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 51 for “"TF binding"”.
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Metal binding to transferrin and immune reactions in Parkinson's disease
The binding of iron (59Fe) and gallium (67Ga) to the plasma protein transferrin (Tf) was investigated by G75 gel filtration chromatography in control patients and treated and untreated patients with Parkinson's disease (PD). Fe-Tf binding was 100% in all controls and PD patients suggesting that a …
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Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
… of gene regulation are Transcription 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 …
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Whole genome regulatory variant evaluation for transcription factor binding
… cell. For example these variants can alter the binding of the transcription factors (TF). In this thesis we present Whole-genome regulAtory Variant Evaluation (WAVE), a computational method that models the TF binding ChIP-seq signal solely from DNA sequence and predicts genetic a variant's …
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Transcription Factor-Centric Approaches to Identify Regulatory Driver Mutations in Cancer
… nucleotide variants on transcription factor (TF) binding. Unlike most of the previous work on driver identification, our method does not require the driver mutations to be highly recurrent; instead, we assess the mutations’ significance by testing if they cause larger TF binding changes than …
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Quantifying the functional and evolutionary relationships among sequences, transcription factor binding and gene expression
… regulatory sequences, transcription factor (TF) binding and gene expression. Many studies have discussed how TFs recognize their DNA binding sites. However, it is not well understood how the various factors that influence TF-DNA binding alter the cascade of gene expression. Moreover, …
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A regulatory role for repeated decoy transcription factor binding sites in target gene expression
… intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in budding yeast to examine if …
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Investigation of transcription factor binding at distal regulatory elements
… contain clusters of transcription factor binding sites, and TF recruitment to them is thought to play a key role in transcriptional control. In this thesis I have addressed two issues regarding gene regulation by enhancers. First, with recent genome-wide enhancer mapping, it is becoming …
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Role of DNA replication timing in gene expression and chromatin organisation
… chromatin structure and transcription-factor (TF) binding events were observed, and a significant number of genes affected are involved in differentiation processes such as sporulation. While some differentially expressed genes showed significant chromatin changes, there were also examples …
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Dissecting the role of CHD4 in the NuRD and ChAHP complexes
CHD4 (chromodomain helicase DNA-binding protein 4) is a widely conserved ATP-dependent chromatin remodeler essential for early mammalian development. Although best known for its role in gene regulation as a core component of the NuRD complex, CHD4 is also found within the ChAHP complex, which …
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Combinatorial gene regulation by transcription factors
… in enhancers and promoters in the form of binding sites for transcription factors (TFs), which collaboratively recruit the transcriptional machinery and drive gene expression. Using high-throughput and quantitative technologies developed by our lab and others, we studied TF binding sites in …
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Statistical methods for variant discovery and functional genomic analysis using next-generation sequencing data
… sequence variants, find transcription factor (TF) binding patterns, and decode the relationship between TF and gene expression levels. Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), plays …
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Insights into transcriptional regulation from natural and induced variation in closely related species
… regulation, focusing particularly on the binding activity of transcription factors (TFs). In the comprised projects and analyses, I use models of closely related mouse species, as in vivo systems that leverage a pool of molecular variation, in order to study the activity and roles of TF …
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Regulation of the kRAS Promoter in Pancreatic Cancer by Proteins and Small Molecules
DNA-binding proteins play a pivotal role in cell biology. The major class of DNA-binding proteins are transcription factors (TFs). TFs are central to almost every fundamental cellular process such as cell development, differentiation, cell growth, and gene expression. They account for 10% of the …
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Computation identification of transcription factor binding using DNase-seq
… the identification of transcription factor (TF) binding sites. Through the use of machine learning techniques, PIQ identified binding sites for >700 TFs from one DNase-seq experiment with accuracy comparable to ChIP-seq for motif-associated TFs (median AUC=0.93 across 303 TFs). We applied PIQ …
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The evolution of gene regulatory landscapes in mammalian tissues
… elements and transcription factor (TF) binding events has diverged at different rates. In this thesis, I investigated several layers of gene regulatory divergence across mammalian species. In the first part of the thesis, I investigated the coevolution of DNA methylation patterns and …
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Towards a Complete Transcriptional Regulatory Code: Improved Motif Discovery Using Informative Priors
… genes. A key component of this process is the binding of proteins called transcription factors (TFs) to corresponding regulatory sites on the DNA. Understanding where exactly these TFs bind, under what conditions they are active, and which genes they regulate is all part of deciphering the …
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The NuRD complex regulates chromatin dynamics driving exit from naïve pluripotency
… role in the regulation of transcription factor (TF) binding dynamics, chromatin accessibility, genome organisation and ultimately gene expression in naive pluripotency through to lineage specification. Single-molecule tracking of pluripotency-associated TFs in live mouse ESCs revealed that …
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Nucleosome repositioning in glioblastoma
… to other features, such as transcription factor (TF) binding, ALU repeats and histone modification changes. I show that the relationship between TF binding and nucleosome positioning in brain tissues, as well as cell-free DNA (cfDNA) from peripheral blood, is a highly promising system to …
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Statistical mechanical modeling of eukaryotic gene regulation
… of the quantities of transcription factors (TFs) bound to genomic regulatory sequences. This thesis work is built on statistical mechanics to study the stochastic interactions of TFs and regulatory sequences. We present a predictive model to learn how TFs interact with cis-regulatory …
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Protein-DNA Recognition Models for the Homeodomain and C2H2 Zinc Finger Transcription Factor Families
Transcription factors: TFs) play a central role in the gene regulatory network of each cell. They can stimulate or inhibit transcription of their target genes by binding to short, degenerate DNA sequence motifs. The goal of this research is to build improved models of TF binding site recognition. …
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