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1
Kokulapalan, Wimalanathan. "Genome-wide Computational Analysis of Chlamydomonas reinhardtii Promoters." Miami University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1320638327.
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Qi, Zhan [Verfasser], and Veit [Akademischer Betreuer] Hornung. "Large-scale analysis of Drosophila core promoter function using synthetic promoters / Zhan Qi ; Betreuer: Veit Hornung." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1188200240/34.
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Phillips, Julian Peter. "Promoter analysis in transgenic sugar beet." Thesis, De Montfort University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391084.
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Oliveira, Junior Silvio De. "Revalorisation des effluents thermiques industriels : analyse exergétique, entropique et économique." Vandoeuvre-les-Nancy, INPL, 1991. http://docnum.univ-lorraine.fr/public/INPL_T_1991_OLIVEIRA_JUNIOR_S_D.pdf.
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ADans la partie 1, nous développons l'analyse entropique et exergétique des processus de transfert de chaleur et de matière de la séparation et du mélangeage d'un mélange binaire, pour définir les conditions optimales de tels systèmes, qui sont les principaux éléments des machines à absorption. Nous présentons une méthode graphique d'élaboration des bilans d'exergie et de calcul des pertes exergétiques lors d'une séparation/mélangeage d'un mélange binaire. Sont présentes les diagrammes exergie-concentration et exergie-enthalpie pour les couples H2O-LiBr et NH3-H2O. Dans la partie 2, nous présentons de nouvelles configurations de structures de promoteurs de turbulence pour des films ruisselants qui provoquent un mélangeage transversal du film en assurant les conditions de mouillabilité film-paroi et ayant des bonnes performances thermiques et des faibles couts de fabrication. L’évaluation du comportement de ces structures est faite à partir de la comparaison de leurs coefficients de transfert de chaleur et de la production spécifique globale d'entropie avec un tube lisse ayant la même géométrie et sous les mêmes conditions d'opération. Dans la partie 3, nous présentons de nouvelles structures et des nouveaux types de thermotransformateurs et frigo-pompes pour la revalorisation des effluents thermiques industriels. Ce sont deux systèmes à absorption pure et deux systèmes hybrides à absorption-compression mécanique et absorption-ejecto-compression. Nous développons une méthode d'analyse exergo-économique de ces systèmes basés sur une fonction de valeur technico-économique qui caractérise la performance combinée thermique et économique des systèmes. Les performances de ces systèmes sont comparées dans des conditions d'opération industrielles à travers l'emploi des logiciels PACA-design. Pour chaque condition d'opération nous identifions les systèmes les plus performants en utilisant la fonction de valeur technico-économique
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Bohne, Alexandra-Viola. "Analyse von Komponenten der organellären Transkriptionsmaschinerien aus Arabidopsis thaliana und Nicotiana tabacum." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2009. http://dx.doi.org/10.18452/15965.
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Die Gesamtheit mitochondrialer Gene sowie ein Teil der plastidären Gene photosynthetischer Eukaryoten wird durch kernkodierte Phagentyp-RNA-Polymerasen transkribiert. In der vorliegenden Arbeit wurden unter Verwendung eines homologen in vitro-Transkriptionssystems, die spezifischen Funktionen der Phagentyp-RNA-Polymerasen RpoTm, RpoTp und RpoTmp aus Arabidopsis untersucht. Während RpoTmp keine Präferenz für die angebotenen Promotoren zeigte, transkribierten RpoTm und RpoTp eine überlappende Gruppe mitochondrialer und plastidärer Promotoren vielfältiger Architektur. RpoTm und RpoTp präsentierten eine Kofaktor-unabhängige Fähigkeit zur Promotorerkennung bei Angebot superhelikaler DNA-Matrizen. Eine selektive Promotornutzung sowie die Unfähigkeit zur spezifischen Transkription linearer Promotormatrizen in vitro implizieren die Assoziation zusätzlicher, in die Promotorerkennung und/oder DNA-Aufschmelzung involvierter Kofaktoren in vivo. Die in vitro-Erkennung mitochondrialer Promotoren durch eine plastidäre Phagentyp-RNA-Polymerase (und umgekehrt) sowie weitere Ähnlichkeiten der Transkriptionsapparate der Mitochondrien und Plastiden, wie die strukturelle Organisation ihrer Promotoren und die phylogenetische Herkunft ihrer kernkodierten Transkriptasen inspirierte in planta Studien zur spezifischen Transkription eines mitochondrialen Promotors in den Plastiden. Hierzu wurde die Expression des nptII-Reportergens unter Kontrolle des mitochondrialen PatpA-Promotors aus Oenothera in transplastomischen