Dissertations / Theses: 'Transcriptional Regulatory Elements'

1

Otto, Wolfgang. "Transcriptional Regulatory Elements." Doctoral thesis, Universitätsbibliothek Leipzig, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-78960.

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A major challenge in life sciences is the understanding of mechanisms that regulate the expression of genes. An important step towards this goal is the ability to identify transcriptional regulatory elements like binding sites for transcription factors. In computational biology, a popular approach for this task is comparative sequence analysis using both distantly as well as closely related species. Although this method has successfully identified conserved regulatory regions, the majority of binding sites can change rapidly even between closely related species. This makes it difficult to detect them using DNA sequences alone. In this thesis, we introduce two new approaches for the detection and evolutionary analysis of transcriptional elements that consider the challenges of binding site turnover. In the first part, we develop a method for detecting homologous motifs in a given set of sequences in order to obtain evidence for evolutionary events and turnover. Based on a detailed theoretical scaffold, we develop a simple, but effective and efficient heuristic for assembling local pairwise sequence alignments into a local multiple sequence alignment. This kind of multiple alignment only contains conserved motifs represented in columns which satisfy the order implied by the underlying sequences. By favoring motifs that are contained in a great range of sequences, our method is additionally able to detect even small conserved motifs. Furthermore, the calculation of the initial local pairwise alignments is generic. This allows the use of fast heuristic methods in case of large data sets while exact alignment programs can be used for small data sets where detailed information is needed. Application to artificial as well as biological data sets demonstrate the capabilities of our algorithm. In the second part, we propose a conceptually simple, but mathematically non-trivial, phenomenological model for the binding site turnover at a genomic locus. The model is based on the assumption that binding sites have a constant rate of origination and a constant decay rate per binding site. The elementary derivation of the transient probability distribution is affirmed by simulations of sequence evolution as well as biological data. Based on the derived distribution, we develop a phenomenological model of binding site number dynamics in order to detect changes in selective constraints acting on transcription factor binding sites. Using a maximum likelihood implementation as well as exploratory data analysis, we show the functionality of the model by identifying functionally important changes in the evolutionary turnover rates on biological data. Each part of this thesis leads to the development of a new program. While Tracker allows the computation of conserved homologous motifs and their representation in a local multiple alignment, Creto determines the evolutionary turnover rates for arbitrary clades of a phylogenetic tree with given binding site numbers at the final taxa. Both software tools are freely available to the scientific community for further research in this important and exciting field.

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Romanish, Mark Taras. "Regulatory elements within repeated elements : a case study of NAIP transcriptional innovation." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/12271.

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Neuronal Apoptosis Inhibitory Protein (NAIP, also known as BIRC1) is a member of the conserved Inhibitor of Apoptosis Protein (IAP) family. However, it is no longer principally considered an apoptosis inhibitor since its domain structure and functions in innate immunity also warrant inclusion in the Nod-Like Receptor (NLR) superfamily. Lineage-specific rearrangement and expansion of this locus have yielded different copy numbers among primates and rodents, providing an interesting case study in which to study transcriptional regulatory changes by a rapidly evolving gene. In the first stage of my thesis, I show that NAIP has multiple promoters sharing no similarity between human and rodents. Moreover, I demonstrate that multiple, domesticated long terminal repeats (LTRs) of endogenous retroviral (ERV) elements provide NAIP promoter function in human, mouse and rat. In human, an LTR serves as a tissue-specific promoter active primarily in testis. However, in rodents, our evidence indicates that an ancestral LTR common to all rodent genes is the major, constitutive promoter for these genes and that a second LTR found in two of the mouse genes is a minor promoter. Thus, independently acquired LTRs have assumed regulatory roles for orthologous genes, a remarkable evolutionary scenario. It is also demonstrated that 5’ flanking regions of IAP family genes as a group, in both human and mouse, are enriched for LTR insertions compared to average genes. In the second stage of my thesis, I demonstrate that several of the human NAIP paralogues are expressed, and that novel transcripts arise from both internal and upstream transcription start sites. Remarkably, two internal start sites initiate within Alu short interspersed element (SINE) retrotransposons, and a third novel transcription start site exists within the final intron of the GUSBP1 gene, upstream of only two NAIP copies. One Alu functions alone as a promoter in transient assays, while the other likely combines with upstream L1 sequences to form a composite promoter. The novel transcripts encode shortened open reading frames and I show that corresponding proteins are translated in a number of cell lines and primary tissues, in some cases above the level of full length NAIP. Interestingly, some NAIP isoforms lack their caspase-sequestering motifs, indicating that they have novel functions. My results support an important role for transposable elements in NAIP evolution, particularly as transcriptional regulatory modules, and illustrate a fascinating example of regulatory innovations adopted by a rapidly evolving gene.

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Schoenborn, Jamie R. "Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing Ifng transcription /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/5098.

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4

Leblanc, Jean-François. "Functional analysis of human interferon-beta gene transcriptional regulatory elements." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=59923.

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One of the main goals of this project was to systematically evaluate the virus-inducible properties of the individual human interferon-beta (IFN-$ beta$) enhansons. Synthetic oligonucleotides representing the different enhansons were subcloned into an enhancerless SV$ sb1$CAT vector; the hybrid plasmids obtained were tested in different human cell lines by transient expression assay. The P2 motif, which is 80% homologous to the NF-$ kappa$B recognition sequence, was inducible by Sendai virus. In contrast, the P1 enhanson was transcriptionally silent. Unexpectedly, a multimer of the P5 motif conferred significant virus inducibility to a heterologous transcription unit. A DNA fragment encompassing P5, P1, and P2 mimicked the transcriptional activity of the whole IFN-$ beta$ promoter, indicating that the three enhansons act synergistically to confer a virus-inducible expression pattern. The effect of certain trans-acting factors on the individual IFN-$ beta$ enhansons was also assessed. Together, these experiments indicate that the synergism between the P5, P1, and P2 enhansons is mediated by at least two distinct transcription factors, NF-$ kappa$B and IRF-1.

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Ewart, Marie-Ann. "Analysis of transcriptional regulatory elements of the human CD23 gene." Thesis, University of Glasgow, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343975.

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Yao, Ya-Li. "Regulation of yy1, a multifunctional transciption [sic] factor /." [Tampa, Fla.] : University of South Florida, 2001. http://purl.fcla.edu/fcla/etd/SFE0000626.

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7

Vangala, Pranitha. "Role of Cis-regulatory Elements in Transcriptional Regulation: From Evolution to 4D Interactions." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1082.

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Transcriptional regulation is the principal mechanism in establishing cell-type specific gene activity by exploring an almost infinite space of different combinations of regulatory elements, transcription factors with high precision. Recent efforts have mapped thousands of candidate regulatory elements, of which a great portion is cell-type specific yet it is still unclear as to what fraction of these elements is functional, what genes these elements regulate, or how they are established in a cell-type specific manner. In this dissertation, I will discuss methods and approaches I developed to better understand the role of regulatory elements and transcription factors in gene expression regulation. First, by comparing the transcriptome and chromatin landscape between mouse and human innate immune cells I showed specific gene expression programs are regulated by highly conserved regulatory elements that contain a set of constrained sequence motifs, which can successfully classify gene-induction in both species. Next, using chromatin interactions I accurately defined functional enhancers and their target genes. This fine mapping dramatically improved the prediction of transcriptional changes. Finally, we built a supervised learning approach to detect the short DNA sequences motifs that regulate the activation of regulatory elements following LPS stimulation. This approach detected several transcription factors to be critical in remodeling the epigenetic landscape both across time and individuals. Overall this thesis addresses several important aspects of cis-regulatory elements in transcriptional regulation and started to derive principles and models of gene-expression regulation that address the fundamental question: “How do cis-regulatory elements drive cell-type-specific transcription?”

