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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 61 for “"Transcription factor binding sites"”.
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Predicting enhancer regions and transcription factor binding sites in D. melanogaster
… and D. melanogaster genomes. The genome- wide binding locations of all known transcription factors as well as of other DNA- binding proteins are currently being mapped within the context of this project [8]. The large quantity of new data that is becoming available through the modENCODE project …
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Integrating Epigenetic Priors For Improving Computational Identification of Transcription Factor Binding Sites
Transcription factors and histone modifications play critical roles in tissue-specific gene expression. Identifying binding sites is key in understanding the regulatory interactions of gene expression. Nave computational approaches uses solely DNA sequence data to construct models known as Position …
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The Mapping of Transcription Factor Binding Sites in the Turkey Prolactin Gene
… not occur in the turkey in vivo. The mapping of transcription factor binding sites in the tPRL 5'-flanking region is the first step toward the identification and isolation of factors that bind to and regulate transcription of the PRL gene.
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Novel Sequence-Based Method for Identifying Transcription Factor Binding Sites in Prokaryotic Genomes
… sequence data in order to determine prokaryotic transcription factor binding specificities. The prototypical prokaryotic transcription factor: TF) contains a helix–turn–helix: HTH) fold and bind DNA as homodimers, leading to their palindromic motif specificities. The connection …
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Zero-Inflated Models to Identify Transcription Factor Binding Sites in ChIP-seq Experiments
<p>It is essential to determine the protein-DNA binding sites to understand many biological processes. A transcription factor is a particular type of protein that binds to DNA and controls gene regulation in living organisms. Chromatin immunoprecipitation followed by highthroughput sequencing …
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A regulatory role for repeated decoy transcription factor binding sites in target gene expression
… studies reveal that many 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 …
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Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
… evolution of lineage-specific traits. Although transcription factor binding events show substantial variation across species, most computational approaches to study regulatory elements focus primarily upon highly conserved sites, and rely heavily upon multiple sequence alignments. However, …
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Exploring transcription patterns and regulatory motifs in Arabidopsis thaliana
… (genes located on opposite strands of DNA, whose transcription start sites are not more than 1000 basepairs apart) are often co-expressed and have similar biological functions. Identification of such genes can be useful in the process of constructing gene regulatory networks. Furthermore, analysis …
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Extraction and identification of frequent sequential patterns in transcription factor binding site organization of enhancers
… has created vast arrays of data correlating binding sites and regulatory elements with genome regions. There has been great interest in developing new computational approaches that leverage these annotations in order to better understand the layout and organization of eukaryotic genomes and …
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Global Microsatellite Content Potentially Distinguishes Humans, Primates, Animals, and Plants
… exhibited no discernible pattern related to transcription factor binding sites or non-microsatellite repetitive sequences (i.e., LINEs, and SINEs). This is the first description of a method for evaluating microsatellite content to classify individual genomes.
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Statistical physics and biological information : hydrophobicity patterns in protein design and differential motif finding in DNA
… essential. Common examples of motifs include transcription factor binding sites in promoter regions of co-regulated genes and exonic and intronic splicing enhancers ...
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THE INTERACTION OF TRANSCRIPTION FACTORS WITH THE LONG CONTROL REGION OF HPV 16
… genes but contains the control elements for transcriptional activation and probably replication of the virus. Research done in our lab previous to the work towards this thesis showed that transcriptional activation of HPV 16 is cell-type-specific, i.e. it was observed in cells derived from a …
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Comparative analysis of the promoters of the CyI-CyIIa-CyIIb actin gene cluster in the sea urchin Strongylocentrotus purpuratus
… region of CyIIa upstream of the ATG and putative transcription start site was subcloned and sequenced. Sites of protein-DNA interaction were identified using DNaseI footprinting. Comparisons of this data with that previously obtained for CyI and CyIIb showed that while CyI and CyIIb share an …
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Developmental Dynamics of 5-Hydroxymethylcytosine and its Role in the Terminal Differentiation of 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 (5hmC), the oxidized form of …
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Identifizierung und funktionelle Analyse der humanen Xylosyltransferase I- und II-Promotoren
… Furthermore, a different response to growth factors of the TGF[beta] family has been observed. The mechanisms underlying the transcriptional regulation of both XYLT genes have not been characterized yet. In my thesis, I identified for the first time the promoter regions of XT-I and XT-II as …
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Defining the Limits and Mapping the Control Sequences of the Gene, Enhancer of Rudimentary, in Drosophila melanogaster
… in Drosophila melanogaster. The gene encodes a transcriptional co-factor of 104 amino acids in length, and although the exact function is still unclear it has been shown to be involved in pyrimidine biosynthesis, oogenesis, and the cell cycle. Mutations in e(r) are characterized by low viability …
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Methods and Mechanisms of DNA Methylation in Development and Disease
<p>DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer and neurological disorders. The goal of this …
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Associative Pattern Recognition for Biological Regulation Data
… recognizing associative patterns between genes, transcription factors, histone modifications and functional labels using heterogeneous data sources (numeric, sequences, time series data and textual labels). </p> <p>In protein-DNA associative pattern recognition, we introduce an efficient …
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