Tabakpflanzen analysiert. Die durchgeführten Studien belegen eine korrekte Transkription des mitochondrialen PatpA-Promotors durch eine plastidäre Phagentyp-RNA-Polymerase in in vitro-Transkriptionsassays sowie in transplastomischen Tabakpflanzen. Diese Resultate enthüllen weitere unerwartete Ähnlichkeiten der organellären Genexpression, die aufschlussreiche evolutionäre Einblicke erlauben und verbesserte Anwendungen zur Manipulation plastidärer Genome ermöglichen könnten.All mitochondrial and a subset of plastidial genes of photosynthetically active eukaryotes are transcribed by nuclear-encoded, phage-type RNA polymerases. In this study, a homologous in vitro transcription system was used to define the specific functions of Arabidopsis phage-type RNA polymerases RpoTm, RpoTp and RpoTmp in organellar transcription. RpoTmp displayed no significant promoter specificity, whereas RpoTm and RpoTp were able to accurately initiate transcription from overlapping subsets of mitochondrial and plastidial promoters of diverse architecture. RpoTm and RpoTp thereby demonstrated an intrinsic capability to recognize promoters on supercoiled DNA templates without the aid of protein cofactors. A selective promoter recognition by the phage-type RNAPs in vitro and the inability to recognize promoters on linear templates imply that auxiliary factors are required for efficient initiation of transcription and/or DNA melting in vivo. Crosswise recognition of organellar promoters by the phage-type RNA polymerases in vitro as well as other similarities of the mitochondrial and plastidial transcription machineries such as promoter structures and the phylogenetic origin inspired in planta studies to investigate specific transcription of a mitochondrial promoter in plastids. Therefore, the expression of an nptII reporter gene under control of the mitochondrial PatpA promoter from Oenothera was analyzed in transplastomic tobacco plants. The data presented here demonstrate the faithful recognition of the mitochondrial PatpA promoter by a plastid RNA polymerase both in in vitro transcription assays and in transplastomic tobacco plants. These findings disclose further unexpected similarities of the organellar gene expression systems which deliver interesting evolutionary insights and might facilitate improved applications for chloroplast genome engineering.
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Featherstone, Mark S. "Structural analysis of the polyomavirus late promoter." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=72778.
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He, Bing. "Systematic analysis of enhancer and promoter interactions." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/1972.
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Transcriptional enhancers represent the primary basis for differential gene expression. These elements regulate cell type specificity, development, and evolution, with many human diseases resulting from altered enhancer activity. To date, a key gap in our knowledge is how enhancers select specific promoters for activation.
To fill this gap, in this thesis, I first developed an Integrated Method for Predicting Enhancer Targets (IM-PET). Leveraging abundant “omics” data, I devised and characterized multiple genomic features for distinguishing true enhancer-promoter (EP) pairs from non-interacting pairs. I integrated these features into a probabilistic predictor for EP interactions. Multiple validation experiments demonstrated a significant improvement over extent state-of-the-art approaches. Systematic analyses of EP interactions across twelve human cell types reveals global features of EP interactions.
Second, we used a well-established viral infection model to map the dynamic changes of enhancers and super-enhancers during the CD8+ T cell responses. Our analysis illustrated the complexity and dynamics of the underlying EP interactome during cell differentiation. Taking advantage of the predicted EP interactions, we constructed stage-specific transcriptional regulatory networks, which is critical for understanding the regulatory mechanism during CD8+ T cell differentiation.
Third, recent progress in mapping technologies for chromatin interactions has led to a rapid increase in this type of interaction data. However, there is a lack of a comprehensive depository for chromatin interactions identified by all major technologies. To address this problem, we have developed the 4DGenome database through comprehensive literature curation of experimentally derived interactions. We envision a wide range of investigations will benefit from this carefully curated database.
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Collins, Malcolm Robert. "Characterisation of the human α2(I) procollagen promoter-binding proteins." Doctoral thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/27139.
