The hundreds of different cell types in the human body arise from a single cell: the zygote. This ability is called totipotency. As a cell becomes more specialised its potency narrows, reducing the number and diversity of its daughter cells. We can derive two pluripotent stem cell populations from mouse pre- and post-implantation embryos: Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs). These cell types respectively represent the naive and primed states of the pluripotency spectrum. A delicately balanced transcriptional network underlies ESCs and EpiSCs, capable of both preserving pluripotency, yet prepared for differentiation. Enhancers act as hubs of transcription factors to focus and promote gene expression. In 2013 Prof Rick Young’s group proposed an ostensibly novel enhancer class: Super Enhancers (SE). In contrast to mere Typical Enhancers (TE), SE purportedly recruit transcription factors at extremely high density to drive strong expression of cell-specific genes.
This thesis examines the regulation and activity of Super Enhancers defined in ESCs during pluripotency maturation. To achieve this, we used an integrated, data-driven approach, analysing sequencing data pertaining to transcription factor occupancy, chromatin accessibility, epigenetic signatures, mRNA expression, and DNA-DNA interactions, to assay SE activity both in vitro and in vivo. We found that the constituent enhancers within SEs divide into two sub-populations based on whether they continue to function as primed pluripotency establishes. We termed the constituent enhancer units Persistently Unmethylated (PU) and Differentially Methylated (DM) Super Enhancelets, reflecting their CpG methylation profiles in naive and primed pluripotent cells. PU and DM enhancers harbour distinct sequence compositions, transcription factor occupancy, and epigenetic profiles. Furthermore DM exhibit a specific chromatin function for the orphan nuclear receptor ESRRB and its co-regulators. We conclude that ESC enhancers represent a heterogenous population of genetic regulatory elements, controlled by distinct transcriptional mechanisms.