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Hilbert, Brendan J. "Structure-based Targeting of Transcriptional Regulatory Complexes Implicated in Human Disease: A Dissertation." eScholarship@UMMS, 2007. http://escholarship.umassmed.edu/gsbs_diss/681.

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Transcriptional regulatory complexes control gene expression patterns and permit cellular responses to stimuli. Deregulation of complex components upsets target gene expression and can lead to disease. This dissertation examines proteins involved in two distinct regulatory complexes: C-terminal binding protein (CtBP) 1 and 2, and Interferon Regulatory Factors (IRF) 3 and 5. Although critical in developmental processes and injury response, CtBP transcriptional repression of cell adhesion proteins, pro-apoptotic factors, and tumor suppressors has been linked to the pathogenesis of multiple forms of cancer. IRFs function in the immune system and have been implicated in autoimmune disorders. Understanding IRF activation is critical to treating pathogens that target IRF function or for future autoimmune disease therapies. We attempted to determine crystal structures that would provide the details of IRF activation, allowing insight into mechanisms of pathogen immune evasion and autoimmune disorders. Although no new structures were solved, we have optimized expression of C-terminal IRF-3 / co-activator complexes, as well as full-length IRF3 and IRF5 constructs. Modifying the constructs coupled with new crystal screening will soon result in structures which detail IRF activation, advancing understanding of the roles of IRF family members in disease. Through structural and biochemical characterization we sought to identify and develop inhibitors of CtBP transcriptional regulatory functions. High concentrations of CtBP substrate, 4-Methylthio 2-oxobutyric acid (MTOB), have been shown in different cancer models to interfere with CtBP transcriptional regulation. We began the process of structure based drug design by solving crystal structures of both CtBP family members bound to MTOB. The resulting models identified critical ligand contacts and unique active site features, which were utilized in inhibitor design. Potential CtBP inhibitors were identified and co-crystallized with CtBP1. One such compound binds to CtBP more than 1000 times more tightly than does MTOB, as a result of our structure-based inclusion of a phenyl ring and a novel pattern of hydrogen bonding. This molecule provides a starting point for the development of compounds that will both bind more tightly and interfere with transcriptional signaling as we progress towards pharmacologically targeting CtBP as a therapy for specific cancers.

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Hilbert, Brendan J. "Structure-based Targeting of Transcriptional Regulatory Complexes Implicated in Human Disease: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/681.

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Transcriptional regulatory complexes control gene expression patterns and permit cellular responses to stimuli. Deregulation of complex components upsets target gene expression and can lead to disease. This dissertation examines proteins involved in two distinct regulatory complexes: C-terminal binding protein (CtBP) 1 and 2, and Interferon Regulatory Factors (IRF) 3 and 5. Although critical in developmental processes and injury response, CtBP transcriptional repression of cell adhesion proteins, pro-apoptotic factors, and tumor suppressors has been linked to the pathogenesis of multiple forms of cancer. IRFs function in the immune system and have been implicated in autoimmune disorders. Understanding IRF activation is critical to treating pathogens that target IRF function or for future autoimmune disease therapies. We attempted to determine crystal structures that would provide the details of IRF activation, allowing insight into mechanisms of pathogen immune evasion and autoimmune disorders. Although no new structures were solved, we have optimized expression of C-terminal IRF-3 / co-activator complexes, as well as full-length IRF3 and IRF5 constructs. Modifying the constructs coupled with new crystal screening will soon result in structures which detail IRF activation, advancing understanding of the roles of IRF family members in disease. Through structural and biochemical characterization we sought to identify and develop inhibitors of CtBP transcriptional regulatory functions. High concentrations of CtBP substrate, 4-Methylthio 2-oxobutyric acid (MTOB), have been shown in different cancer models to interfere with CtBP transcriptional regulation. We began the process of structure based drug design by solving crystal structures of both CtBP family members bound to MTOB. The resulting models identified critical ligand contacts and unique active site features, which were utilized in inhibitor design. Potential CtBP inhibitors were identified and co-crystallized with CtBP1. One such compound binds to CtBP more than 1000 times more tightly than does MTOB, as a result of our structure-based inclusion of a phenyl ring and a novel pattern of hydrogen bonding. This molecule provides a starting point for the development of compounds that will both bind more tightly and interfere with transcriptional signaling as we progress towards pharmacologically targeting CtBP as a therapy for specific cancers.

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10

Christjanson, Lisa J. "Transcriptional regulatory elements in the interleukin-8 receptor type B (IL-8RB) proximal promoter." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/mq21038.pdf.

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11

Wicks, Katherine. "Genetic diversity at the TNF locus and transcriptional regulation : functional characterisation of putative regulatory elements." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.542992.

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12

Richard, Audrey. "Oncolytic H-1 parvovirus NS1 protein : identifying and characterizing new transcriptional and posttranslational regulatory elements." Phd thesis, Université du Droit et de la Santé - Lille II, 2011. http://tel.archives-ouvertes.fr/tel-00826936.

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H 1 parvovirus (H-1PV) is a little single stranded DNA virus that preferentially replicates in a lytic manner in transformed cells due to their expression profile that meets the requirements for the activation of H¬ 1 PV life cycle unlike normal cells. This feature is known as oncotropism. H 1PV genome is constituted by two transcriptional units. The first one is driven by the proliferation and transformation dependent P4 promoter and allows the expression of both non structural proteins NS1 and NS2, and the second one controls the expression of both capsid proteins VP1 and VP2 through the activation of P38 promoter. H-1PV life cycle tightly depends on NS1 protein that is involved in crucial events, including viral DNA replication, P38 promoter activation as well as cytotoxicity.NS1 protein is regulated at both transcriptional and post translational levels.My thesis aimed at identifying new determining elements for both of these regulations and characterizing their involvement in both H-1PV life cycle and oncotropism.

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13

Chang, Whei-meih. "Identification of transcriptional regulatory elements in muscle promoter of Ca⁺⁺-activated potassium channel, slowpoke, in Drosophila /." Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.

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14

Otto, Wolfgang [Verfasser], Peter F. [Akademischer Betreuer] Stadler, and Burkhard [Gutachter] Morgenstern. "Transcriptional Regulatory Elements : Detection and Evolutionary Analysis / Wolfgang Otto ; Gutachter: Burkhard Morgenstern ; Betreuer: Peter. F. Stadler." Leipzig : Universitätsbibliothek Leipzig, 2011. http://d-nb.info/123802047X/34.

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Yancoskie, Michelle N. [Verfasser], and Frank [Akademischer Betreuer] Chan. "Identifying and characterizing transcriptional regulatory elements from chromosome conformation capture data / Michelle N. Yancoskie ; Betreuer: Frank Chan." Tübingen : Universitätsbibliothek Tübingen, 2019. http://d-nb.info/1200916484/34.

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16

Mejia, Guerra Maria Katherine. "Characterization of the Building Blocks of the Maize Gene Regulatory Grid." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1448452906.

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17

Voll, Sarah. "Functional Genetic Analysis Reveals Intricate Roles of Conserved X-box Elements in Yeast Transcriptional Regulation." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30168.