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In an attempt to elucidate the transcriptional mechanisms that regulate the expression of the human α2(I) procollagen gene, cis-acting DNA-elements within the proximal promoter were identified and their corresponding trans-acting factors characterised. The fibroblast cell lines used in this study had previously been transformed with either simian virus 40 (SVWI-38) or by γ-radiation (CT-1). The SVWI-38 fibroblasts do not produce any α2(I) collagen chains, whereas the CT-1 cell line produces normal type I collagen. Previous studies suggested that trans-acting factor(s) may be responsible for the inactivation of the α2(I) procollagen gene in SVWI-38 fibroblasts (Parker et. al. (1989) J. Biol. Chem 264, 7147-7152; Parker et. al. (1992) Nucleic Acids Res. 20, 5825-5830). In this study, the SVWI-38 proximal promoter (-350 to +54) was sequenced and shown to be normal, thereby ruling out any possibility that mutations within this region was responsible for inactivation of the gene.
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Danevad, Margrete. "Functional analysis of the murine LI-Cadherin promoter." [S.l.] : [s.n.], 2004. http://www.diss.fu-berlin.de/2004/165/index.html.
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Chaidir, Nadia. "Whole-genome comparative promoter sequence analysis in plants." Thesis, McGill University, 2014. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=123303.
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Large-scale genome-wide comparative analyses are now made possible by the increasing number of publicly available high-quality genome sequence data for numerous plant species. To understand the mechanisms of transcriptional regulation, computational analysis tools were used to find overrepresented and conserved DNA sequences, i.e. cis-regulatory elements. Datasets used as positive input for computational identification of regulatory regions commonly include promoters of co-regulated genes or promoters of orthologous genes (Wang and Stormo, 2003).We discovered de novo motif using two approaches, seperately; 1) discovery based on orthology relationship of the genes in 18 plant species and 2) discovery based on co-regulated genes in specific tissues from soybean gene expression RNA-Seq data. In the first approach, a combination of several bioinformatics tools were used to predict motifs in promoter region based on clusters of orthologous genes in whole-genome datasets of Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Carica papaya, Chlamydomonas reinhardtii, Glycine max, Linus usitatissimum, Malus domestica, Manihot esculenta, Medicago truncatula, Oryza sativa, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorfii, Sorghum bicolor, Vitis vinivera, Volvox carteri and Zea mays. The results have shown that many promoters of orthologous plant genes contain similar cis-regulatory motifs. In addition, inclusion of more evolutionary distant organism led to detection of very conserved motifs, i.e. motifs that have similar function in wider variety of organisms. In the second approach, bioinformatics tools were used to find motifs in promoter region of co-regulated genes in shoot apical meristem and shoot epidermis of three soybean cultivars. The results have shows that promoters of co-regulated genes in specific tissues contain similar cis-regulatory motifs.Since generating genome-scale datasets requires extensive computational resources that are not always readily available, we created a relational database that houses pre-computed and post-processed whole-genome comparative analysis of promoter regions. The database contains motif sequences, annotations, clusters of orthologous genes and other useful information associated with them, for 18 plant genomes.L'étude d'association pangénomique est maintenant rendue possible par le nombre de séquences génétiques de hautes qualités qui sont disponibles pour plusieurs espèces végétales. Pour comprendre les mécanismes de régulation de la transcription, un nombre d'outils d'analyses informatiques ont été développé pour identifier les éléments cis-régulatoires. Les bases de données utilisées comme saisie positive pour l'identification informatique des régions de régulation incluent communément les promoteurs des gènes co-régulés ainsi que des gènes orthologues (Wang et Stormo, 2003).Pour découvrir les motifs de novo, nous avons utilisé deux techniques; 1) une découverte basée sur la relation orthologue des gènes de 18 espèces végétales et, 2) une découverte basée sur les gènes co-régulés dans certains tissus végétales spécifiques provenant de données de séquençage d'ARN de soja. Dans la première approche nous avons utilisé une combinaison de plusieurs outils bioinformatiques pour prédire les motifs des promoteurs basés sur des groupes de gènes orthologues trouvés dans les bases de données des génomes entiers d'Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Carica papaya, Chlamydomonas reinhardtii, Glycine max, Linus usitissimum, Malus domestica, Manihot esculenta, Medicago truncutula, Oryza sativa, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorfii, Sorghum bicolor, Vitis vinivera, Volvox carteri et Zea mays. Les résultats ont démontré que, dans les plantes, plusieurs promoteurs de gènes orthologues contiennent des motifs cis-régulatoires similaires. En plus, en incluant des espèces évolutivement éloignées dans les analyses, nous avons été capable de démontrer que ces motifs sont conservés. Dans la deuxième partie, nous avons fait une analyse comparant les séquences des promoteurs co-régulés dans les méristèmes apicaux ainsi que dans l'épiderme de trois cultivars de soja; Clark sauvage, mutant a 5-feuilles et mutant glabre. Les résultats ont démontré que les promoteurs des gènes co-régulés en différents tissus contiennent des motifs cis-régulatoires similaires. Générer des données à l'échelle génomique demande une puissance informatique énorme qui n'est pas toujours disponible. En conséquence, nous avons créé une base de données pour 18 génomes de plantes composée de séquences de promoteurs, de motifs, d'annotations et des groupes de gènes orthologues ainsi que d'autres informations associées avec ceux-ci.
