Epigenetic Regulation of Pluripotent and Multipotent Stem Cell Systems

Thesis (Ph.D.)--University of Washington, 2017The epigenome defines what a cell has the potential to do and allows a cell to elicit a response to external cues. This is exemplified in organisms where all the hundreds of different cell types share one genome but differ in their gene expression and response to environmental stimuli. Stem cells with their inherent ability to self-renew and differentiate, are a useful model for studying how the epigenome confers these attribute in a cell. Here I present research performed in two stem cell systems, pluripotent naïve human embryonic stem cells and multipotent ovarian cancer stem cells. I use different next-generation sequencing techniques to quantify changes in gene expression and measure three epigenetic characteristics: DNA methylation, histone modifications and genome three-dimensional architecture. From the data generated, I am able to identify regions that regulate gene expression, identify proteins that potentially target these regions, and predict the genes targets of regulatory regions. I have shown that the pluripotent naïve human embryonic stem cell line, Elf1, has a more open chromatin structure than primed embryonic stem cells, a known feature of early development. This is observed in their less methylated genome and presence of broad domains of active chromatin modifications. I found that architectural differences between the naïve and primed genome can be explained through the presence of histone modifications. I observed that Elf1 naïve embryonic stem cells are also a good model for development due to their ability to gain DNA methylation at imprinted regions and gain repressive histone modifications at key genes when pushed forward to a primed-like state. In our multipotent stem cell system, I was able to identify key genes and protein interactions that distinguish ovarian cancer stem cells from the cells in the bulk of the tumor. I was able to link differentially methylated regions to regulatory elements and identify putative gene targets. Many of the interacting proteins and gene targets have previously been shown to be responsible for chemotherapy resistance and quiescence in cancer stem cells. I uncover evidence that ovarian cancer stem cells use pluripotent cell transcription factors at their regulatory elements, creating a surprising and unexpected connection between the two stem cell systems in this study. There is still much to learn about the epigenetic regulatory network in pluripotent and multipotent stem cells and the work presented here can be viewed as a launching pad for future studies