Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 19 of 19 for “"differentially methylated regions"”.
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Advances in Differentially Methylated Region Detection and Cure Survival Models
… of the dissertation pertains to the detection of differentially methylated regions in the human genome. The varying distribution of gaps between succeeding genomic locations, which are represented on the microarray used to quantify methylation, makes it challenging to identify regions that have …
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Dynamic regulation and functions of locus-specific DNA methylation
… pattern of DNA methylation (tissue-specific differentially methylated regions, T-DMRs) in the distal regulatory elements, such as enhancers. The formation of T-DMRs still remain mysterious, however, one of their interesting features observed in mouse ES cells (mESCs) is the …
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CHARACTERIZATION OF DNA METHYLATION PATTERNS IN HUMAN EMBRYONIC STEM CELLS AND COLORECTAL CANCER USING WHOLE GENOME BISULFITE SEQUENCING
… and histone modifications can identify the differentially methylated regions and genes involved in the regulation of cell differentiation and CRC.
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DNA methylation in early mammalian development
… at fertilization, and discover many, novel differentially methylated regions between the gametes that exist transiently during early development. Notably, the majority of epigenetic events unique to mammalian pre-implantation development are characterized in mouse. In Chapter 2, 1 describe …
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A functional data analytic approach for region level differential DNA methylation detection
… and statistical reasons to test entire genomic regions for differential methylation. The individual loci may be noisy but the overall regions tend to be informative. Also, the biological function of regions is better studied and are more correlated to gene expression, so the interpretation of …
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The effect of age on human monocyte epigenetics and function
… or their transcription. It was determined that differentially methylated regions often mapped to genes involved in phosphorylation, signal transduction, DNA binding and cellular projections. Furthermore, differentially expressed regions mapped to genes involved in immune functions, specifically …
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Investigating the role of epigenetics in rapid adaptation to stress in Arabidopsis thaliana and Sorghum bicolor
… herbicide stresses. Similarly, we found higher differentially expressed genes for clipping as compared to both herbicides. All four stresses changed the methylome in a unique way; where we found 998 differentially methylated regions (DMR) for trifloxysulfuron, 193 for shading, 141 for clipping …
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DNA methylation analysis and identification of a novel antisense transcript in the Peg3 imprinted domain
… genomes. We identified two previously unreported differentially methylated regions (DMR): one in the promoter region of mouse Zim3 and another in the promoter region of human USP29. The PEG3-CpG island is the only DMR that is conserved among these three species. PEG3 has been implicated in several …
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DNA Methylation and Genetic Divergence Associated with an Inducible Defensive Response in Mimulus guttatus
… from Monkeyflower. The first pipeline detects regions that are differentially methylated and identifies adjacent candidate genes, using Nanopore data. This was tested on data from a Monkeyflower recombinant inbred line (RIL) subject to either parental damage or control conditions. The second …
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The DNA methylation landscape of metastatic prostate cancer: from characterization to liquid biopsy applications
… methylation profiling data to nominate robust differentially methylated regions (DMRs). Rocker-meth can retrieve biologically relevant DNA methylation changes, as demonstrated by extensive integrative analyses with gene expression, chromatin states, and genomic annotations. The second …
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Identifying Regional DNA Methylation Patterns in the Human Aorta in Health and Disease
… proximal aortic arch. Identification of these differentially methylated regions (DMRs) in cell-free DNA (cfDNA) will provide a biomarker of aortopathy. We also hypothesized that DNA methylation in the aorta is affected by valve morphology and is related to the pathogenesis of aortopathy. To …
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Investigating the Epigenetic Mechanism Behind Transgenerational Inheritance in Mice with Abnormal Folate Metabolism
… Subsequently, we identified a large number of differentially methylated regions (DMRs) in sperm DNA of $\it{Mtrr^+/+}$, $\it{Mtrr^+/gt}$, and $\it{Mtrr^gt/gt}$ males compared to C57Bl/6 control sperm. Few DMRs were associated with underlying SNPs or SVs. However, no sperm DMRs identified in …
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Molecular characterization of methylated circulating tumour DNA biomarkers and their detection with low-cost biosensor
… classification of cancers. Recently, cell-free methylated DNA immunoprecipitation (cfMeDIP) method was used to distinguish localized from advanced prostate cancers with high sensitivity. The challenge in prostate cancers is that the methylation levels are notoriously heterogeneous, which may …
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The Epigenetic Role of EGR1 during Postnatal Mammalian Brain Development
… that brain methylomes are heterogeneously methylated across different types of cells and the transcription factors play key roles in brain methylome programming. To dissect brain methylome heterogeneity, in Chapter 2, we first focused on the identification of cell-subset specific methylated …
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On the Analysis of DNA Methylation
… possible and estimate that 28% of CpGs, in regions comprising 11% of the genome, show variable methylation and are enriched in regulatory regions. Secondly, we show that WGBS has inherent resulution limitations in a read count dependent manner and that the identification of unmethylated …
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Microfluidic Technology for Low-Input Epigenomic Analysis
… using a transgenic mouse model with microfluidic methylated DNA immunoprecipitation followed by next generation sequencing (MeDIP-seq) assays. Third, I explored negative enrichment of circulating tumor cells (CTCs) followed by microfluidic ChIP-seq technology for studying temporal dynamic histone …
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Epigenetic Response to Low-Dose Ionizing Radiation
… H19, were assessed for methylation changes in differentially methylated regions (DMRs) that regulate their parent-of-origin monoallelic expression using Sequenom technology. Lastly, it was postulated that the epigenetic changes at the Avy locus could be counteracted with dietary alterations. To …
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Defining the Epigenetic Evolutionary Dynamics that Precede Acute Myeloid Leukaemia
… end, the first aim of this work was to identify differentially methylated regions (DMRs) in AML. In Chapter 2, we developed a statistical method for identifying DMRs from whole genome bisulfite sequencing data and applied this to existing datasets of purified AML blasts and healthy hematopoietic …
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Towards a blood-based biomarker for remyelination: Glial cell death and associated byproducts in demyelinating disease
… These results prompted my effort to identify differentially methylated regions in OPCs and microglia by isolating cells from human brain tissue and whole-genome bisulfite-sequencing, resulting in the identification of novel methylation-sensitive ddPCR targets. Next, I completed a thorough, …