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Understanding the functional impact of physical interactions between proteins and DNA on gene expression is important for developing approaches to correct disease-associated gene dysregulation. I conducted a systematic, functional genetic analysis of protein-DNA interactions in the promoter region of the yeast ribonucleotide reductase subunit gene RNR3. I measured the transcriptional impact of systematically perturbing the major transcriptional regulator, Crt1, and three X-box sites on the DNA known to physically bind Crt1. This analysis revealed interactions between two of the three X-boxes in the presence of Crt1, and unexpectedly, a significant functional role of the X-boxes in the absence of Crt1. Further analysis revealed Crt1- independent regulators of RNR3 that were impacted by X-box perturbation. Taken together, these results support the notion that higher-order X-box-mediated interactions are important for RNR3 transcription, and that the X-boxes have unexpected roles in the regulation of RNR3 transcription that extend beyond their interaction with Crt1.

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18

Bharadwaj, Rahul. "Regulation of Higher Order Chromatin at GRIN2B and GAD1 Genetic Loci in Human and Mouse Brain: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/651.

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Little is known about higher order chromatin structures in the human brain and their function in transcription regulation. We employed chromosome conformation capture (3C) to analyze chromatin architecture within 700 Kb surrounding the transcription start site (TSS) of the NMDA receptor and schizophrenia susceptibility gene, GRIN2B, in human and mouse cerebral cortex. Remarkably, both species showed a higher interaction between the TSS and an intronic sequence, enriched for (KRAB) Krueppel associated Box domain binding sites and selectively targeted by the (H3K9) histone 3 lysine 9 specific methyltransferase ESET/SETDB1. Transgenic mice brain cortical nuclei over-expressing Setdb1 showed increased heterochromatin-protein 1 signal at the interacting regions coupled with decreased Grin2b expression. 3C further revealed three long distant chromatin loop interactions enriched with functional enhancer specific (H3K27Ac) histone 3 lysine 27 acetylation signal in GRIN2B expressing tissue (human cortical nuclei and Human Embryonic Kidney - HEK cells). Doxycycline-induced SETDB1 over-expression decreased 2 out of 3 loop interaction frequencies suggesting a possible SETDB1-mediated transcription repression. We also report a specific looping interaction between a region 50Kb upstream of the (GAD1) Glutamic Acid Decarboxylase – 1 gene TSS and the GAD1 TSS in human brain nuclei. GAD1 catalyzes the rate limiting step in (GABA) gamma amino-butyric acid synthesis and is quintessential for inhibitory signaling in the human brain. Clinical studies in schizophrenia brain samples reveal a decreased looping interaction frequency in correspondence with a decrease in gene expression. Our findings provide evidence for the existence of transcription relevant higher order chromatin structures in human brain.

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Bharadwaj, Rahul. "Regulation of Higher Order Chromatin at GRIN2B and GAD1 Genetic Loci in Human and Mouse Brain: A Dissertation." eScholarship@UMMS, 2002. http://escholarship.umassmed.edu/gsbs_diss/651.

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Little is known about higher order chromatin structures in the human brain and their function in transcription regulation. We employed chromosome conformation capture (3C) to analyze chromatin architecture within 700 Kb surrounding the transcription start site (TSS) of the NMDA receptor and schizophrenia susceptibility gene, GRIN2B, in human and mouse cerebral cortex. Remarkably, both species showed a higher interaction between the TSS and an intronic sequence, enriched for (KRAB) Krueppel associated Box domain binding sites and selectively targeted by the (H3K9) histone 3 lysine 9 specific methyltransferase ESET/SETDB1. Transgenic mice brain cortical nuclei over-expressing Setdb1 showed increased heterochromatin-protein 1 signal at the interacting regions coupled with decreased Grin2b expression. 3C further revealed three long distant chromatin loop interactions enriched with functional enhancer specific (H3K27Ac) histone 3 lysine 27 acetylation signal in GRIN2B expressing tissue (human cortical nuclei and Human Embryonic Kidney - HEK cells). Doxycycline-induced SETDB1 over-expression decreased 2 out of 3 loop interaction frequencies suggesting a possible SETDB1-mediated transcription repression. We also report a specific looping interaction between a region 50Kb upstream of the (GAD1) Glutamic Acid Decarboxylase – 1 gene TSS and the GAD1 TSS in human brain nuclei. GAD1 catalyzes the rate limiting step in (GABA) gamma amino-butyric acid synthesis and is quintessential for inhibitory signaling in the human brain. Clinical studies in schizophrenia brain samples reveal a decreased looping interaction frequency in correspondence with a decrease in gene expression. Our findings provide evidence for the existence of transcription relevant higher order chromatin structures in human brain.

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20

Boedicker, Cathinka Verfasser], Simone [Akademischer Betreuer] [Fulda, Rolf [Gutachter] Marschalek, and Simone [Gutachter] Fulda. "Combined inhibition of BET proteins and PI3Kα reallocates BRD4 to transcriptional regulatory elements of BH3-only proteins and triggers mitochondrial apoptosis / Cathinka Boedicker ; Gutachter: Rolf Marschalek, Simone Fulda ; Betreuer: Simone Fulda." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2019. http://d-nb.info/1202297935/34.

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Boedicker, Cathinka [Verfasser], Simone [Akademischer Betreuer] Fulda, Rolf [Gutachter] Marschalek, and Simone [Gutachter] Fulda. "Combined inhibition of BET proteins and PI3Kα reallocates BRD4 to transcriptional regulatory elements of BH3-only proteins and triggers mitochondrial apoptosis / Cathinka Boedicker ; Gutachter: Rolf Marschalek, Simone Fulda ; Betreuer: Simone Fulda." Frankfurt am Main : Universitätsbibliothek Johann Christian Senckenberg, 2019. http://d-nb.info/1202297935/34.

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22

Noyes, Marcus Blaine. "An Omega-Based Bacterial One-Hybrid System for the Determination of Transcription Factor Specificity." eScholarship@UMMS, 2009. https://escholarship.umassmed.edu/gsbs_diss/407.

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From the yeast genome completed in 1996 to the 12 Drosophilagenomes published earlier this year; little more than a decade has provided an incredible amount of genomic data. Yet even with this mountain of genetic information the regulatory networks that control gene expression remain relatively undefined. In part, this is due to the enormous amount of non-coding DNA, over 98% of the human genome, which needs to be made sense of. It is also due to the large number of transcription factors, potentially 2,000 such factors in the human genome, which may contribute to any given network directly or indirectly. Certainly, one of the central limitations has been the paucity of transcription factor (TF) specificity data that would aid in the prediction of regulatory targets throughout a genome. The general lack of specificity data has hindered the prediction of regulatory targets for individual TFs as well as groups of factors that function within a common regulatory pathway. A large collection of factor specificities would allow for the combinatorial prediction of regulatory targets that considers all factors actively expressed in a given cell, under a given condition. Herein we describe substantial improvements to a previous bacterial one-hybrid system with increased sensitivity and dynamic range that make it amenable for the high-throughput analysis of sequence-specific TFs. Currently we have characterized 108 (14.3%) of the predicted TFs in Drosophilathat fall into a broad range of DNA-binding domain families, demonstrating the feasibility of characterizing a large number of TFs using this technology. To fully exploit our large database of binding specificities, we have created a GBrowse-based search tool that allows an end-user to examine the overrepresentation of binding sites for any number of individual factors as well as combinations of these factors in up to six Drosophila genomes (veda.cs.uiuc.edu/cgi-bin/gbrowse/gbrowse/Dmel4). We have used this tool to demonstrate that a collection of factor specificities within a common pathway will successfully predict previously validated cis-regulatory modules within a genome. Furthermore, within our database we provide a complete catalog of DNA-binding specificities for all 84 homeodomains in Drosophila. This catalog enabled us to propose and test a detailed set of recognition rules for homeodomains and use this information to predict the specificities of the majority of homeodomains in the human genome.

