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 20 of 22 for “"Nucleosome positioning"”.
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Statistical analysis and modeling of nucleosome positioning
Nucleosome is the fundamental building block of eukaryotic chromatin. The precise location of nucleosome along the genome plays a central role in gene regulation by controlling the accessibility of genetic information encoded in DNA. Understanding the principles underlying the establishment of …
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Changes of nucleosome positioning and 3D chromatin organization in cell transitions
… chromatin. The basic unit of chromatin is the nucleosome. The positioning of nucleosomes on the DNA determines the accessibility of transcription factors (TFs) and other regulatory molecules. Beyond nucleosome positioning, the higher level of 3D chromatin architecture is constituted by …
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Evolution of nucleosome positioning and gene regulation in yeasts : a genomic and computational approach
… gene expression by measuring mRNA abundance and nucleosome positions genome-wide in 13 Ascomycota yeast species. Our work introduces a host of new computational tools for studying chromatin structure, function, and evolution. We improved on existing methods for detecting nucleosome positions and …
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Nucleosome repositioning in glioblastoma
… genetic or epigenetic causes. In particular, the positioning of nucleosomes along the genome determines the accessibility of DNA to regulatory proteins and therefore modulates gene expression. In this project I investigate nucleosome positioning in relation to other features, such as transcription …
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Autonomous and non-autonomous regulation of chromatin structure during cellular senescence
… accessible chromatin) we demonstrate that nucleosome positioning is substantially altered in RIS and that this re-distribution is also antagonised by NOTCH1, resulting in a distinct chromatin landscape. Importantly, normal or cancer cells that express the NOTCH ligand jagged-1 can drive …
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Leveraging high-throughput datasets for studies of gene regulation
… pre-transcriptional gene regulation through nucleosome positioning, which resulted in the identification of function-specific factors and improved predictive performance. Next, computational analysis enabled the discovery of genome-wide epigenetic modifications that play a foundational role …
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Cross-regulation and interaction between eukaryotic gene regulatory processes
… machinery. We found a marked enrichment for nucleosomes at exonic DNA in human T cells, as compared to surrounding introns, an effect mostly explained by the biased nucleotide content of exons. The use of nucleosome positioning information improved splicing simulation models, suggesting …
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Investigating the role of molecular motors on chromatin organization
… multiple levels of packaging. On one hand, nucleosomes, as the most fundamental packing unit, controls the accessibility of chromatin through their positioning along the DNA sequence, where ATP-driven remodelers, DNA-binding proteins are known to play essential roles. On the other hand, the …
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PHF6 modulates the chromatin landscape in B-cell leukemia
… focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition.
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Towards Models Mesoscale Chromatin Structure and Radiative DNA Damage via Computational Simulation
… of chromatin fiber at the level of several nucleosomes–the mesoscale–is an area of active study. Recent results have shown that it differs between functional states, affects higher orders of chromosome organization, and is likely involved in transcriptional control. However, the …
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Protein-DNA Binding: Discovering Motifs and Distinguishing Direct from Indirect Interactions
… different types of biological information (e.g., nucleosome positioning information) to guide the search for DNA binding sites toward regions where these sites are more likely to occur (e.g., nucleosome-free regions). </p><p>We use transcription factor (TF) binding data from yeast chromatin …
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Role of Nucleosome Remodeling Factor (NURF) in Tumorigenesis Using a Breast Cancer Mouse Model
… they are potential targets for cancer therapy. Nucleosome Remodeling Factor (NURF) is a chromatin-remodeling complex that regulates gene expression by changing nucleosome positioning along the DNA sequence. Previous studies have shown a role for NURF in embryonic development as well as …
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The role of the SWI/SNF ATP dependent chromatin remodelling complex in the regulation of the human hair follicle cell proliferation and control of the human cutaneous wound healing
… covalent DNA and histone modifications, nucleosome positioning and ATP-dependent chromatin remodelling as well as higher order chromatin folding and 3D genome organisation. ATP-dependent chromatin remodelling complexes modulate nucleosome structure, positioning and chromatin de-compaction …
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Mammalian gene regulation through the 3' UTR
… we investigated the potential impact of nucleosome positioning on poly(A) site usage. Using recent, public, Illumina sequencing data from human nucleosome boundaries, we found evidence that greater nucleosome density in regions flanking but not overlapping poly(A) sites is associated with …
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Transcriptional bursting in eukaryotic gene regulation : molecular basis and functional consequences
… the importance of activator residence time and nucleosome positioning on bursting. This investigation exemplifies how we can exploit spontaneous fluctuations in gene expression to uncover the molecular mechanisms and kinetic pathways of transcriptional regulation. At the network level, we …
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Investigating the molecular dynamics of gene re-silencing following treatment with epigenetic therapies
… on DNMT1 depletion and hypomethylation, nucleosome eviction and the acquisition of active histone marks at the MLH1 promoter. However, close inspection of the early stages of gene re-silencing showed that loss of expression occurred despite persistent hypomethylation. Instead, gene …
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Roles of the Histone Chaperone FACT in Drosophila Gene Regulation and Chromatin Architecture
… contribute to the disassembly and reassembly of nucleosomes in the wake of RNA polymerase II passage through chromatin. In yeast, mutation of FACT subunits leads to decreased nucleosome occupancy at the promoters and transcribed regions of genes. In addition, genetic experiments suggest that …
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Investigating DNA G-quadruplex structure function through genome and epigenome engineering
… the local histone methylome. Third, G4s organise nucleosome positioning to influence chromatin accessibility and recruitment of RNA polymerase II. Cells edited to lack the *MYC* G4 lead to loss of *MYC* transcription from the P1 promoter and the deposition of a *de novo* nucleosome that interferes …
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The effect of negative supercoiling on the formation and positioning of nucleosome cores in vitro
… supercoiling of DNA on the formation and positioning of nucleosome cores was investigated in a 1915bp plasmid (pHP2) containing a section of the early H1-H4 histone gene spacer of Psammechinus miliaris, previously shown to position the histone octamer (Retief et al., 1987, Biochemistry, …
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AN EXAMINATION OF THE DOMAIN ARCHITECTURE OF THE IOC2 AND IOC3 SUBUNITS OF THE ISW1 COMPLEXES IN SACCHAROMYCES CEREVISIAE
… remodeling activity and the ability to space nucleosome arrays at ~175bp increments, promoting the formation of a repressive chromatin structure. ISW1b lacks both of these biochemical properties and was found localized within the coding regions of genes functioning in the regulation of …
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