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 138 for “"Cis-Regulatory"”.
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Genomic Cis-Regulatory Map Mining.
Genomic Cis-Regulatory Map Mining.
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Computationally-guided inference of cis-regulatory codes in metazoans
… Deciphering the networks of genes, their regulatory proteins (transcription factors (TFs)) and their regulatory DNA elements (cis-regulatory modules (CRMs)) is fundamental to the understanding of the biological processes they underlie. These processes include the formation and maintenance …
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Computational discovery of Cis-regulatory elements in multiple drosophila species
… factors control gene expression by binding regulatory DNA segments called cis-regulatory modules (CRMs). The increasing number of sequenced genomes of multicellular eukaryotes along with high-throughput methods such as whole genome microarray expression data allows for systematic …
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Cis-regulatory module analysis: inferring regulatory networks and underlying mechanisms
… and annotate the regions that control the precise spatial and temporal expression of the genes. Cis- regulatory modules (CRMs/enhancers), main players of this regulatory process, are typically short (<1kb) sequences that are embedded in non-coding regions of the genome. They harbor …
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Computational Models of Function and Evolution of cis-Regulatory Sequences
Gene expression is controlled by regulatory DNA sequences, often called cis-regulatory modules or CRMs in higher organisms. Even though complete genomes are available in many species, a catalog of CRMs is far from complete. Meanwhile, how basic building blocks of CRMs, called transcription factor …
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Discovering Conserved cis-Regulatory Elements That Regulate Expression in Caenorhabditis elegans
… is two-fold:: 1) To catalog all <italic>cis</italic>-regulatory elements within the intergenic and intronic regions surrounding every gene in <italic>C.elegans</italic>: i.e. the regulome) and: 2) to determine which cis-regulatory elements are associated with expression under specific …
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Characterization of Cis-Regulatory Elements Controlling Repo Transcription in Drosophila Melanogaster
… factors. In 2005, Lee and Jones defined a 4.3 kb cis-regulatory DNA region that recapitulates the endogenous Repo expression pattern dependent on a single Gcm binding site. Within that region, are three different cis-regulatory elements that drive cell-specific expression independent of Gcm …
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Identification of Drosophila heart-specific Cis-Regulatory Modules under Hox control
… aim of our work is to isolate the heart-specific cisregulatory sequences of abd-A direct target genes, the realizator genes granting heart identity. In each segment of the heart, four pairs of cardiomyocytes (CMs) express tinman (tin), homologous to NKX2-5, and acquire strong contractile and …
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ModuleFinder : a computational model for the identification of Cis regulatory modules
… the likelihood that a given genomic region is a cis regulatory module (CRM) for an input set of TFs according to its degree of: (1) homotypic site clustering; (2) heterotypic site clustering; and (3) evolutionary conservation across multiple genomes. Importantly, ModuleFinder obtains all …
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New insights into cis-regulatory module evolution using in-silico evolutionary simulations
Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2014-11-19T15:21:57Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Duque_Thyago.pdf: 5943420 bytes, checksum: 521fa3adb99bf40510252651c6b1dcca (MD5)
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Computational analysis of cis-regulatory mechanisms underlying cellular response to drug perturbations
… subfields of biology: pharmacogenomics and regulatory genomics. The former concentrates on how inherited factors such as SNPs and genes inform the response to medical interventions designed to ameliorate disease states, processes, and phenotypes; ontologically, it resides at the intersection …
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Exploring cis-regulatory models of the genome to predict epigenetic state and variation
… covariate greatly aids in the prediction of cis-regulatory marks. Additionally, we show that by using cell-type specific covariates, CCM+ can generalize across cell-types. Finally, we show CCM+ can be used for downstream analysis that matches state-of-the-art methods when chromatin …
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Genome-wide analysis of transcriptional expression programs, regulatory networks and Cis-regulatory sequences in Saccharomyces cerevisiae
… can also provide clues about the identity of the regulatory regions within DNA, the structure of global regulatory networks and the regulation of DNA-binding proteins. These and other insights are presented here based on our genome-wide studies of transcriptional regulation in the yeast …
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Using a novel large-scale epigenetic analysis method to uncover the cis-regulatory potential of individual transposable elements
… healthy function. In particular, they can act as cis regulatory elements of nearby genes (i.e. enhancers or alternative promoters) in a cell type-specific manner. Epigenetic regulation of TEs is an important feature that our genome has evolved to restrict their transposition potential. One such …
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Characterisation of a conserved motif found within the Dlx cis-regulatory element URE2 and its effect on mouse URE2-lacZ activity in transgenic mice
… as well as their migration to the cortex. The cis-regulatory element URE2 (enhancer) is located upstream of Dlx1 and is thought to regulate the transcription of Dlx1 and/or Dlx2. The objective of this study was to examine a short conserved sequence within the URE2 element, corresponding to …
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Identification and characterization of conserved regulatory elements by comparative genomics
… genes, Six3 and Foxb1, were found to function as cis-regulatory elements by either enhancing or suppressing expression of the reporter gene in a tissue- and developmental-stage specific manner. The regulatory region of orexin (ORX) gene did not contain CNEs but the fugu ORX regulatory region was …
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Genomic Exploration of Transcriptional Regulation and Evolution in Vertebrates
… expression of genes and their interactions. Regulatory sequences encoded in the genome stipulate the necessary instructions interpreted by sequence-specific transcription factors (TFs) to control the spatial-temporal output of gene expression. Detection of cis-regulatory signals is …
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THE DEVELOPMENTAL BASIS AND EVOLUTION OF WING COLOR PATTERN IN BUTTERFLIES
… patterning wing colors, and to characterize the regulatory architecture modulating color pattern-related function of the WntA gene. Our results revealed that WntA is essential to establish multiple pattern elements, even in highly divergent species of nymphalids and papilionids–two distant and …
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Mechanistic Dissection of Tcf7l1-Dependent Enhancer Decommissioning During Exit from Naïve Pluripotency
… the simultaneous dissolution of the naïve gene regulatory network as well as a redirection of transcriptional response to Wnt/β-catenin signaling. Here, we show that Tcf7l1 functions as a linchpin factor that connects the two outcomes via effects at Tcf7l1-bound cis-regulatory elements in mouse …
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Sexual Dimorphism and Consequences of Sex-Specific Selection in Drosophila melanogaster
… In Chapter 2, I examined the nature of cis-regulatory variation in connection to sex-biased gene expression. I detected widespread cis-regulatory variation between the study populations, with unbiased genes being marginally enriched for said variation. In numerous genes, cis-regulatory …
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