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 114 for “"nucleosomes"”.
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The Mi-2 Homolog Mit1 Actively Positions Nucleosomes Within Heterochromatin to Suppress Transcription
… form a dynamic structure known as chromatin. Nucleosomes are the repeating unit of chromatin, and consist of DNA wrapped around an octamer of histone proteins. Nucleosomes can then be modified and spatially arranged to facilitate processes such as transcription, DNA replication, and repair. A …
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Using "Designer" Nucleosomes to Study Enzymatic Crosstalk Between Histone Ubiquitylation and Histone Methyltransferases
… Here, using chemically-defined "designer" mononucleosomes, I tested whether nucleosomal H2BK120ub and H2AK119ub influence the activity of a well-studied histone methyltransferases complex that is repressive to transcription, Polycomb Repressive Complex 2 (PRC2). I also built upon previous …
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SWI/SNF-NUCLEOSOME INTERACTIONS AND DISASSEMBLY OF NUCLEOSOMES: NOVEL METHODOLOGIES FOR MAPPING PROTEIN-PROTEIN AND PROTEIN-DNA INTERACTION
… INTERACTIONS AND DISASSEMBLY OF NUCLEOSOMES: NOVEL METHODOLOGIES FOR MAPPING PROTEIN-PROTEIN AND PROTEIN-DNA INTERACTION MAJOR PROFESSOR: Dr. Blaine Bartholomew The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. A site-directed photoaffinity …
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MODES OF NUCLEOSOME INTERACTION AND MECHANISMS OF THE SACCHAROMYCES CEREVISIAE CHROMATIN REMODELERS INO80 AND ISW1A
… chromatin remodeling complexes, which operate on nucleosomes in concert, to modulate chromatin structure and composition. Exchange of the canonical and variant forms of histones in nucleosomes, and altering the spacing between consecutive nucleosomes, are two major ways which regulate …
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Bioinformatic methods for the analysis of genetic variability and regulation
… different histone PTM combine within individual nucleosomes to encode regulatory information. Regular protocols of chromatin immunoprecipitation followed by sequencing (ChIP-seq) produce fragment sizes that can be several times the length of the DNA needed to wrap a single nucleosome, making them …
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Biophysical studies of chromatin folding and unfolding
… folding is started with a linear long string of nucleosomes, connected by segments of DNA called linker DNA. Further folding forms the higher order structure, 30-nm fibers in which form most DNA in interphase nuclei is maintained. Nucleosomes arrange helically at this level, but the connectivity …
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An experimental approach to determine the binding mode of yeast linker histone, Hho1p
… binding mode of yeast linker histone Hholp to nucleosomes, using magnetic bead pull-down assays. To understand the structural and regulatory role of, Hholp, the linker histone in Saccharomyces cerevisiae, and that of higher eukaryotes (Thoma et al., 1979), it is essential to determine the …
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Chromatin Dynamics During DNA Replication
… of chromatin organisation consists of arrays of nucleosomes that are present across the genetic template. Advances in the post genomics era have made it possible to determine the positions of nucleosomes genome-wide where it has been observed that nucleosomes adopt a distinct organisation with …
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Development of a multiscale coarse-grained chromatin model
… all-atom representations of proteins, DNA, and nucleosomes; a chemically specific coarse-grained model of kb scale chromatin; and a minimal model of sub-Mb scale chromatin. A key feature of this model is its capacity to link the molecular details of nucleosomes to the collective behavior of …
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Effect of Naturally Occurring DNA Modifications on DNA Structure and Packaging
… DNA (dsDNA) coils around histones to form nucleosomes. Arrays of these nucleosomes bundle together to generate chromatin. Most DNA-related processes require interactions between chromatin-protected DNA and cellular machinery. Access of cell machinery to genomic DNA is partially regulated by …
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GENOME-WIDE PROTEIN MOLECULAR ARCHITECTURE OF HUMAN PROMOTERS
… complex (PIC), TFs, cofactors, and nucleosomes within the human genome—and their interactions on a genomic scale—has yet to be thoroughly investigated. In this study, we developed an advanced version of the ChIP-exo assay (v6), utilizing a combination of nucleases as high-precision …
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Building the 3D Genome from the Ground Up: Local Interactions Give Rise to Global Order
… an active area of study. Interactions between nucleosomes—modulated by histone tail post-translational modifications, histone sequence variants, and the DNA sequence itself—are thought to be a major driver of this emergent structure. In this thesis, I address the question of how these intrinsic …
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Biochemical, biophysical and structural study of the nucleosome-MeCP2 complex
… to understand the interactions between MeCP2 and nucleosomes, the fundamental component of chromatin. We used biochemical and biophysical approaches to study the interplay between MeCP2 and nucleosomes. Gel mobility assays showed that although MeCP2 can interact with a nucleosome with or without …
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Structural and functional effects of histone variant, H2A.Bbd, on the nucleosome core particle
… incorporation on the structure and stability of nucleosomes. It was found that Bbd-NCP has a more relaxed structure in which only 118+/-2 bp of DNA was protected against digestion with micrococcal nuclease. Furthermore, absence of fluorescence resonance energy transfer (FRET) between the ends of …
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Centromere Identity and the Nature of the Cenp-A-Containing Nucleosome
… centromere protein A (CENP-A) replaces H3 in nucleosomes at the centromere and is the best candidate to provide this epigenetic mark. This thesis aims to understand the features of the CENP-A nucleosome that impart its ability to mark and stabilize functional centromeres. In the first part of …
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Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data
… proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and …
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Changes of nucleosome positioning and 3D chromatin organization in cell transitions
… 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 chromatin architecture is constituted by relatively large loops of DNA such as …
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On the physics of intranuclear organization
… histone proteins, which DNA wraps around to form nucleosomes, are key determinants of nucleosomes’ condensability and chromatin’s higher-order structure. Chromatin structure, by regulating access of transcriptional machinery to the genome, in turn, has broad implications for cellular processes …
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THE MECHANISMS OF ISW1A, ISW1B AND ISW2 CHROMATIN REMODELERS
… remodeling, and detailed remodeling mechanism of nucleosomes by ISW1a. ISW1a and ISW1b share the same catalytic subunit, but in vivo they are localized at different locations and is also known to have different roles. This suggests that the accessory subunits play a very crucial role in …
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AN INSIGHT INTO DIFFERENT MODES OF REMODELER REGULATION: FOCUS ON SACCHAROMYCES CEREVISIAE SWI/SNF
… to move, disassemble or alter the composition of nucleosomes. Though all remodelers share a conserved ATP hydrolysis and DNA translocase domain, their biochemical actions and in-vivo characteristics differ because of their subunits and accessory domains in the catalytic subunit that regulate its …
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