Abstract
The development and function of the mammalian brain requires precise control of transcription to specify neuronal subtypes, form and refine circuits, and respond to dynamic changes in neuronal activity. This makes neurons extremely dependent on epigenetic modifications, such as histone modifications and direct modifications of DNA. Accumulating evidence outside the nervous system suggests interdependence between histone methylation and DNA methylation during establishment of the neuronal epigenetic landscape, and indeed, mutations in genes encoding histone- and DNA-modifying enzymes present with striking overlapping clinical phenotypes. Interestingly, much of this overlap is neurological, raising the question as to whether there are brain-specific mechanisms that govern the molecular crosstalk between histone and DNA methylation. Though DNA methylation is classically considered to only occur in mammalian cells in the CG context, neurons are uniquely enriched for methylation in non-CG contexts established by DNA methyltransferase 3A (DNMT3A). This non-CG methylation primarily occurs at CA dinucleotides (mCA) and is read out by the methyl binding protein MeCP2 to control neuronal gene expression and function. Notably, mCA is disrupted in DNMT3A- and MeCP2-associated neurodevelopmental disorders. Previous studies in non-neuronal cells have revealed that histone modifications play a central role in directing DNMT3A-mediated CG methylation across the genome, but it is not known to what extent these histone modifications influence DNMT3A and mCA throughout the neuronal genome. Recently, large-scale exome studies have identified neurodevelopmental disease-associated genes that indeed implicate a predictive role for histone modifications on neuronal DNA methylation by modulating DNMT3A recruitment or activity. Here, I explore the coordinated interplay of histone modifications to ultimately establish patterns of non-CG methylation in neurons and examine how disruption of histone-mediated DNMT3A recruitment mechanisms disturbs critical patterns of mCA across the neuron genome to disrupt brain development and function. I identify H3 lysine 36 dimethylation (H3K36me2) mediated by the NSD1 enzyme to be required for establishing megabase-scale, regional mCA levels in neurons that are correlated with topologically-associating domains (TADs) of chromatin folding across the neuronal genome. Disruption of NSD1 is known to cause Sotos Syndrome, a NDD with neurodevelopmental phenotypes similar to Tatton-Brown Rahman Syndrome (TBRS), caused by mutations to DNMT3A. I detect concordant alterations in mCA, mCG, and transcriptomes between adult brains of NSD1 and DNMT3A mutant mouse models. This is the first demonstration of a convergent molecular mechanism involving neuronal DNA methylation that can begin to explain the shared neuropathology between TBRS and Sotos Syndrome and offer targetable paths for treatment of these disorders. Notably, H3K36 methylation is catalyzed by distinct sets of proteins, including NSD1, NSD2, and ASH1L for H3K36me2 and SETD2 for H3K36me3, all of which have been shown to be mutated in NDDs. I outline preliminary findings dissecting the degree to which different H3K36 methyltransferases have redundant or unique roles in H3K36me-mediated establishment of the neuronal mCA landscape. Finally, I present initial studies on Polycomb repressive complex (PRC)-associated histone modifications that have been found to interact with DNA methylation patterning mechanisms to mediate gene repression, but that are poorly understood in the maturing brain. Notably, two PRC-mediated histone modifications H2AK119ub1 and H3K27me3 are highly correlated with H3K36me2, DNMT3A binding, and mCA levels genome-wide in the early postnatal cortex, and my preliminary findings support a dynamic interplay between these two modes of epigenetic repression to confer a robust gene expression program during postnatal brain development. Overall, these insights build an integrative framework for the coordinated role of histone modifications on the neuronal mCA pathway in neurodevelopment and disease.
Committee Chair
Harrison Gabel
Committee Members
Benjamin Garcia; John Edwards; Nima Mosammaparast; Ting Wang
Degree
Doctor of Philosophy (PhD)
Author's Department
Biology & Biomedical Sciences (Molecular Genetics & Genomics)
Document Type
Dissertation
Date of Award
3-13-2026
Language
English (en)
DOI
https://doi.org/10.7936/yzwt-c912
Recommended Citation
Hamagami, Nicole, "Elucidating the Coordinated Role of Histone Modifications on the Establishment and Regulation of a Neuronal-specific Methylome" (2026). Arts & Sciences Theses and Dissertations. 3719.
The definitive version is available at https://doi.org/10.7936/yzwt-c912