Doctor of Philosophy (PhD)
Over evolutionary time, mammalian genomes have accumulated a large number of retrotransposons, making up about half of the genome in any given species. These retrotransposons are typically repressed by epigenetic mechanisms, one of the main ones being DNA methylation. It is well known that improper DNA methylation of retrotransposons can have unwanted consequences on nearby gene expression, and hypomethylation of retrotransposons has been frequently observed in various cancers. Nevertheless, it has been notoriously difficult to study retrotransposon loci individually due to the highly repetitive nature of their sequences. To address this issue, we have developed a novel protocol termed HT-TREBS (High-Throughput Targeted Repeat Element Bisulfite Sequencing), which is designed to survey the DNA methylation levels of a large number of interspersed repeat elements on an individual-locus basis. Here we have used this technique on two mammalian retrotransposon families: IAP LTRs in mouse, and the AluYa5 and AluYb8 subfamilies of Alu elements in humans. According to the results, the majority of retrotransposons (~95%) are heavily methylated in mammalian somatic cells. Moreover, only a fraction of loci appear to be sensitive to cell state in both species. Approximately 25% IAP LTRs showed hypomethylation in mouse ES cells, and ~50% in mouse cancer (Neuro2A) cells. In humans, however, the level of response to tumorigenesis in the breast was much more constrained, with only 1% AluYb8 elements being expected to show hypomethylation at an early stage. Interestingly, our results also revealed extensive (up to 10-fold) inter-individual variation in the level of DNA methylation of AluYa5 and AluYb8 elements in humans, similar to the variation previously noted regarding IAP LTRs in mice. Overall, these results highlight the dynamic nature of DNA methylation at retrotransposons, which further leads us to speculate its unique contribution to mammalian evolution and disease susceptibility by allowing for epigenetic variation within one species. Furthermore, it also suggests the potential utility of some of these elements which are sensitive to cell state, but show less variability between individuals, to be used as epigenetic biomarkers for tracking disease progression.
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Bakshi, Arundhati, "Epigenetic Profiling of Mammalian Retrotransposons" (2017). LSU Doctoral Dissertations. 4357.