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Burbridge, Stephen Anthony. "Analysis of the Xenopus N-cadherin promoter region." Thesis, University of Warwick, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362548.
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Marden, Chloe Maria. "Functional analysis of the P47 PHOX gene promoter." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.392359.
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Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3656.
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This thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
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Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." University of Sydney, 2008. http://hdl.handle.net/2123/3656.
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Master of EngineeringThis thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
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Khan, H. "Mutational analysis of the Klebsiella pneumoniae nifLA promoter." Thesis, University of Sussex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372054.
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Childs, Kevin. "Combinatorial motif analysis in yeast gene promoters: the benefits of a biological consideration of motifs." Thesis, Texas A&M University, 2004. http://hdl.handle.net/1969.1/1351.
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There are three main categories of algorithms for identifying small transcription regulatory sequences in the promoters of genes, phylogenetic comparison, expectation maximization and combinatorial. For convenience, the combinatorial methods typically define motifs in terms of a canonical sequence and a set of sequences that have a small number of differences compared to the canonical sequence. Such motifs are referred to as (l, d)-motifs where l is the length of the motif and d indicates how many mismatches are allowed between an instance of the motif and the canonical motif sequence. There are limits to the complexity of the patterns of motifs that can be found by combinatorial methods. For some values of l and d, there will exist many sets of random words in a cluster of gene promoters that appear to form an (l, d)-motif. For these motifs, it will be impossible to distinguish biological motifs from randomly generated motifs. A better formalization of motifs is the (l, f, d)-motif that is derived from a biological consideration of motifs. The motivation for (l, f, d)-motifs comes from an examination of known transcription factor binding sites where typically a few positions in the motif are invariant. It is shown that there exist (l, f, d)-motifs that can be found in the promoters of gene clusters that would not be recognizable from random sequences if they were described as (l, d)-motifs. The inclusion of the f-value in the definition of motifs suggests that the sequence space that is occupied by a motif will consist of a several clusters of closely related sequences. An algorithm, CM, has been developed that identifies small sets of overabundant sequences in the promoters from a cluster of genes and then combines these simple sets of sequences to form complex (l, f, d)-motif models. A dataset from a yeast gene expression experiment is analyzed with CM. Known biological motifs and novel motifs are identified by CM. The performance of CM is compared to that of a popular expectation maximization algorithm, AlginACE, and to that from a simple combinatorial motif finding program.
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Lorson, Christian. "An analysis of transcriptional regulation of the MVM capsid gene promoter." free to MU campus, to others for purchase, 1997. http://wwwlib.umi.com/cr/mo/fullcit?p9841319.
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Soanes, Darren Mark. "Regulation of the pathogenicity gene MPG1 in the rice blast fungus Magnaporthe grisea." Thesis, University of Exeter, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368367.
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Kirk, Jane A. E. "Region specific expression of a Dictyostelium discoideum prestalk marker." Thesis, Open University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262113.
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Eristi, Can M. "Investigation of Transcriptional Regulation of 5'-Nucleotidase in Dictyostelium Discoideum." Diss., Virginia Tech, 2003. http://hdl.handle.net/10919/28822.
