Factors shaping the 3D genome

The nuclear organization of chromosomes has been suggested to be associated with regulation of gene expression. In embryonic stem cells, chromosomes were shown to segment into topological domains. However, many questions remain how transcriptional control is related to nuclear positioning. This thesis describes the experiments trying to unraveling the functional role of a few protein factors in the 3D organization of the genome. Chapter 2 describes the application of LacO/LacR platform in studying the role of different types of repressive chromatin regulators in targeting to transcriptionally active genomic loci. We found trans-acting factors can re-shape a locus according to their functional roles, however, genomic contexts do have a strong influence in this reposition phenomenon. This spatial repositioning is uncoupled from gene expression, indicating nuclear organization is not a major determinant of gene expression. Chapter 3 investigates that pluripotency factors have a unique role in organizing the higher-order genome structure in pluripotent stem cells. Pluripotency factors binding sites are found to cluster in the nucleus, which may facilitate their robust control of the pluripotent state. Linker histone H1 is studied in Chapter 4. Here, we combined various genome-wide data sets including DNA methylation, histone modification, DNaseI hypersensitivity profiling and Hi-C to investigate the role of histone H1 in chromatin folding and function. Our analysis suggests that histone H1 is essential for cell to maintain normal gene expression and chromatin structure. Partial depletion of histone H1 causes massive epigenetic changes and alteration of topological organization at specific sites. This local structure changes are uncoupled with transcriptional changes, supporting the emerging concept that gene expression and higher-order chromosome topology beyond that of topologically associating domains are not causally related, but independently controlled by the locally associated trans-acting factors