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Burdin, Dmitry V., Alexey A. Kolobov, Chad Brocker, Alexey A. Soshnev, Nikolay Samusik, Anton v. Demyanov, Silke Brilloff, et al. "Diabetes-linked transcription factor HNF4α regulates metabolism of endogenous methylarginines and β-aminoisobutyric acid by controlling expression of alanine-glyoxylate aminotransferase 2." Nature Publishing Group, 2016. https://tud.qucosa.de/id/qucosa%3A30404.

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Elevated levels of circulating asymmetric and symmetric dimethylarginines (ADMA and SDMA) predict and potentially contribute to end organ damage in cardiovascular diseases. Alanine-glyoxylate aminotransferase 2 (AGXT2) regulates systemic levels of ADMA and SDMA, and also of beta-aminoisobutyric acid (BAIB)-a modulator of lipid metabolism. We identified a putative binding site for hepatic nuclear factor 4 α (HNF4α) in AGXT2 promoter sequence. In a luciferase reporter assay we found a 75% decrease in activity of Agxt2 core promoter after disruption of the HNF4α binding site. Direct binding of HNF4α to Agxt2 promoter was confirmed by chromatin immunoprecipitation assay. siRNA-mediated knockdown of Hnf4a led to an almost 50% reduction in Agxt2 mRNA levels in Hepa 1–6 cells. Liver-specific Hnf4a knockout mice exhibited a 90% decrease in liver Agxt2 expression and activity, and elevated plasma levels of ADMA, SDMA and BAIB, compared to wild-type littermates. Thus we identified HNF4α as a major regulator of Agxt2 expression. Considering a strong association between human HNF4A polymorphisms and increased risk of type 2 diabetes our current findings suggest that downregulation of AGXT2 and subsequent impairment in metabolism of dimethylarginines and BAIB caused by HNF4α deficiency might contribute to development of cardiovascular complications in diabetic patients.

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Burdin, Dmitry V., Alexey A. Kolobov, Chad Brocker, Alexey A. Soshnev, Nikolay Samusik, Anton v. Demyanov, Silke Brilloff, et al. "Diabetes-linked transcription factor HNF4α regulates metabolism of endogenous methylarginines and β-aminoisobutyric acid by controlling expression of alanine-glyoxylate aminotransferase 2." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-226882.

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Elevated levels of circulating asymmetric and symmetric dimethylarginines (ADMA and SDMA) predict and potentially contribute to end organ damage in cardiovascular diseases. Alanine-glyoxylate aminotransferase 2 (AGXT2) regulates systemic levels of ADMA and SDMA, and also of beta-aminoisobutyric acid (BAIB)-a modulator of lipid metabolism. We identified a putative binding site for hepatic nuclear factor 4 α (HNF4α) in AGXT2 promoter sequence. In a luciferase reporter assay we found a 75% decrease in activity of Agxt2 core promoter after disruption of the HNF4α binding site. Direct binding of HNF4α to Agxt2 promoter was confirmed by chromatin immunoprecipitation assay. siRNA-mediated knockdown of Hnf4a led to an almost 50% reduction in Agxt2 mRNA levels in Hepa 1–6 cells. Liver-specific Hnf4a knockout mice exhibited a 90% decrease in liver Agxt2 expression and activity, and elevated plasma levels of ADMA, SDMA and BAIB, compared to wild-type littermates. Thus we identified HNF4α as a major regulator of Agxt2 expression. Considering a strong association between human HNF4A polymorphisms and increased risk of type 2 diabetes our current findings suggest that downregulation of AGXT2 and subsequent impairment in metabolism of dimethylarginines and BAIB caused by HNF4α deficiency might contribute to development of cardiovascular complications in diabetic patients.

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Sandelin, Albin. "In silico prediction of CIS-regulatory elements /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-879-3/.

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Hay, Deborah. "The role of regulatory elements in alpha globin transcription." Thesis, University of Oxford, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.665159.

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Understanding the mechanisms of transcriptional control by cis-acting regulatory elements is one of the major goals in current molecular biology. Estimates of enhancer numbers in mammalian genomes extend to hundreds of thousands, outnumbering genes by an order of magnitude or more. Yet current high throughput methods for enhancer identification give only indirect insights into their function, and are unable to demonstrate heterogeneity, redundancy, or cooperativity between regulatory elements. The a-globin locus has been extensively characterized with regard to transcriptional output, chromatin marks and chromosome conformation throughout erythroid maturation, and offers an excellent model for the investigation of enhancer function. Such analysis at this locus has previously been undertaken in heterologous transgenic models, including a 'humanized' mouse bearing the entire human aglobin cluster. Through the investigation of a rare naturally occurring mutation in a patient with thalassaemia, we demonstrate that heterologous transgenic models do not accurately recapitulate normal transcriptional control at this locus. This allows us to revise the prevailing view of human a-globin transcription control, in which a reliance on a single regulatory element (HS-40, or R2) was assumed. An analysis of the transcriptional contribution of the five regulatory elements at this locus (RI-4 and R[m]) has therefore been undertaken, using knockout mouse models. Assessment of the haematological impact of each regulatory element knockout demonstrates that none is indispensable for a-globin transcription; however, analysis of double knockouts proves functional non-equivalence of the elements, with RI and R2 together being critically required for viability. Quantification of nascent transcripts from each model shows a significantly different contribution to a-globin transcription from each of the five putative enhancers, with two providing no transcriptional contribution despite chromatin marks and transcription factor binding profiles suggestive of enhancer activity. RI and R2 are defined as the minor and major enhancers for a-globin; their deletion in concert also shows an unexpected impact on nascent transcription more widely across chromosome 11, challenging current views on enhancer-promoter specificity. This locus-specific study highlights heterogeneity in regulatory element biology that would be undetectable in current genome-wide studies. The models generated provide a platform for the further investigation of general principles of enhancer function, and will also permit us to examine the regulation of a-globin transcription in non-erythroid tissues.

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Mitchelmore, Joanna. "Investigation of transcription factor binding at distal regulatory elements." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/277805.

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Cellular development and function necessitate precise patterns of gene expression. Control of gene expression is in part orchestrated by a class of remote regulatory elements, termed enhancers, which are brought into contact with promoters via DNA looping. Enhancers typically 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 increasingly apparent that genes are commonly regulated by multiple enhancers in the same cell type. How a gene’s regulatory information is encoded across multiple enhancers, however, is still not fully understood. Second, numerous recent studies have found that enhancers are enriched for expression-modulating and disease-associated genetic variants. However, understanding and predicting the effects of enhancer variants remains a major challenge. I focussed on a human lymphoblastoid cell line (LCL), GM12878, for which ChIP-Seq data are available for 52 different TFs from the ENCODE project. Significantly, Promoter Capture Hi-C data for the same LCL are available, making it possible to link enhancers to target genes globally. In the first part of the thesis, I investigated how gene regulatory information is encoded across enhancers. Specifically, I asked whether a gene tends to use multiple enhancers to bring the same or distinct regulatory information. I found that there was a general trend towards a “shadow” enhancer architecture, whereby similar combinations of TFs were recruited to multiple enhancers. However, numerous examples of “integrating” enhancers were observed, where the same gene showed large variation in TF binding across enhancers. Distinct groups of TFs were associated with these contrasting models of TF enhancer binding. To investigate the functional effects of variation at enhancers, I additionally took advantage of a panel of LCLs derived from 359 individuals, which have been genotyped by the 1000 Genomes Project, and for which RNA-Seq data are publically available. I used TF binding models to computationally predict variants impacting TF binding, and tested the association of these variants with the expression of the target genes they contact based on Promoter Capture Hi-C. Compared to the standard eQTL calling approach, this offers increased sensitivity as only variants physically contacting the promoter and predicted to impact TF binding are tested. Using this approach, I discovered a set of predicted TF-binding affinity variants at distal regions that associate with gene expression. Interestingly, a large proportion of these binding variants fall at the promoters of other genes. This finding suggests that some promoters may be able to act in an enhancer-like manner via long-range interactions, consistent with very recent findings from alternative approaches.

