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 14 of 14 for “"DNA accessibility"”.
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Impact of DNA accessibility and sequence on eukaryotic origin licensing
Eukaryotic DNA replication is a complex process that requires the coordination of many different proteins to ensure duplication of the genome occurs rapidly and only once during each cell cycle. Establishing a pair of replication forks moving apart from a single starting location is essential for …
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Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
… Factors (TFs), proteins which bind to DNA in a sequence specific manner and drive the activation or repression of genes. Statistical thermodynamics has shown to be a promising avenue to describe the binding mechanisms of TFs. Here, I present ChIPanalyser, an R/Bioconductor package that …
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Probabilistic models to resolve cell identity and tissue architecture
… chromatin with sequencing (ATAC-seq), DNA accessibility provides a readout of intermediate gene regulation steps at single-cell resolution, with technologies measuring both RNA and ATAC providing the necessary evidence to build mechanistic models of regulation. Existing methods address …
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Single-molecule FRET study on the RecA-mediated DNA repair
… provides insights into how RecA might control DNA accessibility in vivo. Next, we estimate that about five monomers are sufficient for filament nucleation. Using a vesicle encapsulation assay, we find that the nucleation is likely to occur through the binding of a pre-assembled oligomer rather …
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Molecular mechanisms of pioneer factor ELF2 interactions with the nucleosome
… subfamily of TFs consisting of 29 members. The DNA binding domains (DBD) of ETS family TFs are highly conserved. ELF2 is a ETS family pioneer factor that has a strong preference for oriented binding on nucleosomes. The functionality of ELF2 in genome is, however, unknown. In this study, by …
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ZSCAN4 AND REPLICATION STRESS: SAFEGUARDING GENOME STABILITY IN MOUSE EMBRYONIC STEM CELLS
The accuracy of DNA replication is essential for maintaining genome stability. However, replication can be disrupted by both endogenous and exogenous factors, leading to a condition known as replication stress (RS). RS slows down and eventually stalls replication forks. If stalled forks are not …
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The Polycomb Complex 2 contributes to developmental delay when histone methylation is inappropriately inherited
… tails of histone core proteins that regulates DNA accessibility, and consequently, gene expression. Like DNA, histone methylation can be inherited between generations, and is highly regulated during embryonic development. At fertilization, histone methylation must undergo maternal reprogramming …
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Computational analysis of cis-regulatory mechanisms underlying cellular response to drug perturbations
… binding to the (d) genes immediate upstream DNA sequence, but rather, that the span of regulators ranges from protein DNA binding factors to other such nuclear factors (including the DNA itself) up and through various signaling molecule networks to the various components of the cell, …
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STRUCTURAL INSIGHTS INTO RNA POLYMERASE III PRE-INITIATION COMPLEX AND THE PIONEER ROLE OF OCT1
… U6 snRNA promoter. Captured in melting and open DNA states (3.2–4.2 Å resolution), these structures reveal distinct SNAPc conformations when engaging Pol III versus Pol II. Through integrative modeling and crosslinking mass spectrometry, we structurally localized the SNAPC2 and SNAPC5 subunits …
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Regulation of nucleosome dynamics
… called nucleosomes, where 147 base pairs of DNA are wrapped around a protein core. Stable packing of DNA in nucleosomes imposes a barrier for accessibility of genetic code on DNA for replication, transcription, and repair. The dynamics of nucleosomal DNA provide a mean for gene regulation by …
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Epigenetic Determinants of CRISPR-Cas9 genotoxicity
… that occur without altering the underlying DNA sequence. Cas9 interacts directly with the genome to introduce double strand breaks at targeted locations. However, the efficiency and specificity of Cas9- mediated editing can be significantly influenced by the epigenetic landscape of the …
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REPAIR AND EFFECTS OF THE 8-OXOG LESION IN DNA
Eukaryotic DNA is packaged in a condensed state with histone proteins. The minimal structural unit within packaged eukaryotic DNA is the nucleosome core particle (NCP). The NCP consists of a 146 bp DNA fragment wrapped around an octamer of histone core proteins. Nucleosome core particle formation …
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REPAIR AND EFFECTS OF THE 8-OXOG LESION IN DNA
Eukaryotic DNA is packaged in a condensed state with histone proteins. The minimal structural unit within packaged eukaryotic DNA is the nucleosome core particle (NCP). The NCP consists of a 146 bp DNA fragment wrapped around an octamer of histone core proteins. Nucleosome core particle formation …