Date of Award

Fall 2013

Project Type

Dissertation

Program or Major

Biochemistry

Degree Name

Doctor of Philosophy

First Advisor

W Kelley Thomas

Abstract

Recent large-scale comparative analysis of cytosine DNA methylation across diverse eukaryotes suggest that early features of DNA methylation present in the last common ancestor of all eukaryotes some 1.6 to 1.8 billion years ago included the methylation of gene bodies and transposable elements (Zemach, McDaniel et al. 2010; Parfrey, Lahr et al. 2011). These potentially ancient patterns may reflect a primitive role of methylation in transcriptional fidelity and as a mechanism to protect the germ line from transposon, or repeat, mediated mutation. Because spurious transcription and mutation are hypothesized to be among the critical limiting factors to genome size, an ancient role for methylation in support of fidelity of transcription and genome stability suggests a possible link with the origin of eukaryotes. As a consequence, understanding the roles of methylation across diverse eukaryotes will be critical to understanding the evolution of methylation and its role in the evolution of genome complexity.

In light of these observations it is perplexing that one of our key model eukaryotes, the nematode (Caenorhabditis elegans) is assumed to lack active DNA methylation. In fact, C. elegans is often invoked to suggest the dispensability of methylation in multicellular animals (Feng, Cokus et al. 2010; Zemach, McDaniel et al. 2010). Historically, this view has been based on crude assays using methylation sensitive restriction enzymes (Simpson, Johnson et al. 1986) that lack the sensitivity to identify low levels of methylation.

While it is clear that the genome of C. elegans is not highly methylated, in this thesis we used comparative genomics and genome wide bisulfite sequencing to show that: 1) The genome of C. elegans appears to encode at least three DNA methyltrasferases and a DNA methyltransferase associated protein; 2) the genome of C. elegans is methylated in a pattern consistent with the proposed basal eukaryotic pattern and 3) that that cytosine methylation is not a major contributor to the basal rate and pattern of mutation in the genome of C. elegans. Based on these observations we contend that C. elegans represents an ideal model for the study of the basal roles of DNA methylation shared by all eukaryotes.

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