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Fulton, Debra Louise. "Computational prediction of regulatory element combinations and transcription factor cooperativity." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/17429.

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Cellular identity and function is determined, in part, by the subset of genes transcribed. Gene transcription regulation is directed by a subgroup of proteins called transcription factors (TF), which can interact directly or indirectly with DNA to promote transcription initiation. In multi-cellular eukaryotes, gene expression often derives from synergistic and/or antagonistic interplay of multiple TFs with coordinate activity in response to physiological, developmental, and environmental stimuli. Sequence-specific interactions of TFs with DNA occur at TF binding sites (TFBS). Such TFBS can be predicted based on previously observed target DNA sequence specificity of a TF. Experimental studies have confirmed that proximally situated TFBS are often associated with synergistic interactions of multiple proteins that lead to cooperative regulation. The identification of clustered TFBS combinations (often called cis-regulatory modules) in a set of co-expressed genes can implicate regulatory roles for homologous groups of TFs that may contribute to co-regulation of a gene cohort. The identification of the specific TFs that interact with TFBS motifs is an important step in deciphering mechanisms of co-regulation. My thesis research addressed these challenges, firstly, through the design and development of a Combination Site Analysis (CSA) algorithm to identify over-representation of combinations of TFBS in co-expressed genes and, secondly, the assembly of a comprehensive wiki-based catalog of human-mouse TFs (TFCat) using literature curation and homolog prediction approaches. These applications were incorporated within a new promoter sequence analyses procedure for the identification of TFs that may be acting cooperatively to co-regulate expression of myelin-associated genes during myelin production in the CNS. Dysregulation of gene expression is frequently implicated in human pathologies and development of approaches that identify the molecular components of transcriptional regulatory systems is an important step towards the elucidation of molecular mechanisms for the design of therapeutic interventions.

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Xu, Xiaohong. "SHARED LONG-RANGE REGULATORY ELEMENTS COORDINATE EXPRESSION OF THE NACHR BETA4/ALPHA3/ALPHA5 CLUSTER." Case Western Reserve University School of Graduate Studies / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1157660172.

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Suciu, Maria C. "Analysis of transcription factor binding at cis-regulatory elements during blood development and differentiation." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:bc5d0f0a-814b-4f5f-85ea-19c6624ca387.

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The overall aim of this work is to understand how regulatory sequences (enhancers, promoters) are bound and interpreted by TFs during erythroid development and differentiation. This is becoming increasingly important as DNA sequence variants in enhancers may alter protein binding and consequently may contribute to changes in gene expression that affect susceptibility to common diseases. We hypothesised that by using high-resolution analysis of chromatin accessibility data, we would identify relevant differences in sequence usage at regulatory regions in erythroid cells at various stages of development and differentiation. To test this, we developed a robust and efficient method to isolate HS regions in erythroid cells by performing DNase-Seq and ATAC-Seq. When analysed at high resolution, open-chromatin assays, namely DNase-Seq, reveal a genome-wide profile of 'footprints' - transcription factor bound sites at regulatory elements in different erythroid cell types. The two dynamic contexts, development and differentiation, in which we analysed the changes in HS regions share a common pattern: we identified approximately 10% cell specific HS regions. The differential open-chromatin regions correspond mainly to enhancers, but also promoters. Majority of these elements (~80%) occur in different genomic regions. These observations reinforce the fact that differentiation and development are driven by TF binding at distal elements. At the α-globin locus, the quantitative changes of HS regions are correlated with the activity of gene promoters. The level of HS enrichment refines the chromatin signature of functional enhancers. Novel analysis of HS genome-wide data, "average footprinting", provides a constrained set of transcription factor binding sites ranked by their usage in a specific cell type. We also adapted this approach to predict the effect of a variant in a sequence on altering affinity to TF and potentially causing changes in gene expression. This predicted damage score approach can be used to prioritise variants for functional analysis. Finally, we have identified families with unexplained anaemia, which have a SNP in a binding site of the major enhancer of the human α-globin cluster. This variant has a high damage score based on our prediction analysis. We are currently investigating if, and how, this non-coding SNP affects gene expression as an example of how regulatory SNPs in general may contribute to human genetic disease.

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31

Adam, Muhammed Saleem. "A knowledgebase of stress reponsive gene regulatory elements in arabidopsis Thaliana." Thesis, University of the Western Cape, 2011. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_9599_1362393100.

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Stress responsive genes play a key role in shaping the manner in which plants process and respond to environmental stress. Their gene products are linked to DNA transcription and its consequent translation into a response product. However, whilst these genes play a significant role in manufacturing responses to stressful stimuli, transcription factors coordinate access to these genes, specifically by accessing a gene&rsquo
s promoter region which houses transcription factor binding sites. Here transcriptional elements play a key role in mediating responses to environmental stress where each transcription factor binding site may constitute a potential response to a stress signal. Arabidopsis thaliana, a model organism, can be used to identify the mechanism of how transcription factors shape a plant&rsquo
s survival in a stressful environment. Whilst there are numerous plant stress research groups, globally there is a shortage of publicly available stress responsive gene databases. In addition a number of previous databases such as the Generation Challenge Programme&rsquo
s comparative plant stressresponsive gene catalogue, Stresslink and DRASTIC have become defunct whilst others have stagnated. There is currently a single Arabidopsis thaliana stress response database called STIFDB which was launched in 2008 and only covers abiotic stresses as handled by major abiotic stress responsive transcription factor families. Its data was sourced from microarray expression databases, contains numerous omissions as well as numerous erroneous entries and has not been updated since its inception.The Dragon Arabidopsis Stress Transcription Factor database (DASTF) was developed in response to the current lack of stress response gene resources. A total of 2333 entries were downloaded from SWISSPROT, manually curated and imported into DASTF. The entries represent 424 transcription factor families. Each entry has a corresponding SWISSPROT, ENTREZ GENBANK and TAIR accession number. The 5&rsquo
untranslated regions (UTR) of 417 families were scanned against TRANSFAC&rsquo
s binding site catalogue to identify binding sites. The relational database consists of two tables, namely a transcription factor table and a transcription factor family table called DASTF_TF and TF_Family respectively. Using a two-tier client-server architecture, a webserver was built with PHP, APACHE and MYSQL and the data was loaded into these tables with a PYTHON script. The DASTF database contains 60 entries which correspond to biotic stress and 167 correspond to abiotic stress while 2106 respond to biotic and/or abiotic stress. Users can search the database using text, family, chromosome and stress type search options. Online tools have been integrated into the DASTF
database, such as HMMER, CLUSTALW, BLAST and HYDROCALCULATOR. User&rsquo
s can upload sequences to identify which transcription factor family their sequences belong to by using HMMER. The website can be accessed at http://apps.sanbi.ac.za/dastf/ and two updates per year are envisaged.

