Allelic effect on transcription factor binding affinity
Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
... the binding affinity of the PhoB two-component response regulator (RR) to target promoters impacts the level and timing of expression of PhoB-regulated ...for transcription factor ...
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Determination of transcription factor binding specificities
... though binding of essentially any TF will by itself compete against the binding of the histones, it is clear that in most cases the major effect is mediated by enzymes that are recruited by the TFs ...
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Statistics for Transcription Factor Binding Sites
... advantageous effect on the removal of redundancies, the dependence of the result on the parameter choices is unwanted for ...minor effect by changing the composition of one cluster ...
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Transcription Factor Binding Site Analysis
... hits. Effect of desoxyribonuclease on the biological activity of the transforming ...TF binding and TF motifs but also for determining cellular ...DNA binding specificity across a target ...a ...
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Effect of positional dependence and alignment strategy on modeling transcription factor binding sites
... produced by these two algorithms from the same input sequences. Pairwise score (PS) is a measure of the dependence of nucleotides at two positions that are situated within a given distance in an alignment of TFBS. ...
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Computational Approaches for Transcription Factor Binding Prediction
... the transcription and translation. Transcription factors make a major role in determining how the proteins are formed and metabolic activities are ...scription factor binding sites are ...
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The Genetics of Transcription Factor DNA Binding Variation
... DNA binding dependencies between these TFs were maintained over a relatively long ...DNA binding in which two or more TFs compete with a nucleosome to access DNA (Biggin, 2011; Mirny, 2010; Spitz and ...
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Stochastic Modeling of Transcription Factor Binding Fluctuations
... corresponding to a specific gene is assayed. The level of gene product is observed to change in a smooth, dose-dependent manner. Based on this observation, it seems reasonable to assume that the production of transcript ...
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Dynamics of transcription factor binding site evolution
... key factor for an enrichment in presite ratio may arise through variation in GC content or through simple sequence repeats (especially if the preferred sequence has some repetitive or palindromic ...to ...
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Transcription Factor Binding Site Prediction Software
... and transcription factors. Classically computational prediction of TF binding sites TFBSs is based on basic position weight matrices PWMs which quantitatively score binding ...with ...
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Influence of DNA methylation on transcription factor binding
... Investigating binding site restriction by nucleosomes thus requires an alternative ...the effect of nucleosomes on binding of TFs with a massively parallel reporter assay (MPRA) of ...
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Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding
... companion factor HNF4A did not materially affect nucleosomal H3K4me2 marks at thousands of sites where it occupies DNA, regardless of nearby CDX2 ...erful effect on chromatin, which we observed at the ...
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Structural fingerprints of transcription factor binding site regions
... When dealing with lengths of DNA comprising fewer than 1024 octamers, the process is similar, except that the structural parameter vector is padded with zeroes to give 1024 values, prior to taking its Fourier transform. ...
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Computational prediction of transcription factor binding site locations
... nitrocellulose binding assays, gel-shift analysis that monitors the change in mobility when DNA and protein bind, Southwestern blotting of both DNA and protein, or reporter ...high-affinity binding ...
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Functional Consequences of mtDNA Methylation on Mitochondrial Transcription Factor Binding and Transcription Initiation
... 46 mitochondrial localization, a mtDNMT1 construct was designed in which the MLS from DNMT1 was replaced with the TFAM MLS, and the NLS was replaced by a nuclear export signal (NES) (Figure 2-10). However, plasmid ...
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DNA Replication Efficiency Depends on Transcription Factor-Binding Sites
... AP-1 transcription factor-binding site had a greater effect on the RRE of the ...Sp1 transcription factor-binding sites; squares with an “x” represent AP-1 ...
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Mapping the YY1 and p65 binding sites on the transcription factor LSF
... of Factor Xa Cleavage Since an aim of the study was to determine the specific LSF peptide sequence or sequences responsible for binding p65 and YY1, I developed a new assay to investigate this ...DNA ...
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Functional analysis of transcription factor binding sites in human promoters
... transcriptional effect of TFBS disruption in one cell line with that in another cell line implies an underly- ing dependence on TF concentration: an n-fold effect in one cell line is consistently matched to ...
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Analysis of variation at transcription factor binding sites in Drosophila and humans
... deleterious effect of TFBS variation depends on how much it perturbs the motif ...deleterious effect of TFBS mutations in terms of ‘muta- tional load’, a known population genetics metric that combines the ...
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Explicit equilibrium modeling of transcription factor binding and gene regulation
... cooperative binding of proteins X and Y to DNA can be separated thermodynamically into the formation of an XY dimer and the binding of that dimer to DNA; this is thermo- dynamically equivalent to protein X ...
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