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Computational Analysis Of Non-Cpg Dna Methylation In The Mammalian Nervous System, Dennis Yawen Wu

Arts & Sciences Electronic Theses and Dissertations

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 …

Transcription Factor-Mediated Epigenetic Regulation In The Healthy Brain And Neurological Disease, Alexander J. Cammack

Arts & Sciences Electronic Theses and Dissertations

Proper cellular development and function is a complex process established by elaborate gene expression networks. These networks are regulated by epigenetic processes, which alter chromatin states and coordinate the binding of transcription factors (TFs) to regulatory elements (REs), such as enhancers, across the genome to facilitate gene expression. It follows then that a major experimental effort is to profile and understand the binding patterns of TFs to REs in various cellular types and contexts. Critically however, current TF profiling techniques are limited in their abilities to profile TF occupancy in targeted cellular populations and temporal windows, hindering investigations into epigenetic …

Developing Tools For Identifying Tissue-Specific Epigenetic Marks And Predicting Dna Hydroxy/Methylation, Yu He

Arts & Sciences Electronic Theses and Dissertations

A single genome can derive phenotypically unique cell types through various epigenetic modifications that instruct specific gene expression patterns. Histone modifications, DNA methylation, and DNA hydroxymetylation are the most common epigenetic modifications. To understand the mechanisms how these epigenetic modifications regulate gene expression, one often needs to map these marks genome-wide through profiling methods. Firstly, for histone modifications, Roadmap Epigenomics Consortium generated The Human Reference Epigenome Map, containing thousands of genome-wide histone modification datasets that describe epigenomes of a variety of different human tissue and cell types. This map has allowed investigators to obtain a much deeper and more comprehensive …

Deciphering Mechanisms Governing The Development Of The Rod Epigenome, Philip Andrew Ruzycki

Arts & Sciences Electronic Theses and Dissertations

Precisely coordinated expression of distinct sets of genes is essential for cellular development and function, especially in complex multicellular organisms. This regulation is achieved by the action of transcription factors (TF), proteins that bind specific genomic locations and alter the activity state and packaging of the DNA to promote or repress gene expression. However, while tremendous effort has defined networks of transcription factors that work together to drive specific phenotypes, little is known about their differential activity at the hundreds or thousands of sites where they bind. There are also many questions regarding the basic principles of the packaging of …

Brain Enriched Micrornas Open The Neurogenic Potential Of Adult Human Fibroblasts, Daniel Gene Abernathy

Arts & Sciences Electronic Theses and Dissertations

The seemingly limitless capacities of mammals to sense, respond, and manipulate their environments stems from their structurally and functionally diverse nervous systems. Establishing these complex behaviors requires the integration of many biological phenomena including, morphogenetic gradients, cell-cell signaling, transcriptional networks, cell migration and epigenetic gene regulation. As mammalian development progresses, these pathways coordinate the production of highly specialized neuronal and glial cells, that connect and communicate with another in an even more complex manner. While evolution has shaped a multitude of pathways to produce numerous favorable traits, it has also created an intricate system vulnerable to disease. The loss of …

The Effect Of Dietary Fat On Obesity, Gene Expression, And Dna Methylation In Two Generations Of Mice, Madeline Rose Keleher

Arts & Sciences Electronic Theses and Dissertations

As obesity rates continue rising nationally and globally, it is crucial to understand how a high-fat diet disrupts the regulation of the genome and leads to adverse health effects. Uncovering the underlying gene expression and DNA methylation changes induced by an individual’s high-fat diet and a maternal high-fat diet can pinpoint new targets for epigenetic therapies and reveal the physiological and behavioral changes in obesity. The goal of this dissertation is to gain deeper insight into the DNA methylation and gene expression changes that occur in response to a high-fat diet.