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A 5' AMP-degrading activity appears during the course of development in Dictyostelium discoideum between the prestalk and prespore zones. This enzyme is referred as 5'-Nucleotidase (5NT). Given the critical role of cyclic AMP in cell differentiation in this organism, 5NT is thought to be involved in cell positioning during development. Southern blot analysis showed a single form of the gene. The expression of the 5nt gene is known to be developmentally regulated. The message appears first at about 5 hr of the Dictyostelium development and remains constant throughout the rest of the development. Primer extension indicated two potential transcriptional start sites (118 bp and 148 bp upstream of the ATG initiation codon) for the 5nt expression. The 5nt promoter region was cloned and analyzed to investigate the expression of 5nt. Analysis of the cloned 5nt promoter fused to lacZ enabled the localization of the 5nt expression in pstAB cells during development. To identify cis-acting regulatory sequences, a series of 5' and internal promoter deletions were generated and fused to a luciferase reporter gene. The reporter activity driven by the 1,212 bp promoter started at the early aggregation stage, in agreement with temporal expression of the 5nt gene. Also, the expression was induced by exogenous cAMP. The reporter activity was high and relatively equivalent for all deletion constructs that contained 547 bp or more of the promoter region. No luciferase activity was detected using 365 bp or less of the promoter. A gradual decrease in activity was observed when three deletion constructs between -547 and -365 bp were tested suggesting the presence of at least two cis-regulatory elements within this region. Internal deletion analysis indicated another potential regulatory region located between -307 and -226 bp. To identify protein factor(s) that bind specifically to these regulatory sequences, gel shift assays were performed. Two bands, 0.33 Rf and 0.13 Rf, were detected in both cytoplasmic and nuclear extracts using radiolabeled DNA fragments located between -227 and -198 bp and -252 and -203 bp of the promoter region, respectively. Competition experiments confirmed the specificity of binding. The protein factors in these DNA binding activities were purified using various chromatography techniques. Mass spectrometry analysis of the purified 70 kDa protein corresponding to the 0.33 Rf band activity and a subsequent search in the Dictyostelium genomic database revealed that the purified protein was a putative formyltetrahydrofolate synthase.Ph. D.
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Brown, Anthony Peter Colin. "A biomolecular analysis of the control of expression and function of a low temperature responsive barley gene." Thesis, University of Newcastle Upon Tyne, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245079.
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Malik, Yousaf Amir. "Functional analysis of the human immunodeficiency virus type-1 long terminal repeat." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343172.
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edu, Kim Rice@mssm, and Kim Lee Rice. "Functional Analysis of the HOX11 Target Genes ALDH1A1 and FHL1." Murdoch University, 2004. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20051012.93820.
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HOX11 is a developmental regulator that plays a crucial role in the normal development
of the spleen and is also aberrantly activated by the t(10;14)(q24;q11) and variant
t(7;10)(q35;q24) translocations in a subset of T-cell acute lymphoblastic leukaemias (TALLs).
The recent finding that HOX11 is deregulated in up to 40% of childhood TALLs
when abnormalities not detected by cytogenetics are included, suggests that the
over-expression of HOX11 and subsequent deregulation of downstream target genes are
critical events in the progression of this tumour type. To date, three candidate HOX11
target genes have been reported, two of which are Aldehyde Dehydrogenase 1a1
(ALDH1A1) and Four and a Half LIM domain Protein 1 (FHL1). This investigation
focused on two aspects of HOX11 function, namely its roles as a transcriptional
regulator and as a nuclear oncoprotein capable of inducing neoplastic transformation.
More specifically, we sought to further understand the role of HOX11 in tumorigenesis
by 1) Confirming target gene status of ALDH1A1 and FHL1 by assessing whether their
proximal promoter regions are transcriptionally regulated by HOX11, 2) Investigating
the regulatory elements/transcriptional complexes involved in the response of
ALDH1A1 to HOX11 in both a T-cell and an erythroid cell line in order to gain an
insight into the mechanism(s) responsible for mediating a HOX11 activity and 3)
Assessing the ability of ALDH1A1 and FHL1 to perturb normal patterns of
haematopoiesis, on the basis that the transforming capabilities of HOX11 are thought to
derive from its ability to affect haematopoietic cell differentiation.
