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 15 of 15 for “"DamID"”.
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Characterizing the Nuclear Function of the Cell Adhesion Molecule Fat and Chromatin Regulation by the Inner Nuclear Membrane Protein Speg
… nucleus, Ft is associated with chromatin. Using DamID-microarray, a DNA binding site mapping technique, I showed that Ft binds to specific genomic loci in vivo. Through ChIP-seq, I characterized the genome-wide DNA binding profile of Ft in vivo. ChIP-seq results suggested that nuclear Ft binds …
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Exploring the Role of Long Non-Coding RNA in Neural Stem Cell Reactivation from Quiescence: A Functional Genomics Approach
… potential target genes. To do this, I used RNA-DamID to identify in vivo targets of pron. I correlated this genome-wide binding data with differential gene expression and chromatin accessibility, using a combination of single-cell RNA sequencing and chromatin accessibility DamID, to better …
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Modelling chromatin dynamics in neural stem cell quiescence and reactivation
… wealth of genomic profiling tools such Targeted DamID makes it an ideal model for studying chromatin transitions in vivo. In this project, I used a selection of DamID tools to generate a comprehensive dataset of Drosophila neural stem cell chromatin landscape in early proliferating, quiescent and …
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The role of Dichaete in transcriptional regulation during Drosophila embryonic development
… binds in the genome, I generated whole genome DamID data for embryos and followed this with a detailed comparative analysis, combining my data with three newly published ChIP-chip datasets. The combined studies identify thousands of binding regions, mostly in the vicinity of developmentally …
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Exploiting Lentiviral Integrations to Profile Chromatin
… while other antibody-free techniques like DamID are limited by the availability of specific DNA sequences. Here, I describe the development of ChILI-seq (Chromatin Interactions by Lentiviral Integration Sequencing), an antibody-free and sequence-independent method to profile the genomic …
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Genomic and microscopic dissection of large-scale chromatin compaction
… LAD/innerLAD boundaries defined by lamin B1 DamID, and rapid transitions in the Hi-C principal eigenvector signal. Moreover, cluster analysis reveals DLCDs map most frequently to divisions between chromatin domains of varying epigenetic marks. To validate the existence of DLCDs, I have …
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Systemic and local signalling regulating neural stem cell proliferation
… signals sent to the brain, I used Targeted DamID to generate transcriptional profiles of the fat body under fed and starved conditions. I discovered upregulation of *dpp (decapentaplegic)*, a transforming growth factor (TGFβ) secreted morphogen, after feeding. Knockdown of Dpp in the fat …
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Investigating the functional and evolutionary significance of Group B Sox genes in arthropods
… within the beetle genome (a technique known as DamID). Unfortunately, these last set of experiments have proved unsuccessful, despite several attempts which have made use of different promoters, different DNA enrichment methodologies, and tackling unforeseen DNA contamination issues. …
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Hypoxia signalling regulates human lung epithelial cell fates
… Combining transcriptomic and targeted DamID-sequencing analyses, my collaborators and I identified direct HIF target genes, including KLF-family transcription factors. I further examined functions of KLF4 and KLF5 in lung epithelial progenitors with CRISPRi. KLF4 and KLF5 facilitated …
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Genomic and microscopic dissection of nuclear compartmentalization and function
… to the center. Sequencing-based methods (Hi-C, DamID) suggest the genome could be partitioned into two compartments: transcriptionally active and inactive chromatin positioned at the interior and periphery of the nucleus, respectively. Newer genomic methods (SPRITE, GAM) suggest multi-way …
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Multiscale Modeling of Genome Organization: Bridging Polymer Physics, Molecular Dynamics, and AI
… reproduces experimental data from Hi-C, TSA-seq, DamID, and DNA-MERFISH. The developed software is fully open-source and GPU-accelerated, enabling large-scale simu- lations and mechanistic explorations. In Chapter 3, we explore the impact of genome organization on various biological phe- nomena …
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Evolutionary patterns of group B Sox binding and function in Drosophila
… features of group B Sox binding, I performed DamID-seq for SoxNeuro and Dichaete in four species of Drosophila, D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura. I also performed FAIRE-seq in D. pseudoobscura embryos to compare the chromatin accessibility landscape between two fly …
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Investigating the underlying mechanisms of axis formation in Drosophila melanogaster
… this process. The transcriptomic method Targeted DamID was used to quantify gene expression in these cells, compared to their lateral follicle cells counterparts. This resulted in the identification of 140 genes which were either uniquely expressed or upregulated in posterior follicle cells. …
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Identifying regulators of neural stem cell fate and tumourigenesis
… regulated by Tll in type II NSCs I used Targeted DamID to determine the genome-wide binding sites of Tll in vivo. My results showed that Tll binds to many of the genes required for type II NSC identity, suggesting that Tll is a master regulator of type II NSC fate. To test if the tumourigenic …
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Exploring a Nuclear Insulin Receptor Signalling Pathway in Drosophila Neural Stem Cells
… recently published technology based on Targeted DamID, was used to profile the chromatin association of InR in NSCs *in vivo* genome‐wide. NanoDam was performed at endogenous levels of InR expression in the InR‐GFP background, and under misexpression conditions in the UAS‐*InR‐CFP* background. …