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 54 for “"genome organization"”.
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Dynamics of Genome Organization
… 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 dynamics, working towards a full four-dimensional characterization of genome organization. First, by pulling on a genomic locus …
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Genome organization in transcriptional regulation
… of cell identity, development, and disease. Genome organization contributes to transcriptional regulation in multiple ways. At a fundamental level, the genome is organized into distinct active and repressive chromatin states that facilitate transcriptional regulation. These chromatin states …
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Genome organization by loop extrusion
… We show that, in prophase, the interphase organization is rapidly lost in a condensin-dependent manner and chromosomes become compacted into arrays of consecutive loops. During prometaphase, these loops grow in size and become further split into series of smaller loops. The compacted …
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Unfolding genome organization in interphase
Genomic contact frequency 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 …
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Genome Organization And Expression Of Selected Potexviruses
… also examined the relationship of these viral genomes at the level of nucleotide sequence. Using RNA-cDNA hybridization we found that no homology exists between all members of the potexvirus group tested, not with unrelated members. As a further means of characterizing the genomes of these …
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How Chromosome-Nuclear Envelope Attachments Affect 3D Genome Organization
… for gene expression and regulation. Thus, genome sequences must be understood in the context of their 3D organization which critically influences the flow of information. The effort to understand this added complexity now encompasses an entire field of chromosome biology and is reshaping …
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Analysis of 3D Genome Organization in 4-Cell Mouse Embryos
… has shown a tight coupling between the spatial organization of the genome inside the cell nucleus and a cell’s gene expression profile, in order to gain insights into cell fate determination, we studied the 3D genome organization; in particular how chromosomes are arranged in the 3D space of the …
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Initiating international collaboration: a study of the human genome organization
The formation of the Human Genome Organization, nicknamed HUGO, in 1988 was a response by scientists to the increasing number of programs designed to examine in detail human genetic material that were developing worldwide in the mid 1980s and the perceived need for initiating international …
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Linking genome organization to nuclear function in astrocytes and muscle cells
… 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 chromatin …
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Modeling Genome Organization in Eukaryotic and Prokaryotic Cells Using Folding Determinant Interactions
The three-dimensional organization of genomes is fundamental to gene regulation, DNA replication, and cell identity. A key challenge, however, lies in disentangling stochastic folding driven by polymer physics from specific interactions mediated by nuclear landmarks and regulatory factors. In this …
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Computational methods for analyzing and modeling gene regulation and 3D genome organization
… and linking gene expression with the 3D organization of the genome. First, I describe methodologies for elucidating gene regulatory mechanisms by considering multiple data modalities. I design a computational framework for identifying colocalized and coregulated chromosome regions by …
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Multiscale Modeling of Genome Organization: Bridging Polymer Physics, Molecular Dynamics, and AI
The human genome is intricately organized within the nucleus, and its spatial arrangement plays a critical role in gene regulation, cellular function, and disease. Recent advances in high- throughput experiments have unveiled the heterogeneous and dynamic nature of chromatin organization at …
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Single-Molecule Investigation of Chromatin-Associated Factors in Genome Organization and Epigenetic Maintenance
… acids in the nucleus, forming reaction hubs for genome maintenance. This work also provides a new perspective to understand how various H1 subtypes and disease-associated mutations affect chromatin structure and function. In summary, we have gained a greater understanding of the biophysical basis …
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Aphid Transmission, Replication, and Transcription of BYDV -Pav -Il and Genome Organization of RhPV
… the 3' non-coding region of the BYDV-PAV-IL genome was found to be required for replication. These results illustrated that in vivo-transcribed cDNA clones can be effective tools for the analysis of the expression and replication of the BYDV-PAV genome. A Rhopalosiphum padi cDNA expression …
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Toward sequence-to-structure predictions of chromatin: Generative AI sheds light on genome organization
The secrets of the genome have captivated scientists for well over a century, though the active role its spatial organization plays in gene regulation, cell determination, and disease formation has become clear only in recent decades. Significant strides have been made toward characterizing and …
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The role of MLL4 in the chromatin framework: from the epigenome to 3D genome organization
… haploinsufficiency, TrxG members show reduced genome binding, while PcG strengthens its enrichment and genome occupancy. This chromatin state rearrangement is also reflected on a three-dimensional scale. Genome Architecture Mapping (GAM) experiments reveal distinct changes in 3D chromatin …
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"""TSA-Seq"": a novel proximity mapping approach for studying three dimensional genome organization and function"
"The organization of chromatin and its localization in the eukaryotic cell nucleus plays a critical role in gene regulation (Agarwal and Rao, 1998; Brown, 2003; Ferrai et al., 2010) and is important for maintaining normal genome function. However, although it is known that the distribution of …
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Analysis of the genome organization and fitness traits of non-pathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1)
In the last years more than one hundred microbial genomes have been sequenced, many of them from pathogenic bacteria. The availability of this huge amount of sequence data enormously increases our knowledge on the genome structure and plasticity, as well as on the microbial diversity and evolution. …
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Genomic and microscopic dissection of nuclear compartmentalization and function
The spatial genome organization in the cell nucleus is non-random and important for gene expression regulation. Abnormal nuclear organization is related to disease. Microscopy measurements of individual genes reveal a population-based, statistical gradient of increased gene activity from the …
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Scalable Methods for In Situ Genomics
… remains challenging, and accordingly the role of genome structure and organization in determining cellular function is an open question. Mapping cellular genome organization is difficult because it requires joint measurement of linear DNA sequence and 3D spatial context, however, existing …
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