| Summary: | Thesis (Ph.D.)--University of Washington, 2019 Epigenetic processes, which contribute to gene regulation without affecting underlying DNA sequences, are increasingly recognized as molecular mechanisms that shape phenotypes. DNA methylation is the best understood epigenetic process and has been shown to mediate environmental effects on gene expression and phenotype in a wide range of taxa. However, most of what is known about DNA methylation is based on model organisms, particularly vertebrates, while much less is known about DNA methylation in other organisms such as invertebrates. Tropical reef corals are long-lived, sessile invertebrates that are thought to be particularly reliant on physiological acclimatization and phenotypic plasticity to cope with environmental variation. The underlying basis of this plasticity could lie, at least in part, in epigenetic mechanisms like DNA methylation. The aim of this dissertation research is to examine DNA methylation in corals with respect to its patterns, variability, response to change, and involvement in phenotypic and transcriptional plasticity. Chapter one explores patterns of evolutionary-scale DNA methylation in corals, using CpG depletion analysis to estimate methylation levels in publicly available transcriptome data from six coral species. Consistent with what has been documented in most other invertebrates, all corals exhibited bimodal distributions of germline methylation suggestive of distinct fractions of genes with high and low levels of methylation. The hypermethylated fractions were enriched with genes with housekeeping functions, while genes with inducible functions were highly represented in the hypomethylated fractions. In three of the coral species, genes differentially expressed in response to thermal stress and ocean acidification exhibited significantly lower levels of methylation. These results support a link between gene body hypomethylation and transcriptional plasticity that may point to a role of DNA methylation in the response of corals to ...
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