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 7 of 7 for “"MNase seq"”.
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Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data
… including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the …
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Bioinformatic methods for the analysis of genetic variability and regulation
Next-generation sequencing (NGS) technologies have put within our reach several biological inquiries. In this thesis, we exploited NGS data to address questions related to how cell's genetic and epigenetic makeups give rise to phenotypic traits and regulatory processes. We started analyzing the …
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Role of DNA replication timing in gene expression and chromatin organisation
… DNA replication timing (RT) is a cause or a consequence of cellular fate changes. During my thesis I used a conditional system to perturb DNA RT in a single cell cycle in budding yeast, in combination with whole-genome sequencing techniques such as replication profiles, RNA-Seq and MNase-Seq in …
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Nucleosome repositioning in glioblastoma
… analysis performed here is based on experimental MNase-seq data in paired normal and tumour brain tissues from GBM patients as well as cfDNA from GBM patients and healthy individuals. I have determined GBM-specific changes in nucleosome occupancy profiles around binding sites of 20 …
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Deciphering genome-wide chromatin occupancy, dynamics, and their connections to gene regulation
… the chromatin configurations for the same genome sequence give rise to distinct cell types. Likewise, cells of the same type also undergo changes in chromatin configurations under different environmental conditions. Key changes to the occupancy profile of the chromatin may dictate changes in gene …
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The Animal-fungi Hybrid Cell Cycle of the Zoosporic Fungus Spizellomyces punctatus - a New Model to Understand Evolution of Eukaryotic Cell Cycle Control
… nucleosomal and TF-footprints generated from MNase-seq data.</p><p>Finally, I developed Agrobacterium-mediated transformation in Spizellomyces, allowing me to describe basic characteristics of its developmental program using live-cell and fluorescence microscopy. By following nuclear dynamics …
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DISTINCT GENOME WIDE FUNCTIONS OF CHROMATIN REMODELERS IN NUCLEOSOME ORGANIZATION AND TRANSCRIPTION REGULATION
… the nucleosome free region (NFR). Our RNA-seq analysis shows SWI/SNF positively regulates the bi-directional transcription of non-coding RNA (ncRNA) which are activated when the AT hook motifs are deleted. Moreover, AT hooks regulate such activities of SWI/SNF through direct protein-protein …