Summary: | 5-hydroxymethylcytosine was first discovered in mammalian DNA in 1972, but its biological significance only became appreciated in 2009 when the TET enzymes responsible for producing this epigenetic mark were identified. Since then, work has identified a role for these enzymes in regulating gene expression in diverse systems especially within the fields of development, hematopoiesis, and cancer biology. I tested for a function of 5-hydroxymethylcytosine in mediating the transcriptional response to extracellular stimuli in two systems: the response of neuroblastoma cells to hypoxia, and spontaneous differentiation of T84 colon cancer cells. In both of these systems, I find that TET1 is induced, and is required for regulation of gene expression changes that occur in response to the environmental stimulus. Genome-wide mapping of 5-hydroxymethylcytosine in these systems reveals that this epigenetic mark clusters at highly expressed or induced genes, and associates with transcription factor binding sites. Finally, I have studied changes in 5-hydroxymethylcytosine in the context of broader chromatin remodeling within these systems by either testing for changes in global levels of histone modifications or by overlaying changes in 5-hydroxymethylcytosine with available histone chromatin immunoprecipitation-sequencing data. Combined, my results show that 5-hydroxymethylcytosine plays a role in the transcriptional response elicited by both of these environmental stimuli, and that changes in 5-hydroxymethylcytosine occur within the broader context of chromatin remodeling. In addition to testing more environmental stimuli, future work should determine how the TET enzymes are regulated, and how 5-hydroxymethylcytosine affects changes in gene expression at different genetic locations.
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