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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.

Microbial biogeography explores the spatial and temporal distribution of microorganisms at multiple scales and is influenced by environmental selection and passive dispersal. Understanding the relative contribution of these factors can be challenging as their effects can be difficult to differentiate. Dormant thermophilic endospores in cold sediments offer a natural model for studies focusing on passive dispersal. Understanding distributions of these endospores is not confounded by the influence of environmental selection; rather their occurrence is due exclusively to passive transport. Sediment heating experiments were designed to investigate the dispersal histories of various thermophilic spore-forming Firmicutes in the River Tyne, a tidal estuary in North East England linking inland tributaries with the North Sea. Microcosm incubations at 50-80°C were monitored for sulfate reduction and enriched bacterial populations were characterised using denaturing gradient gel electrophoresis, functional gene clone libraries and high-throughput sequencing. The distribution of thermophilic endospores among different locations along the estuary was spatially variable, indicating that dispersal vectors originating in both warm terrestrial and marine habitats contribute to microbial diversity in estuarine and marine environments. In addition to their persistence in cold sediments, some endospores displayed a remarkable heat-resistance surviving multiple rounds of autoclaving. These extremely heat-resistant endospores are genetically similar to those detected in deep subsurface environments, including geothermal groundwater investigated from a nearby terrestrial borehole drilled to >1800 m depth with bottom temperatures in excess of 70°C. The ability of these endospores to survive extreme temperatures whilst in a dormant state may enable them to withstand adverse conditions for long periods of time and then germinate in response to changing surroundings. This was investigated further in the context of seawater injection during secondary oil recovery, where cold seawater is injected into hot oil reservoirs, resulting in a cooler reservoir temperature near the injection well bore. Microcosm experiments designed to simulate this showed that cooling triggered the germination of endospores of sulfate-reducing Desulfotomaculum leading to the onset of souring in this model system. The results presented here, indicate that bacterial endospores are transported between terrestrial and marine, surface and subsurface environments. Their survival and distribution therefore has ii relevance to understanding deep biosphere processes, and factors shaping microbial diversity in the marine environment.