To confirm ALDH1A1 and FHL1 as target genes, they were both characterised in terms
of the ability of their proximal promoters to be transcriptionally regulated by HOX11
using luciferase reporter assays. Significant repression of the proximal promoters of
ALDH1A1 and FHL1 by HOX11 was observed in PER-117 T-cells which provided
further evidence for their status as target genes. In the case of ALDH1A1, a CCAAT box
(-74/-70bp) was identified as the primary cis-regulatory element involved in ALDH1A1
transcription and repression by HOX11 appeared to occur, either directly or indirectly,
via interactions at the CCAAT box. Electromobility shift assays (EMSAs) revealed the
disruption of a specific complex at this site by HOX11, which also altered the formation
of complexes at a non-canonical TATA box (a GATA box at -34/-29bp). Significantly,
HOX11 was shown to have the potential to interact with TFIIB, a member of the basal
transcriptional complex. This, together with the presence of a TFIIB responsive element
immediately 5 of the GATA box, suggested that HOX11 may repress transcription by
interfering with members of a preinitiation complex on the ALDH1A1 promoter. The
transcriptional repression by HOX11 demonstrated in T-cells was dependent on DNA
binding helix 3 of the homeodomain, suggesting that repression may require DNA
binding. Alternatively, this region may be required for stable protein-protein
interactions. In support of this, the in vitro association of HOX11 with TFIIB was
disrupted upon deletion of helix 3, and the HOX11∆H3 mutant switched from a
transcriptional repressor to a potent activator of transcription. Together, this data
supports a model whereby HOX11 represses transcription by interfering with activation
complexes at the CCAAT box and at the GATA box possibly via protein-protein
interactions involving the homeodomain helix 3, whereas deletion of the region disables
repressor-specific interactions, resulting in potent activation by HOX11.
Luciferase reporter gene assays investigating the response of nested deletions of the
ALDH1A1 promoter to HOX11 in the HEL900 erythroleukaemic cell line, also
identified the CCAAT box (-74/-70bp) as the primary cis-regulatory element involved
in ALDH1A1 transcription. However, in stark contrast to the its effect in T-cells,
HOX11 was shown to activate transcription in the HEL cell line, both from the empty
pGL3Basic luciferase reporter vector and from the ALDH1A1 promoter, in a manner
independent of the homeodomain DNA binding helix 3. HOX11 thus appears to be a
dichotomous regulator, capable of both transcriptional activation and repression
depending on the circumstances. The mechanisms underlying these two functions are
also appear to be distinct, with repression but not activation requiring the presence of
homeodomain helix 3.
ALDH1A1 encodes an enzyme involved in the irreversible conversion of retinaldehyde
to the biologically active metabolite, retinoic acid (RA) and appears to be
physiologically regulated by Hox11 in the developing spleen. Since RA is a potent
modulator of cellular differentiation, proliferation and apoptosis, the dysregulation of
RA synthesis is likely to have severe consequences for the cell and may constitute a
mechanism whereby overexpression of HOX11 predisposes T-cells to malignant transformation.
FHL1 also appears to have potential relevance to tumorigenesis, given
that it encodes protein isoforms with suspected roles in transcriptional regulation. As a
starting point to investigate a possible link between these HOX11 target genes and
leukaemogenesis, the effect of overexpressing ALDH1A1 and FHL1 on murine
haematopoiesis was assessed following reconstitution of lethally irradiated mice with
retrovirally-transduced primary murine bone marrow cells. The enforced expression of
ALDH1A1 in bone marrow was associated with a marked increase in myelopoiesis and a
decrease in B and T-lymphopoiesis. By contrast, overexpression of FHL1 was not
associated with perturbations in myelopoiesis or lymphopoiesis, although a slight
increase in erythropoiesis was observed in the bone marrow. While further work is
required to clarify the possible oncogenic roles of both of these HOX11 target genes,
these findings have served to identify ALDH1A1 in particular, as a gene which could
potentially be involved in HOX11-mediated tumorigenesis.
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Sawaya, Rana. "Promoter analysis of the porA gene of Neisseria meningitidis." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0025/MQ50871.pdf.
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Rogers, David Howard. "Analysis of the rat Tal a-tubulin gene promoter." Thesis, McGill University, 2000. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=36831.
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The mature nervous system is composed largely of two cell types, glial cells and postmitotic neurons. All postmitotic neurons of the mature nervous system derive from proliferating neural precursor cells. To generate a neuron, a precursor must cease dividing and express a number of genes that are characteristic of the neuronal phenotype. How these changes in cell behaviour and phenotype are brought about in mammals is still poorly understood.This thesis describes experiments that were designed to explore cell intrinsic mechanisms regulating the generation of neurons from neural precursor cells. Specifically, the regulatory region of the rat Talpha1 alpha-tubulin gene, which encodes an isoform of alpha-tubulin expressed in neurons throughout the nervous system immediately following cell cycle exit, was analyzed to identify DNA sequences directing early neuronal gene expression.
