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 114 for “"chromatin accessibility"”.
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Chromatin Accessibility Beyond the Peaks
Chromatin state resides at the intersection of trans-acting factors that operate globally over the genome but respond to changing conditions, and DNA sequence which is invariant across conditions but varies locally around genes. Assays that measure features of chromatin state can help us understand …
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Chromatin Accessibility Dynamics Underlying Development and Disease
… are incredibly malleable. Comparative studies of chromatin features between different cell types, tissues, and species have revealed tremendous differences in how the genome is accessed, transcribed, and replicated. However, how the dynamics of chromatin accessibility contribute to development, …
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Control of chromatin accessibility during CD4+ T cell development and activation
… in the genome, which is tightly controlled by chromatin structure, is required to acquire a specific gene expression profile and a new cell identity. The dynamic changes of the chromatin landscape during Treg differentiation are largely unknown. To study this, I measured chromatin accessibility …
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Small Molecules Modulate Chromatin Accessibility to Promote NEUROG2-Mediated Fibroblast-to-Neuron Reprogramming
… SOX4 expression, and promote SOX4-dependent chromatin remodeling. Genome-wide occupancy analysis revealed that SOX4 targets numerous SWI/SNF complex subunits and co-binds with NEUROG2 to enhance the expression of diverse neurogenic factors. The overexpression of SWI/SNF chromatin remodeling …
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Chromatin accessibility informs cell identity: studies in silico, in vitro, and in vivo
Chromatin accessibility provides key regulation in defining cell identity as it exhibits control over the ability of transcription factors and transcriptional machinery to bind to regulatory elements and initiate changes to gene expression. In this thesis I elaborate on the intricate relationships …
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Sequence-driven gene regulation across cellular contexts
… of the DNA. Transcription factors can induce chromatin accessibility and recruit co-factor proteins, leading to the indirect recruitment of RNA polymerase II to activate transcription. Observational screens and genetic data have given insights into which parts of the genome are likely involved …
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Estimating transcription factor binding properties in human cell lines using statistical methods and genomics datasets
… interact with the genome. Besides DNA sequence, chromatin accessibility, CpG methylation and cooperative binding with other transcription factors or themselves also impacts transcription factor binding. The era of high throughput sequencing has brought large amounts of genomic data, including …
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Dissecting the role of CHD4 in the NuRD and ChAHP complexes
… protein 4) is a widely conserved ATP-dependent chromatin remodeler essential for early mammalian development. Although best known for its role in gene regulation as a core component of the NuRD complex, CHD4 is also found within the ChAHP complex, which contributes to silencing of transposable …
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Exploring cis-regulatory models of the genome to predict epigenetic state and variation
… show that the addition of base-pair resolution chromatin accessibility covariate greatly aids in the prediction of cis-regulatory marks. Additionally, we show that by using cell-type specific covariates, CCM+ can generalize across cell-types. Finally, we show CCM+ can be used for downstream …
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On the Origins of Genetic Novelty in Drosophila
… originate and subsequently evolve; second, how chromatin accessibility maintains evolutionary lability while remaining conserved across broad sequence divergence. The study of the origins of new genes has flourished in the genomic era with the sequencing of genomes. De novo gene birth, where a …
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Leveraging Single-Cell ATAC-Seq for Genomic Language Models and Multimodal Foundation Models
Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful tool for profiling chromatin accessibility at single-cell resolution. By capturing epigenomic landscapes, scATAC-seq provides critical insights into the regulatory elements that govern …
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Epigenetic Regulation Controls Intrinsic and Extrinsic Drivers of Gastrointestinal Development
… gut development by mapping the genome-wide chromatin accessibility profile of the developing gut tube at a single-cell resolution, revealing that at the level of chromatin, individual cells are primed to acquire specific lineage fates. I further mapped epigenetic changes throughout gut …
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Deciphering genome-wide chromatin occupancy, dynamics, and their connections to gene regulation
… DNA is bound by a myriad of proteins to form the chromatin inside the nucleus of the cell. The proteins can bind to the genome in different combinations leading to a combinatorial explosion in the number of possible chromatin configurations. The differences in the chromatin configurations for the …
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OMICs based identification of the mechanisms that underpin FAK’s regulation of gene expression
… programmes, as well as FAK’s role in regulating chromatin accessibility and transcription factor binding. Integration of these datasets predicted that FAK regulates the binding of AP-1 and ETS transcription factors to chromatin. Furthermore, our findings indicate that a subset of FAK-regulated …
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Spatiotemporal control of gene expression in Caenorhabditis elegans
… characterize the dynamics of gene expression and chromatin activity across development and aging. Follow- ing this, I aimed to identify and characterize the regulatory elements involved in tissue-specific control of transcription in C. elegans. I jointly profiled chromatin accessibility and gene …
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The NuRD complex regulates chromatin dynamics driving exit from naïve pluripotency
… and in vivo. However, the specific mechanisms of chromatin modulation by NuRD in this process have not been fully characterised. This study used rapid, auxin-inducible removal of NuRD components in mouse ESCs to dissect its role in the regulation of transcription factor (TF) binding dynamics, …
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PHF6 modulates the chromatin landscape in B-cell leukemia
… in leukemia and define its role in regulating chromatin accessibility to lineage-specific transcription factors. We show that loss of Phf6 in B-cell leukemia results in systematic changes in gene expression via alteration of the chromatin landscape at the transcriptional start sites of B- and …
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Principled Methods and Models for Deep Learning Based Functional Genomics
… to study the determinants of cell type-specific chromatin accessibility, with an ensemble of neural networks trained on DNase-seq data to predict chromatin accessibility, and MIAA, the multiplexed integrated accessibility assay, to validate, experimentally, these in silico predictions. The third …
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Role of host chromatin remodelling in Mycobacterium leprae-induced Schwann cell fate change
… Sox2 binding sites in order to define changes to chromatin accessibility and Sox2 binding. Cultured mSwCs, along with fixed ML-mSwC models, were validated and phenotypically characterised through microscopy with additional immunofluorescence staining for Schwann cell lineage markers (p75-NTR, …
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Investigation of transcriptional regulation by C. elegans SET-2/SETD1 H3K4 methyltransferase through single-nucleus profiling
… in different ways, depending on the cell type, chromatin environment and locus. In this thesis, I investigated the consequences of loss of SET-2, the C. elegans orthologue of mammalian SETD1, in early embryogenesis using single-cell profiling of nuclear transcription and chromatin accessibility. …
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