regulating domain structure. CTCF appears to affect both intra- and inter- domain interactions, whereas Cohesin appears to primarily affect intra-domain interactions. When we compare topological domain interaction patterns across a variety of embryonic stem cell derived lineages, we observe that the interactions appear to be regulated on a domain-wide scale. Increases in domain-wide interaction frequency within domains correlates with active histone modifications, DNaseI hypersensitivity, and increased gene expression. In addition, we observe a wide-spread re- organization of inter-domain interactions between cell types. This correlates with a re-structuring of the "A" and "B" compartments in the nucleus. The alterations of the A/B compartments appear to modestly correlate with changes in gene expression, most notably for particular subsets of genes. We anticipate that these studies will lay the ground work for future experiments to elucidate the impact of higher order chromatin structures on diverse fields of biology, ranging from human disease to the evolution of genomes