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Title: Role of DNA methylation and Polycomb machineries in directing higher-order chromatin architecture in embryonic stem cell
Author: McLaughlin, Kathryn Anne
ISNI:       0000 0004 7429 5518
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2018
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Mouse embryonic stem cells (mESCs) are an excellent model to study epigenetics and chromatin structure, owing to their self-renewal capabilities and tolerance of dynamic changes to DNA and histone modifications. Culturing conditions impact on the ability of mESCs to effectively recapitulate in vivo developmental states, and this is exemplified by refined culture conditions (termed 2i) that promote a pluripotent ground state. 2i-cultured mESC populations are homogeneous, naïve, and distinct from conventional (serum/LIF-cultured) cells, which exist as a metastable population. Remarkably, 2i-cultured mESCs also display global DNA hypomethylation, with methylation patterns more comparable to the cells of the E3.5 pre-implantation blastocyst. This is distinct from conventional serum-cultured cells, which display DNA methylation profiles that resemble later-stage E6.5 post-implantation epiblasts. The ability to transition between 2i- and serum-culture states is an attractive model for studying the dynamic role of DNA methylation in a variety of processes. DNA hypomethylation has been linked with depletion of the Polycomb-mediated repressive histone mark H3K27me3 from its normal target loci. Polycomb repressive complexes (PRC1 and PRC2) are important developmental regulators that maintain the repression of lineage-specific genes through generating compact higher-order chromatin structures. Polycomb target sites are primarily unmethylated CpG islands (CGIs). However, under conditions of DNA hypomethylation, new (previously methylated) binding sites are unveiled, and Polycomb is redistributed from its normal CGI target regions to intragenic regions. Thus, shifting mESCs to ground state conditions results in both DNA methylation and Polycomb patterns that are quite distinct from their serum-cultured counterparts. In my PhD, I sought to investigate the effect of DNA hypomethylation and Polycomb redistribution on higher-order chromatin structure in the ground state. I used a targeted, single-locus approach (FISH) as well as a genome-wide approach (Hi-C) to analyse differences in chromatin structure between conventionally cultured and ground state mESCs. My work suggests that chromatin structure is globally altered in hypomethylated 2icultured mESCs, with a similar state present in E3.5 mouse blastocysts. Using mESC lines in which DNA methylation levels can be directly manipulated, I was able to dissect the molecular mechanism driving higher-order structure changes in 2i medium, and showed the importance of DNA methylation in directing Polycomb-mediated chromatin compaction. My results may be important in considering the impact of DNA-methylation mediated reprogramming in multiple developmental, disease and regenerative medicine contexts.
Supervisor: Meehan, Richard ; Bickmore, Wendy Sponsor: Medical Research Council (MRC)
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: epigenetics ; chromatin ; stem cells ; higher order chromatin compaction ; decompact architecture ; gene expression ; 3D ; Polycomb patterns ; DNA methylation