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32

Ritter, Deborah Irene. "Coding and Noncoding Regulatory Enhancers in Vertebrate Development." Thesis, Boston College, 2011. http://hdl.handle.net/2345/3721.

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Thesis advisor: Jeffrey H. Chuang
Gene regulation is perhaps least understood among vertebrate species, where cell differentiation, tissue-types and body-plans indicate a complexity in need of careful coordination to achieve such hierarchical design. Recent studies reveal the intricacy of vertebrate gene regulation through diverse events including transcriptional regulatory histone modifications and non-coding DNA [1-5]. Almost 98% of the human genome is noncoding DNA, much of which may be actively involved in regulating healthy and disease-state gene expression and environmental response [6]. Conserved noncoding elements (CNEs) are sequences of noncoding DNA that are known to regulate gene expression [7-9]. The CNEs identified thus far are a small percentage of the total noncoding DNA in the human genome, and many identified CNEs still lack experimental characterization [10]. Thus, there is a need for functional characterization and streamlined identification of CNEs in order to more fully annotate vertebrate genomes and understand gene expression. The work in this thesis identified over 6000 CNEs and experimentally characterized over 150 CNEs conserved between zebrafish and human (> 60% DNA sequence conservation), using the experimental model Danio rerio (zebrafish). Functional, tissue and time-specific CNEs were identified through analysis of conservation, accelerated evolution, distance, GC content, motifs, transcription factors and gene function. In addition, a searchable database and website was created to host data and facilitate collaborative research between experimental and computational labs. While non-coding DNA is an important area of discovery for gene regulation, protein-coding DNA also has the potential to contain non-coding transcriptional information. DNA is typically conceptualized as either noncoding or protein coding. An underlying assumption to this framework assumes that the function of noncoding DNA is "regulatory" and coding DNA is "protein coding." Consequently, the potential for DNA to harbor both types of information in one sequence has been minimally researched. For the second-half of this thesis, I identified and experimentally tested 31 conserved coding exons ( > 60% zebrafish and human DNA sequence conservation) in zebrafish. To improve annotation of live embryonic expression, a novel voice-recognition expression analysis system was developed that allows quick comparison and annotation of embryonic expression at the microscope. In addition, a website and webtool to calculate significant expression was created as a resource for experimental research on anatomical analysis in whole organisms. The experimental results show that a large number of protein-coding DNA sequences can act as non-coding enhancers. This knowledge may impact methods to identify noncoding signals and, further, the scientific conceptualizations of coding and noncoding DNA in the genome
Thesis (PhD) — Boston College, 2011
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

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33

Wolfe, Richard A. "In Silico Discovery of Pollen-specific Cis-regulatory Elements in the Arabidopsis Hydroxyproline-Rich Glycoprotein Gene Family." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1408383003.

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34

Chen, Liang. "Motif Selection Using Simulated Annealing Algorithm with Application to Identify Regulatory Elements." Ohio University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1531343206505855.

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35

Fu, Wai. "In silico prediction of cis-regulatory elements of genes involved in hypoxic-ischaemic insult." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36986896.

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36

Langer, Björn. "Phenotype-related regulatory element and transcription factor identification via phylogeny-aware discriminative sequence motif scoring." Doctoral thesis, Center for Systems Biology Dresden, 2017. https://tud.qucosa.de/id/qucosa%3A31172.

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Understanding the connection between an organism’s genotype and its phenotype is a key question in evolutionary biology and genetics. It has been shown that many changes of morphological or other complex phenotypic traits result from changes in the expression pattern of key developmental genes rather than from changes in the genes itself. Such altered gene expression arises often from changes in the gene regulatory regions. That usually means the loss of important transcription factor (TF) binding sites within these regulatory regions, because the interaction between TFs and specific sites on the DNA is a key element of gene regulation. An established approach for the genome-wide mapping of genomic regions to phenotypes is the Forward Genomics framework. This approach compares the genomic sequences of species with and without the phenotype of interest based upon two ideas. First, the initial loss of a phenotype relaxes selection on all phenotypically related genomic regions and, second, this can happen independently in multiple species. Of interest are such regions that diverged specifically in phenotype-loss species. Although this principle is general, the current implementation is only well-suited for the identification of phenotype related gene-coding regions and has a limited applicability on regulatory regions. The reason is its reliance on sequence conservation as divergence measure, which does not accurately measure functional divergence of regulatory elements. In this thesis, I developed REforge, a novel implementation of the Forward Genomics principle that takes functional information of regulatory elements in the form of known phenotype-related TF into account. The consideration of the flexible organization of TF binding sites within a regulatory region, both in terms of strength and order, allows the abstraction from the region’s sequence level to its functional level. Thus, functional divergence of regulatory regions is directly compared to phenotypical divergence, which tremendously improves performance compared to Forward Genomics, as I demonstrated on synthetic and real data. Additionally, I developed TFforge which follows the same approach but aims at identifying the TFs relevant for the given phenotype. Given a multi-species alignment with a phenotype annotation and a set of regulatory regions, TFforge systematically searches for TFs whose changes in binding affinity between species fit the phenotype signature. The reported output is a ranking of the TFs according to their level of correspondence. I prove the concept of this approach on both biological data and artificially generated regions. TFforge can be used as a standalone analysis tool and also to generate the input set of TFs for a subsequent REforge analysis. I demonstrate that REforge in combination with TFforge is able to substantially outperform standard Forward Genomics, i.e. even without foreknowledge of relevant TFs. Overall, the in this thesis introduced methods are examples for the power of computational tools in comparative genomics to catalyze biological insights. I did not only show a detailed description of the methods but also conducted a real data analysis as validation. REforge and TFforge have a wide applicability on endless phenotypes, both on their own in the association of TF and regulatory region to a phenotype. Moreover, particularly their combination constitutes in respect to gene regulatory network analyses a valuable tool set for evo-devo studies.

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Lam, Ka-man Amy. "Osmotic response element binding protein (OREBP) is an essential regulator of urine concentrating mechanism and renal protection." Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B3127402X.

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Fu, Wai, and 符慧. "In silico prediction of cis-regulatory elements of genes involved in hypoxic-ischaemic insult." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B36986896.

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39

Wourms, Michael J. "The Aryl Hydrocarbon Receptor Regulates an Essential Transcriptional Element in the Immunoglobulin Heavy Chain Gene." Wright State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=wright1389551618.

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40

Lam, Ka-man Amy, and 林嘉敏. "Osmotic response element binding protein (OREBP) is an essential regulator of urine concentrating mechanism and renal protection." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B3127402X.

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41

Banerjee, Chaitali. "The Osteocalcin Gene: Transcriptional Elements and Factors Regulating TGF-β1 Responsiveness and Tissue-Specific Expression in Bone Cells: A Dissertation." eScholarship@UMMS, 1998. http://escholarship.umassmed.edu/gsbs_diss/145.

