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 43 for “"Chromatin state"”.
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Classification of genes using clustering of chromatin state segmentations in human epigenomes
Combinatorial patterns of chromatin marks have been shown to play a significant role in gene regulation activities by changing the landscape of the DNA through chemical means. Recent work has expanded on this observation using ChIP-seq signals of chromatin marks and supervised algorithms to build …
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The Analysis of the MCF7 Cancer Model System and the Effects of 5-AZA-2'-Deoxycytidine Treatment on the Chromantin State Using a Novel Microarray-Based Technology for High Resolution Global Chromatin State Measurement
A microarray method to measure the global chromatin state of the human genome was developed in order to provide a novel view of gene regulation. The 'chromatin array' employs traditional methods of chromatin isolation, microarray technology, and advanced data analysis, and was applied to a cancer …
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The Role of Genomic Sequence in the Spatial and Temporal Propagation of Heterochromatin
… packaging of DNA into distinct types of chromatin. While chromatin state exerts a major influence on gene expression, the extent to which cis-acting DNA sequences contribute to the specification of chromatin state remains incompletely understood. To address this, we have used a fission …
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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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Modelling chromatin dynamics in neural stem cell quiescence and reactivation
… quiescent, remaining in an actively maintained state of cell cycle arrest. Quiescent and actively proliferating neural stem cells can be distinguished by their transcriptional state, however, the understanding of how these gene signatures are established at the epigenomic level remains lacking. …
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The role of MLL4 in the chromatin framework: from the epigenome to 3D genome organization
… (PcG) proteins, which enforce repressive states. Proper TrxG-PcG crosstalk is critical for various cellular processes and for determining cell fate. Although the balance between Trithorax and Polycomb has been recognized for decades, the mechanisms achieving and sustaining this …
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Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
… in their binding. While BEAF-32 binds in open chromatin, CTCF and su(Hw) showed increased binding is less accessible DNA. Furthermore, the model was able to recover binding preferences of three Hox TFs with respect to DNA accessibility. However, DNA accessibility showed some limitations to …
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Establishment of the epigenetic landscape in mammalian embryonic stem cells
… cis elements in the establishment of repressive chromatin domains. To this effect, we determined the genetic basis for localization of Polycomb repressive complexes (PRCs) in mammalian embryonic stem (ES) cells. First, by generating genomewide chromatin state maps in mouse and human by high …
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Multi-Omics Investigation to on the Effect of Replication Stress on Leukemia Cells
… replication stress leads cells to adopt a cell state similar to oncogene knockdown. Replication stress is likely not acting through chromatin state directly given that upregulated genes did not vary in their H3K27 modification or polymerase pausing, and many chromatin modifier genes that …
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REGULATION OF TELOMERASE EXPRESSION IN STEM CELL REPROGRAMMING
… opposing di-methylation, indicative of a closed chromatin state at the hTERT promoter. Subsequent treatment of cells with TSA alone showed an upregulation of hTERT mRNA without telomerase activity. However, telomerase activity was found when ASCs, but not BJs were treated with TSA and all four …
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Super-resolution Imaging of Chromatin and Functional Nuclear Architecture
… features of the genome, however, imaging chromatin within the nucleus is traditionally very difficult due to the dense packaging with a small nuclear volume. The nuclei of Drosophila melanogaster primary spermatocytes have unique properties that can circumvent these limitations, with …
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A C. elegans histone methyltransferase promotes spermatocyte gene expression, spermatid production and fertility
… understand the tissue-specific regulation of chromatin state in cell-fate determination and development, we defined the tissue-specific expression of all 36 lysine methyltransferase (KMT) genes by endogenous mRNA detection in C. elegans. We found that most KMTs are expressed in only one or two …
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Developmental Dynamics of 5-Hydroxymethylcytosine and its Role in the Terminal Differentiation of Neurons
… about how postmitotic neurons regulate their chromatin state. Modulation of transcription through the regulation of accessibility of transcription factor binding sites is essential for the regulation of migration, synapse formation and terminal differentiation. Although 5-hydroxymethylcytosine …
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Computational epigenomics : gene regulation, comparative methodologies, and epigenetic patterns
… theoretic computational methodology to identify chromatin state differences in groups of samples. In our methodology, we use correction for external covariates to isolate the relevant signal, and as a result, we find that our method outperforms existing computational methods, with further …
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Functional analysis of the histone variant H2A.Z during lineage commitment
… of H2A.Z ubiquitylation leads to a disrupted chromatin state and derepression of key developmental regulators in mESCs. Furthermore, we show that H2A.Zub is a crucial component required for regulating canonical Wnt signaling, a key pathway in early embryogenesis. Consistent with …
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Computational personal genomics : understanding the functional effects of sequence variation
… expression, transcription factor binding, or chromatin state. In this thesis, we use data from the ENCODE project to conduct a unique examination of allele-specific activity jointly across many layers of regulation including chromatin structure and modifications, occupancy by transcription …
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Changes of nucleosome positioning and 3D chromatin organization in cell transitions
… the nucleus in a highly condensed form called chromatin. The basic unit of chromatin is the nucleosome. The positioning of nucleosomes on the DNA determines the accessibility of transcription factors (TFs) and other regulatory molecules. Beyond nucleosome positioning, the higher level of 3D …
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Investigating the role of chromatin modifications in CRISPR/Cas9 gene editing
Precisely positioned nucleosomes and heterochromatin have been shown to impede CRISPR/Cas9 editing efficiency. Conversely, Cas9 can open previously inaccessible regions of DNA, and transcriptionally silent targets can usually be edited without difficulty. In order to address this paradox, we have …
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Chromatin-based memory of prolonged cold exposure in Arabidopsis thaliana
… to environmental conditions. In recent years, chromatin has emerged as an important player in orchestrating gene regulation. This thesis focuses on the role of chromatin in the maintenance of gene expression states and their inheritance through cell division. FLOWERING LOCUS C (FLC) in the …
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A Proteomic and Genomic Investigation Into Replication Fork Dynamics in Saccharomyces Cerevisiae
… with components of the replicative helicase and chromatin during S —phase. Previous studies have led to a picture wherein the replication of DNA progresses at variable rates over different parts of the budding yeast genome. It is widely held that the dynamics of replication fork progression are …
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