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.
Results
Showing 1 to 20 of 26 for “"chromatin interactions"”.
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Identifying chromatin interactions at high spatial resolution
… two computational approaches for identifying chromatin interactions at high spatial resolution from ChIA-PET data. We introduce SPROUT which is a hierarchical probabilistic model that discovers high confidence interactions between binding events that it accurately locates. We apply SPROUT to …
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UNCOVERING LNCRNA-CHROMATIN INTERACTIONS SHAPING HUMAN MONOCYTE TO MACROPHAGE DIFFERENTIATION
… non-coding transcripts, that can associate with chromatin and contribute to the regulation of genome organization and gene expression. However, the functional roles of most chromatin-associated RNAs, particularly long non-coding RNAs (lncRNAs), are still being elucidated, with new functions …
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Making Molecular Movies: Using Single-Molecule Techniques to Unveil Hidden Features of Protein-Chromatin Interactions
… of physical regulation for proteins operating on chromatin. Previously, tracking these protein behaviors on DNA and chromatin had been technically challenging, dependent on tools that could access short-lived, heterogenous, and out-of-equilibrium interactions. It is now possible to observe these …
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Identificazione e analisi funzionale di fattori regolatori dei geni globinici
… whether they are involved in long range physical interactions able to modulate HBS1L-MYB and BCL11A expression. As a first step we optimized a Hi-C protocol in the K562 fetal erythroid cell line and we set up the conditions for the new method based on the selective enrichment of target regions. We …
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Investigating the function of DNA G-quadruplex structures in human enhancers
… I explore the folding of G4 structure in 3D chromatin interactions, and dissect the function of a G4 in the control of enhancer-promoter communication for accurate gene regulation at the human β-globin locus. First, a new methodology, viewpoint Hi-C on accessible regulatory DNA (ViCAR), was …
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The evolution of gene regulatory landscapes in mammalian tissues
… bisulfite sequencing (WGBS) and matched chromatin immunoprecipitation assays followed by sequencing (ChIP-seq) of five TFs from the livers of five mammals. I first characterized DNA methylation patterns at transcription factor binding regions and found four prototypical methylation …
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RNA in the nucleus: insight into location and biological function
… Currently used technologies to study RNA chromatin interactions pull down individual RNAs and sequence the associated DNA. However, it remains challenging to identify chromatin associated RNAs and their genomic target sites. In this thesis, I will describe MARGI-seq, a method to identify …
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Data-driven Mechanistic Modeling of 3D Human Genome
… we introduce a computational model to simulate chromatin structure and dynamics. The model defines chromatin states by taking one-dimensional genomics and epigenomics data as input and quantitatively learns interacting patterns between these states using experimental contact data. Once learned, …
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The Sumoylation of General Transcription Factors Regulates Transcription in Saccharomyces cerevisiae
… or reduced TFIID or TFIIF sumoylation. Using chromatin immunoprecipitation (ChIP), we found that GTF sumoylation does not substantially impact GTF-chromatin interactions but can impact the promoter-wide sumoylation level. Notably, TFIID and TFIIF sumoylation enhances RNAPII recruitment at …
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From Protein Folds to Chromatin: Topological Data Analysis and Deep Learning at Multiple Scales
… folds to the three-dimensional architecture of chromatin—structural organization governs molecular function and regulation. We present two complementary computational frameworks that integrate geometric, topological, and spatial modeling with deep learning to elucidate these structure–function …
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Integrative analysis of transcriptional regulatory programs in mammalian systems
… Finally, we study the mechanisms underlying the interactions between lncRNAs and chromatin. Given the experimental loss of function studies and considering the RNA-first hypothesis, it is hard not to imagine a central role for RNAs in fundamental cellular processes such as transcription and DNA …
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Transcript Regulation within the Kcnq1 Domain
… In addition, this regulation involves complex interactions between enhancers, insulators and other regulatory elements to control the amount of silencing by the Kcnq1ot1 ncRNA. First, through a series of experiments looking at the Kcnq1 promoter, the mechanism of Kcnq1 paternal expression was …
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Linking genome organization to nuclear function in astrocytes and muscle cells
Higher-order chromatin structures have been identified in the genome. These structures have been linked to nuclear processes, including transcription. However, how dynamic these chromatin structures change throughout mammalian development remains to be determined. I have mapped genome-wide …
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Exploiting Lentiviral Integrations to Profile Chromatin
… modifications and protein localisation along chromatin suffer from critical limitations: the gold standard, ChIP-seq, relies on high-quality antibodies, while other antibody-free techniques like DamID are limited by the availability of specific DNA sequences. Here, I describe the development …
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Non-Parametric Analyses of the Regulatory Roles of LINE-1 Retrotransposons during Motor Neuron Differentiation
… some low-complexity regions may participate in chromatin interactions with cis-regulatory sequences in a cell-type specific manner analogous to enhancer-promoter interactions. Conclusion: The thesis elucidates a set of functional hypotheses concerning putative regulatory roles of repetitive …
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Chromatin Architecture Aberrations Contribute and Acute Lymphoblastic Leukemia Relapse
… These aberrations can be found within the chromatin architecture of cancer cells that includes the genome, molecular modifications to the genome, and the three-dimensional organization of the chromatin fiber. The majority of genetic variants target non-coding regions of the genome and many …
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P53 Maintains Hepatic Cell Identity During Liver Regeneration
… and RNA sequencing) and profiling of p53 interactions with chromatin (ChIP sequencing) at the G1-S transition of normal cell cycle, corresponding to 24h post-PH in mice liver regeneration, will reveal p53 functions during cell cycle regulation in normal cells and during tissue …
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THE ROLE OF TRANSCRIPTION FACTOR DYNAMICS IN GENE EXPRESSION: DOES TIME MATTER?
… the nuclear microenvironment and interact with chromatin to activate or silence genes remains poorly understood. I used state of the art microscopy and genomic techniques to show that binding times of TFs to chromatin are power-law distributed. I proposed a new theoretical framework to …
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Development of a multiscale coarse-grained chromatin model
… the structure of biomolecules inside nano-scale chromatin. In this thesis, we develop a multiscale coarse-grained chromatin model, which integrates all-atom representations of proteins, DNA, and nucleosomes; a chemically specific coarse-grained model of kb scale chromatin; and a minimal model of …
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Integrative statistical methods for the genomic analysis of immune-mediated disease
… of GWAS summary statistics within PCHi-C chromatin contact maps I developed a novel statistical method, blockshifter. I applied \textit{blockshifter} to a compendium of GWAS summary statistics for 31 traits and PCHi-C data across 17 primary blood tissues, and found convincing evidence for …
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