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Osteocalcin (OC) is a bone specific protein expressed during differentiation and mineralization of the bone extracellular matrix. The Osteocalcin gene is transcriptionally regulated by several basal, hormone- and cytokine-responsive elements. To address the potential role of TGF-β1 regulation and tissue-specific expression of the OC gene, we defined regulatory elements and factors mediating the transcriptional activity of the rat OC (rOC) promoter. TGF-β1 modulates the differentiation of cells of the osteogenic lineage and downregulates the osteoblast-specific expression of OC. By promoter deletion and mutational analyses, a TGF-β1 responsive element at nt -146 to -139 and a contiguous tissue-specific enhancer element at nt -136 to -130 on the rOC promoter were identified. These studies show that Fra-2, a member of the AP-1 family of proteins, binds to the TGF-β1 responsive element and activates basal OC expression. TGF-β1 induced phosphorylation of Fra-2 inhibits this activation, resulting in repression of OC gene transcription. The tissue-specific enhancer element contiguous to the TGF-β1 responsive element contains an AML (Cbfa) binding sequence. This element, designated OC Box II, contributes to 75% of the basal OC promoter activity and forms an osteoblast-specific protein-DNA complex in in-vitro assays. The activation potential of this binding sequence was established by overexpressing AML (Cbfa) transcription activator proteins in osteoblastic as well as in non-osseous cell lines. Interestingly, overexpression not only enhances rOC promoter activity in osteoblasts but also mediates promoter activity in a non-osseous human fibroblastic cell-line. Subsequently, we identified AML-3 (Cbfa1) as the major AML family member present in the osteoblast specific complex and demonstrate that AML-3 (Cbfa1) is expressed predominantly as a 5.4 kb transcript in rat bone tissues. Finally, to establish the functional involvement of AML (Cbfa) transcription factors in osteoblast differentiation, we utilized antisense strategies to demonstrate that blocking expression of all AML (Cbfa) related genes in primary osteoblast cultures significantly decreased several parameters which are linked to differentiation of normal diploid osteoblasts. These results indicate that AML-3 (Cbfa1) is a key transcription factor in bone cells and that the activity of the AML (Cbfa) family of proteins is required for completion of osteoblast differentiation.

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42

Xu, Jing. "Polyunsaturated fatty acids suppress hepatic lipogenic gene transcription by accelerating sterol regulatory element binding protein-1 transcript decay /." Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3008476.

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43

Watanabe, Mitsuhiro. "Bile acids lower triglyceride levels via a pathway involving SHP (small heterodimer partner) and SREBP-1c (sterol regulatory element binding protein)." Université Louis Pasteur (Strasbourg) (1971-2008), 2004. http://www.theses.fr/2004STR13031.

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Les souris KK-Ay représentent un bon modèle pour étudier les effets d'une alimentation riche en graisse dans le développement des hyperlipidémies de type IIb et IV. Les acides biliaires réduisent l'accumulation des TG dans le foie ainsi que dans le sérum. LXR et LRH-1 induisent l'expression de SREBP-1c, les acides biliaires induisent l'expression de SHP en activant FXR. Ensuite, SHP diminue l'activité transcriptionnelle de LXR et LRH-1 sur le promoteur murin de SREBP-1c. Les acides biliaires réduisent l'accumulation hépatique de TG en réduisant l'expression de SREBP-1c via SHP. La diminution de la sécrétion des VLDL, et donc de TG sérique, est diminuée. Mes résultats suggèrent que des stratégies en vue d'augmenter l'activité de FXR et l'effet répresseur de SHP doivent être explorées pour corriger l'hypertriglycéridémie
KK-Ay mice are useful model to study high fat diet induced type IIb and IV hypertriglyceridemia. Bile acids reduced TG accumulation in liver and TG level in serum. LXR and LRH induce SREBP1c gene expression and bile acids induce mRNA expression of SHP by activating FXR. SHP decreases LXR and LRH transcriptional activity in mouse SREBP1c promoter region. Bile acids reduced liver TG accumulation by suppressing SREBP1c gene expression via SHP. This decreases VLDL secretion and as a result serum TG is reduced. Our results and these data suggest that strategies aimed at increasing FXR activity and the repressive effects of SHP should be explored to correct hypertriglyceridemia

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Murphy, Charlotte. "Studies on the regulatory roles of cholesterol and bile acids /." Stockholm, 2007. http://diss.kib.ki.se/2007/978-91-7357-173-9/.

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45

Jäkel, Heidelinde. "Régulation transcriptionnelle de l'apolipoprotéine A5 par les facteurs de transcription "Peroxisome proliferator activated receptor α", "Liver X Receptor" et "Sterol regulatory element binding protein 1c"." Lille 2, 2005. http://www.theses.fr/2005LIL2S007.

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Les études épidémiologiques démontrent qu’une concentration élevée en triglycérides plasmatiques constitue un facteur de risque indépendant dans le développement des maladies cardiovasculaires. L’apolipoprotéine A-V (apoA-V), récement découverte, présente un nouveau déterminant de la concentration en triglycérides plasmatiques. D’autre part, le rôle joué par des récepteurs nucléaires PPARα et LXR, qui régulent la concentration en triglycérides et ont un effet anti-athérogène, a été étudié dans la régulation de l’expression de l’APOA5. Nous avons montré que las activateurs de PPARα induisent l’expression de l’APOA5 par l’intermédiaire d’un élément de réponse à PPAR situé dans son promoteur. Inversement, nous avons pu mettre en évidence une transrépression de l’APOA5 par les ligands de LXR via la fixation du gène cible, SREBP-1c, sur son promoteur. En résumé, ces résultats obtenus soulignent l’implication de PPARα et LXR dans la régulation de l’expression de l’apoA-V et le métabolisme des triglycérides
Epidemiological studies revealed that an elevated plasma triglyceride concentration constitue an independent risk factor for cardiovascular disease. The recently discovered apolipoprotein A-V (apoA-V) emerged as a new determinant of plasma triglyceride levels. In our study we assessed the regulation of APOA5 by PPARα and LXR ligands, since these nuclear receptors play a crucial role in plasma triglyceride metabolism with an over-all antiatherogenic effect. We showed that PPARα activators elevate APOA5 gene expression via a PPRE in its proximal promoter. Furthermore, we demonstrated that a LXR ligand down-regulates APOA5 gene expression via the fixation of its target gene SREBP-1c on a specific element on its promoter. In conclusion, our results indicate that PPARα and LXR ligands may be implicated in apoA-V gene expression

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46

Rodda, David J. "Characterization of the repression of glucocorticoid-induced transcription of the mouse mammary tumor virus through negative regulatory element 1." Thesis, University of Ottawa (Canada), 2001. http://hdl.handle.net/10393/9190.