A novel 10-nucleotide regulatory sequence, named the neuronal restriction element (NRE), has been identified. In the context of the Talpha1 gene, the NRE inhibits precocious expression in neural precursor cells. Interestingly, the NRE is conserved in the alpha-1 alpha-tubulin gene and is found in a number of neural genes expressed widely and early in development. As such, the NRE may affect the onset time of a battery of neuronal genes and modulate the timing of neuronal differentiation. In vitro , the NRE binds Su(H), a highly conserved transcription factor involved in the repression of neuronal differentiation.
A second novel regulatory element has been identified, the forebrain response element (FRE), which acts to enhance gene expression specifically in the neocortex. The FRE overlaps the NRE and also contains a conserved 30-nucleotide sequence constituting a putative homeodomain recognition sequence. We speculate that the FRE consists of two subelements that act synergistically to promote gene expression in newborn and mature neocortical neurons.
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Kim, S. "Structural analysis of the TRPI promoter in Saccharomyces cerevisiae." Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.306685.
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Ahmed, Nadeem M. "Transgenic analysis of the endodermin promoter in Xenopus laevis." Thesis, University of Warwick, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269083.
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Hellen, Elizabeth H. B. "Identification of co-regulated candidate genes by promoter analysis." Thesis, University of Brighton, 2010. https://research.brighton.ac.uk/en/studentTheses/68e2d36a-1d90-4e21-b407-2e67df1e351c.
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Genes which are co-expressed in tissues or processes are often regulated by the same transcription factors. In this thesis, the analysis of transcription factors predicted to regulate a gene is conducted to attempt to discover co-regulated, possibly co-expressed, genes. The initial problem tackled in the thesis is to determine an accurate method of predicting transcription factor binding sites (TFBS), and therefore regulatory transcription factors. Three TFBS prediction methods are developed; one consensus method combining pairs of prediction algorithms, one consensus method combining 6 algorithms through a Naïve Bayes classifier and a phylogenetic footprinting method combining data from multiple organisms using a Naïve Bayes classifier.
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Gosemärker, Anna Teresa. "Charakterisierung der humanen und murinen I-kappa-B-Kinase-beta--Promotoren zur Analyse der gewebsspezifischen Variationen in der Zusammensetzng des I-kappa-B-Kinase-Komplexes." [S.l. : s.n.], 2008. http://nbn-resolving.de/urn:nbn:de:bsz:289-vts-64393.
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Guillocheau, Gabriel. "Etude des polymorphismes altérant la régulation de l'expression des gènes chez le bovin." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLA045.
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Un nombre croissant de gènes et régions génomiques sont associés à des pathologies ou des phénotypes d’intérêt, soit par analyse de liaison ou analyse d’association. Il est crucial d’arriver à identifier les variants génétiques causaux. Les régulateurs ayant l’effet le plus important sont le plus souvent des polymorphismes régulateurs exerçant un effet en cis, près des gènes pour lesquels le niveau d’expression est altéré. L’objectif global de la thèse est d’identifier à grande échelle les polymorphismes chez la vache qui potentiellement altèrent la régulation de l’expression des gènes et affectent des phénotypes d’intérêt.Nous avons développé une approche pour déterminer les SNPs (Single Nucleotide Polymorphisms) causant ou étant impliqué dans une régulation de l’expression des gènes. Dans cet objectif, nous avons analysé chez 19 taurillons Limousin le génome et le transcriptome musculaire et chez 6 vaches Holstein le génome et le transcriptome de 8 tissues dont utérus et ovaire. Chez les mâles Limousin, nous avons identifié 5 658 SNPs montrant une expression allèle spécifique (ASE-SNPs) dans 13% des gènes exprimés dans le muscle et avons lié certains d’entre eux à des SNPs dans une région régulatrice. On a aussi identifié des gènes d’intérêt liés à la qualité de la viande (AOX1, PALLD et CAST) qui présente un déséquilibre allélique. Chez les femelles Holstein, nous avons identifié 33 527 ASE-SNPs dans les 8 tissus dont 3 369 ASE-SNPs pour les données de muscle, 5 771 pour les données d’ovaire et 5 499 pour les données d’utérus. L’analyse de ces deux jeux de données bovins a permis une nouvelle cartographie des gènes