I studied the response to dietary fat within two …

Designing Epigenome Editing Tools To Understand The Functional Role Of Dna Methylation Changes In Cancer, James Mcdonald

Arts & Sciences Electronic Theses and Dissertations

DNA methylation is known to silence gene expression in the context of imprinting, X-chromosome inactivation, and retrotransposon silencing. However, the role of DNA methylation in silencing gene expression outside of these contexts is not fully understood. This is especially true in diseases such as cancer, where normal DNA methylation patterns are significantly altered. In breast cancer as well as nearly all cancer types, most of the genome loses DNA methylation while small regions of the genome gain methylation. DNA methylation generally correlates with decreased gene expression when present at a gene promoter. Therefore, these regions of hypo- and hyper-methylation may …

Epigenetic Regulation Of Lymphocyte Development And Transformation, Yue Huang

Arts & Sciences Electronic Theses and Dissertations

Cell identity and function rely on intricately controlled programs of gene regulation, alterations of which underlie many diseases, including cancer. Epigenetic analyses of normal and diseased cells have started to elucidate different facets of epigenetic mechanisms for gene regulation. These include changes in nucleosome density, histone modifications, factor binding and chromosomal architecture. All of these aspects contribute to the activities of regulatory elements conferring promoter, enhancer and insulator functions and the cis-regulatory circuits formed by these elements. Despite this progress, an urgent need remains to profile these features and to study how they cooperatively function in normal and pathogenic settings. …

Molecular And Epigenetic Regulation Of Stem Cell Radiosensitivity, Keith Michael Jacobs

Arts & Sciences Electronic Theses and Dissertations

Normal tissue injury resulting from ionizing radiation (IR) during cancer radiotherapy has been attributed to reduced regenerative capacity of stem cell compartments. Utilizing multiple in vivo tissue niches and primary culture models, we demonstrate that normal stem cells are highly radiosensitive while their isogenic, directly differentiated progeny are radioresistant. Stem cell dropout is therefore likely responsible for the resulting radiation injury in these niches. This differential radiosensitivity is independent of proliferation status, and increased IR-induced apoptosis in stem cells is more broadly distributed across the cell cycle.

We elucidate that stem cells exhibit an attenuated DDR resulting in aberrant cell …

Origin Of Maternal Age Effect In Congenital Heart Disease Risk For Offspring, Claire Elaine Schulkey

Arts & Sciences Electronic Theses and Dissertations

Increasing maternal age is widely acknowledged to lead to greater likelihood of pregnancy complications and congenital abnormalities, but the basis of this effect has not been well studied. Often dismissed as the product of oocyte ageing, the mechanistic basis of this maternal age effect is likely more complex.

Congenital heart disease is a classic complex disease with multiple genetic and environmental modifiers, including maternal age. Maternal ageing is a known risk-factor in humans, and has been shown to exist in an Nkx2-5 haploinsufficient mouse model for the disease. This mouse model's maternal age risk is dependent upon strain background, with …

On The Origin Of Phenotypic Variation: Novel Technologies To Dissect Molecular Determinants Of Phenotype, Francesco Vallania

All Theses and Dissertations (ETDs)

This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of …

Mutations Of Pdd1 Chromo- And Chromoshadow Domains Reveal Critical Functions For Each During Development Of Tetrahymena Thermophila, Rachel Schwope

All Theses and Dissertations (ETDs)

Pdd1 is a developmentally expressed HP1-like protein of Tetrahymena thermophila that is required during conjugation, when a copy of the cell's transcriptionally silent germline micronucleus differentiates into an active somatic macronucleus. Differentiation of these somatic chromosomes involves genome-wide fragmentation and amplification. These DNA rearrangements are facilitated by an RNAi mechanism, in which small RNAs target silencing histone modifications, H3K9 and H3K27 methylation, to Internal Eliminated Sequences: IESs), which are bound by Pdd1 and later excised from the genome. Pdd1 features two chromodomains, one of which shares homology with that of HP1, and a C-terminal chromoshadow domain. In this study, we …