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The physiological effects of steroid hormones are mediated by their cognate receptors which regulate expression of target genes in response to binding of their steroid ligand. The mouse mammary tumor virus (MMTV) promoter is a widely used system for studying the effects of steroid hormones due to its strong activation by several classes of steroids. MMTV induces mammary tumors in female mice following lactation. T-cell lymphomas are also induced at much lower frequency and all cases of lymphoma that have been examined have deletions spanning a region of the long terminal repeat (LTR) from -421 to -364. This region has a transcriptional negative regulatory element called NRE1. Characterization of NRE1 revealed nuclear factors binding to the double-stranded (ds) form, as well as each of the single strands (up, lo - upper and lower strands respectively). A truncated element (MT) was also recognized but only the ds form. Kinetic studies showed binding occurred to the ds, up, to and MT with t1/2s of 11, 1.5, 3 and 4 min respectively. The off-rates (t1/2) were determined to be 60 min, 30 min, 12 h and 4 h respectively. Four factors were observed to bind NRE1 in southwestern analysis, while only one was observed binding to MT, that corresponded in mobility to the smallest NRE1 binding factor. The four factors appeared to cross-react with an octamer motif. The dsNRE1 binding factor was confirmed to recognize an octamer motif in EMSA. The dsNRE1 binding factor was identified as the Ku autoantigen heterodimer. It was demonstrated to bind directly to NRE1 with an affinity of Kd = 0.84 +/- 0.24 mum. Ku also bound upNRE1 with an affinity of K d = 3.5 +/- 1.3 mM. In kinetic analyses of purified Ku binding to upNRE1 the on-rate was determined to be t1/2 = 1.6 min, while the off rate was t1/2 = 68 min. Transient transfection assays using MMTV reporters either containing or lacking NRE1 were performed. Using cell lines not expressing functional Ku or its associated factor DNA-PK it was shown that both factors were required for the NRE1 mediated repression of glucocorticoid-induced transcription of MMTV. DNA-PK was shown to specifically phosphorylate a myc-tagged glucocorticoid receptor (GR) on serine 527 (5527) in vitro. A second phosphorylation site was determined to result from the addition of the myc tag, while a native receptor was phosphorylated only on S527. Transient transfections using 5527 mutants of GR demonstrated that substitution of S527 for alanine abrogated NRE1 mediated repression. The same effect was observed for glutamic acid and aspartic acid substitutions. We therefore conclude that binding of DNA-PK to NRE1 through its DNA binding subunit, Ku, allows it to phosphorylate GR on serine 527 resulting in a repression of glucocorticoid-induced transcription.

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Cowie, Philip David. "Analysis of the effects of disease-associated variation within a cis-regulatory element of the CNR1 locus on CNR1 promoter dynamics." Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=225652.

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Genetic variation within the cannabinoid 1 receptor (CB1R) locus (CNR1) has been repeatedly associated with drug addiction pathologies. Genomic annotation of CNR1 indicates the vast majority of this genetic variation likely results in altered transcriptional regulation of the CNR1 gene as a mechanistic link to the disease phenotype. There is a lack of information describing the regulation of CNR1 transcription and the potential impact of disease-associated variation within the CNR1 locus on its transcriptional regulation. This study investigates the impact of an evolutionary conserved regulatory region of CNR1, termed ECR1, and the disease-associated variation contained within, on the transcriptional activity of the cognate CNR1 promoter region. Reporter assays conducted in primary hippocampal cells demonstrate that CNR1 promoter exhibits variable transcriptional activity during periods of CB1R signalling and cell depolarisation. Coupled to allelic variants of ECR1, the CNR1 promoter shows significant changes in transcriptional activity under resting conditions indicating that disease-associated variation within ECR1 may decrease CNR1 transcription. Further, alleles of ECR1 can drive allele-specific transcriptional responses from the CNR1 promoter during periods of CB1R stimulation and cell depolarisation. The results highlight the potential for disease-associated regulatory variation of the CNR1 locus to create stratified transcriptional responses to specific cell signalling scenarios and putatively to clinical strategies employing pharmacological agents. Furthermore, investigation of DNA-protein interactions at the allelic ECR1 region demonstrate that disease-associated variation within ECR1 alters DNA-protein interactions within the nucleus consistent with a decrease in transcriptional activity in the disease-associated allele variant. Collectively the current work supports the hypothesis that disease-associated variation within the ECR1 regulatory region of the CNR1 locus has the capacity to significantly impact on CNR1 promoter transcriptional activity. It is posited that allele-specific transcriptional effects may have a major impact on the susceptibility of individuals to drug addiction or on responses to clinical pharmacological treatments.

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48

Li-Kroeger, David. "Integration of regional and neural transcription factors controls EGF signaling from sensory organ precursor cells during Drosophila development." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1337351052.

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49

Schoenfelder, Sonja Melanie Kerstin. "Gene expression control in healthcare-associated Staphylococci : characterisation of a T-box regulatory RNA element governing methionine biosysthesis gene transcription." Thesis, Queen's University Belfast, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.549686.

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Gram-positive bacteria of the genus Staphylococcus are known commensals of the human skin and mucosa, but also opportunistic pathogens especially for immunocompromised patients. The rapid development of antibiotic multiresistance poses a great problem for the treatment of staphylococcal infections and results in an ongoing need for novel antibiotic targets. The first part of this work addressed the phenotypic and genetic characteristics of a set of S. epidermidis samples which had been isolated from a leukaemia patient over the course of an eventually fatal infection. Molecular typing methods (PFGE and MLST) were used to identify a single S. epidermidis strain of the widespread sequence type ST2 as the cause of infection. The strain displayed a high phenotypic variability during the infection with regard to oxacillin resistance and biofilm formation. The underlying mechanism is most likely the high genetic variability of this particular S. epidermidis clonal lineage. The same genomic deletion observed in vivo could be triggered in an in vitro experiment and occurred with a very high frequency (10-²) The second part of this thesis concerned the characterisation of a recently identified putative T-box transcriptional control system for methionine biosynthesis genes. The nucleotide sequence alignment revealed high homologies between staphylococcal species and predicted structural elements associated with Bacillus T-box systems. In vitro binding assays with this met leader RNA and tRNA Met demonstrated the binding interaction between the two RNA species and mutational studies of the T-box motif revealed the importance of single nucleotides for tRNA binding. Transcript levels of the met leader RNA and the downstream genes were shown to vary between different staphylococcal strains, but to be generally induced under methionine starvation. From various S. aureus RNase mutants investigated mainly RNase Y, RNase J2 and RNase III seem to be involved in met leader RNN mRNA processing and degradation.

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Bernard, Virginie. "Relations entre l'organisation des sites de fixation des facteurs de transcription, la fonction des gènes et l'expression des gènes : vers une annotation des sites de fixation chez Arabidopsis thaliana." Phd thesis, Université d'Evry-Val d'Essonne, 2009. http://tel.archives-ouvertes.fr/tel-00444896.

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Abstract:

Les sites de fixation des facteurs de transcription ou éléments régulateurs sont impliqués dans la régulation de l'expression des gènes. Une meilleure connaissance de l'architecture des promoteurs est aujourd'hui accessible via l'annotation des génomes et les données transcriptomiques. Certains éléments régulateurs sont conservés à une position préférentielle dans les promoteurs. Chez A. thaliana, nous avons mis au point une approche pour caractériser de tels motifs. Ce travail a permis de proposer une cartographie des promoteurs en identifiant 5105 motifs caractérisés par une sur-représentation locale dans les promoteurs proximaux. L'étude du promoteur central où est observée la boîte TATA, élément régulateur conservé entre eucaryotes, a été approfondie. Une liste de 15 variants fonctionnels de la boîte TATA a été identifiée, ainsi qu'une nouvelle classe d'éléments régulateurs qui sont caractérisés par des mêmes contraintes topologiques que la boîte TATA : les motifs-TC. Ils sont conservés chez A. thaliana et le riz, Oryza sativa, mais absents chez les mammifères. Les 18% de gènes d'A. thaliana contenant un motif-TC ont tendance à être exprimés dans des conditions expérimentales spécifiques. Ces éléments pourraient participer à la régulation de l'expression des gènes. L'étude de l'élément initiateur YR chez A. thaliana a mis en évidence une extension de ces 4 dinucléotides dans l'UTR 5'. Des associations entre ces éléments régulateurs peuvent montrer une collaboration fonctionnelle. La recherche de caractéristiques fonctionnelles communes aux gènes possédant une même organisation d'éléments régulateurs pourra permettre de contribuer à l'annotation fonctionnelle de ces éléments.

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Dissertations / Theses on the topic 'Transcriptional Regulatory Elements'

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