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 29 for “"conformation-capture"”.
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Investigating 3D genome organisation in Caenorhabditis elegans with Accessible Region Conformation Capture (ARC-C)
… a variant of Hi-C, named Accessible Region Conformation Capture (ARC-C), in C. elegans, which interrogates genome organisation at multiple scales genome-wide - from domains and compartments to high resolution interactions between regulatory elements. I applied ARC-C in wild-type Bristol N2, …
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Unfolding genome organization in interphase
… maps obtained from high throughput chromosome conformation capture technologies have revealed several organizing patterns of mammalian interphase chromosomes, including self-interacting topologically associating domains (TADs) which are believed to function as coherent gene regulatory …
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UNCOVERING STRUCTURE-FUNCTION RELATIONSHIPS IN CHROMATIN ARCHITECTURE
… inner subTADs in high resolution Chromosome-Conformation-Capture Hi-C data. We then apply our method to chromatin dynamics during mitosis, uncovering how TADs and subTADs evolve temporally. Afterwards, we classify TADs/subTADs by the presence of other genome folding features, compartments and …
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Dynamics of Genome Organization
… 15 years, following the advent of chromosome conformation capture techniques. The fourth dimension---time---however, has remained elusive and the dynamics underlying the organization of the genome are much less known. In this thesis I present my contributions to our understanding of these …
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Genomic Regulation of the Shox2 Gene during Mouse Limb Development
… profiling, we have utilized circular chromosome conformation capture (4C-seq) technology to probe the entire cis-regulatory organization of the Shox2 gene during limb development. We show five of numerous genomic regions within a 1.5 megabase (Mb) chromosomal territory surrounding the Shox2 gene …
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Linking genome organization to nuclear function in astrocytes and muscle cells
… Therefore, I evaluated chromosomal interactions captured by HiC and Circular Chromosome Conformation Capture (4C) for mito-nDNA interactions in order to determine if they are random. I show that the mito-nDNA interactions captured in mammalian cells are statistically significant and shared …
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Characterizing 3D epigenomes in pathological conditions
… cells and neurons. By employing chromatin conformation capture methodologies, I have detailed the 3D genome structures across different layers in Trisomy 21 neural stem cells.</p> <p>Turning to SARS-CoV-2, I charted the three-dimensional chromatin structure and comprehensive epigenomes …
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Identificazione e analisi funzionale di fattori regolatori dei geni globinici
… at these loci we applied “Genome Wide Chromosome Conformation Capture” (Hi-C), followed by a novel technique for a selective enrichment at these target regions, to characterize whether they are involved in long range physical interactions able to modulate HBS1L-MYB and BCL11A expression. As a …
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Computational Methods for Integrating Microscopy with Chromatin Structures
… understood, but the development of chromatin conformation capture (3C) techniques has enabled the first thorough study of intermediate scales. These methods provide information about the distances between pairs of genomic loci, which gives indirect information about their positions. By …
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Patterns and processes driving chromosome organization
… of interaction maps generated from Chromosome Conformation Capture (3C) technologies. We begin by analyzing data generated using a novel Micro-C protocol and assess its performance in comparison to established Hi-C. New computation tools are developed to extract, quantify and compare patterns …
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Chromatin Architecture Aberrations Contribute and Acute Lymphoblastic Leukemia Relapse
… intervention. Secondly, I used chromatin conformation capture of 12 primary prostate cancer tumours and 5 benign prostate tissues to characterize the three-dimensional genome organization. We found that large-scale organization, including topologically associated domains and compartments, …
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Genome-Wide and Multi-Scale Mapping of DNA Supercoiling in Differentiating Human Stem Cells
… then integrating this dataset with a chromatin conformation capture Hi-C map, we studied DNA supercoiling across multiple scales: from kilobase genes, through larger-scale topologically associating domains, to megabase epigenomic compartments. Crucially, we observed the formation of supercoiling …
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Single-molecule G-quadruplex visualisation in live cells and 3D chromatin
… Hi-C method. Hi-C is a fixed nucleus chromatin conformation capture technique that can simulate 3D chromatin structure via high-throughput sequencing of DNA strands in close proximity. 3D imaging of G4s has revealed their localisation throughout the nucleus volume with several regions showing …
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Computational Analysis of Transcriptional Regulation
… cervical carcinogenesis with a novel Chromosome Conformation Capture (3C) method that specifically enriches for interactions involving viral integrants. Integration occurs without disrupting host 3D chromatin structure but alters the expression of many neighbouring host genes. The advent of …
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Linker Histone Medicated Regulation of Mitotic Chromosome Compaction and Individualization
… Xenopus egg extract chromosomes using chromosome conformation capture technique Hi-C. Using Hi-C analysis, I showed that condensin I organizes both mitotic loops and loop layers of mitotic chromosomes and that H1.8 mediated suppression of condensin I increases both mitotic loop and layer sizes. …
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Integrative analysis of transcriptional activity and genome architecture changes upon viral infections
… infections, I employed a genome-wide chromosome conformation capture approach (Hi-C) on infected murine and human cells and further enriched those libraries for genomic loci of interest and the viral genomes with biotinylated RNA baits. In parallel, I profiled newly transcribed RNA throughout the …
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An Investigation Into The Role Of Cfia 3' End Processing Complex In The Termination And Initiation/reinitiation Of Transcription
… a functional Clp1 protein. Using the chromosome conformation capture approach, CCC, we observed a role for Clp1 in gene loop formation. We found a strong correlation between the Clp1 function in gene looping, and its role in promoter-associated transcription which implies gene looping as the …
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The Nucleosome Remodelling & Deacetylase complex: Genome folding & transcriptional regulation
… of nucleosomes. Until the advent of Chromosome Conformation Capture (3C), and related experiments, relatively little was known at scales between these two. In particular, the Hi-C experiment provides genome-wide pairwise information about the frequency with which two genomic loci come into …
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The interplay of global chromosomal organisation, promoter-enhancer interactions and transcription
… In recent years, the emergence of chromosome conformation capture and related methodologies has dramatically increased our understanding of chromosomal organisation. In particular, high-throughput Hi-C analyses across cell types have led to the identification of spatial genomic structures, …
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Microfluidic technology for cellular analysis and molecular biotechnology
… in one step. Enhancement in cell isolation (high capture efficiency or high selection purity) is experimentally observed and the former is explained by computational model. In the final part of the dissertation, microfluidic device incorporating valves and mixers for sensitive study of chromosome …
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