Date of Award
Doctor of Philosophy (PhD)
Noncanonical forms of DNA methylation, especially non-CpG DNA methylation, play essential roles in the neuronal epigenome, and have only recently begun to be characterized. While most DNA methylation within mammals is found in a CG context and maintained by DNMT1, neurons contain uniquely high levels of non-CpG methylation, such that the total amounts of methylation in non-CpG contexts equals or surpasses the total amounts of methylation in CG contexts. Non-CpG methylation, unlike CpG methylation, cannot be maintained by DNMT1, and must be established by the de novo methyltransferase DNMT3A.One unique characteristic of non-CpG methylation compared to canonical CpG methylation is the extremely wide range of biological signal it exhibits across large regions of the genome. This may enable MeCP2, a critical methyl-binding protein whose disruption causes
multiple neurodevelopmental diseases, to repress regulatory elements across entire domains of the genome. How these patterns of varied methylation are established throughout the genome and what factors direct methylation to one location versus another, however, are unknown. In addition, the mechanisms by which these methyl binding proteins function and the transcriptomic effects when non-CpG methylation is lost are not well understood. As such, my dissertation work centers around the patterning, function, and consequences of this unique neural regulatory mark.Firstly, by applying multiscale analysis of bisulfite-sequencing and high-throughput chromatin conformation capture data in the cerebral cortex of mice we find that megabase-scale regions of high non-CG methylation can correspond with topologically-associating domains of chromatin folding, identifying a new mechanism influencing mCA deposition across the neuronal genome. We find that MeCP2 represses enhancers found in these domains when they are enriched for non-CG and CG methylation, with the strongest repression occurring for enhancers located within MeCP2-repressed genes. These alterations in enhancer activity provide a mechanism for how MeCP2 disruption in neurodevelopmental disorders can lead to widespread changes in gene expression. In light of our findings that enhancer-based repression by MeCP2 and mCA is disrupted in models of MeCP2 disorders, we investigated whether this pathway is affected in a new model of NDD caused by DNMT3A disruption.We find that multiple transcriptomic and epigenomic changes are shared between a knockout of MeCP2, and a heterozygous knockout of DNMT3A, the enzyme that establishes neuronal non-CpG methylation.
Together these findings demonstrate a previously unrecognized role for non-CpG DNA methylation in the regulation of enhancer activity in neurons, and a role for enhancer dysregulation, stemming from disruption of non-CpG DNA methylation, in multiple disorders. This highlights non-CpG methylation as a possible convergence point between multiple neurodevelopmental disorders.
Chair and Committee
Harrison Gabel, Kristen Kroll, Tychele Turner, Ting Wang,
Wu, Dennis Yawen, "Computational Analysis of Non-CpG DNA Methylation in the Mammalian Nervous System" (2021). Arts & Sciences Electronic Theses and Dissertations. 2385.