soumis à ASE. Il s’agit de la première analyse de cette ampleur pour la race Limousine.Les résultats de ces études permettent d’approfondir la compréhension de la régulation de l’expression des gènes chez le bovin, notamment en identifiant des polymorphismes causaux candidats et en apportant des nouvelles méthodes pour les détecterAn increasing number of genes and genomic loci have been associated with diseases or phenotypes of interest, by either linkage or association studies. Identifying causative genetic variants is crucial. The regulators with the strongest effect tend to be cis-acting regulatory polymorphisms, close to genes for which altered mRNA expression was detected. The overall objective of this PhD project is to develop a large-scale approach to identify regulatory polymorphisms that potentially alter the regulation of gene expression and impact phenotypes of interest, in cattle.We have developed an approach to ascertain causative SNPs (Single Nucleotide Polymorphisms) of gene expression regulation. To this end, we analysed genome and muscle transcriptome from 19 Limousine bull calves and genome and transcriptome of eight tissues (including ovary and uterus) transcriptome from 6 Holstein cows. For the Limousine breed, we identified 5,658 SNPs showing an allele-specific expression (ASE-SNPs) in 13% of genes with detectable expression in muscle; we linked some of them to SNPs in a regulatory region. Interestingly, we found genes involved in meat quality traits (AOX1, PALLD and CAST) with an allelic imbalance. For the Holstein breed, we identified 33, 527 ASE-SNPs across 8 tissues including 3,369 ASE-SNPs from muscle data, 5,771 from ovary data and 5,499 from uterus data. By analysing these two data records, we discovered genes impacted by ASE. This study is the first done for the Limousine breed and the second for thr Holstein breed.The results of these studies provide a best understanding of gene expression regulation in cattle, in particular by identifying candidate causal polymorphisms and by proposing new methods to detect them
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Kühn, Kristina. "Analysis of components of the mitochondrial transcription machinery in Arabidopsis thaliana." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2006. http://dx.doi.org/10.18452/15453.
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In der vorliegenden Arbeit wurde die Transkription mitochondrialer Gene durch die kernkodierten Phagentyp-RNA-Polymerasen RpoTm und RpoTmp der Pflanze Arabidopsis untersucht. Im Mitochondriengenom von Arabidopsis wurden f r 12 Gene Promotoren bestimmt. Diese zeigten verschiedene Sequenzelemente und wichen meist von der f r Dikotyle publizierten Konsensussequenz ab. F r die Mehrheit der Gene wurden multiple Promotoren identifiziert. Es wurden weiterhin Promotoren nachgewiesen, welche die Transkription vermutlich nicht funktioneller Sequenzen aktivieren. Architektur, Lokalisation und Nutzung mitochondrialer Promotoren implizieren eine wenig stringente Kontrolle der Transkriptionsinitiation in Arabidopsis-Mitochondrien. Zur Analyse der Funktionen von RpoTm und RpoTmp wurde ein in vitro-Transkriptionssystem entwickelt. Da RpoT-Enzyme m”glicherweise Kofaktoren ben”tigen, wurde in Arabidopsis nach Genen potentieller mitochondrialer Transkriptionsfaktoren gesucht. Als mitochondriales Protein mit Žhnlichkeit zu mtTFB, einem essentiellen Transkriptionsfaktor in Hefemitochondrien, wurde MetA identifiziert. In in vitro-Assays initiierte RpoTm an verschiedenen Promotoren die Transkription, w„hrend RpoTmp keine signifikante Promotorspezifit„t zeigte. Die spezifische Promotornutzung durch RpoTm erforderte superhelikale DNA. Weder RpoTm noch RpoTmp wurde durch MetA stimuliert. Eine mtTFB-„hnliche Funktion von MetA ist daher unwahrscheinlich. F r MetA wurde ausserdem eine engere phylogenetische Beziehung zu nukle„ren rRNA-Dimethylasen als zu mtTFB ermittelt. Die hier vorgestellten Studien belegen die Transkription mitochondrialer Gene in Arabidopsis durch RpoTm; f r RpoTmp ist eine nicht-redundante Transkriptionsfunktion denkbar. Die Kofaktor-unabh„ngige Spezifit„t von RpoTm f r verschiedene Promotoren und die wenig stringente Initiationskontrolle in vivo legen nahe, dass eine individuelle Regulation mitochondrialer Gene in Arabidopsis auf Transkriptionsebene nicht erfolgt.Mitochondria depend on a nucleus-encoded transcription machinery to express their genome. The present study examined the transcription of mitochondrial genes by two nucleus-encoded phage-type RNA polymerases, RpoTm and RpoTmp, in the plant Arabidopsis. For selected mitochondrial genes in Arabidopsis, transcription initiation sites were determined. Most genes were found to possess multiple promoters. The identified promoters displayed diverse sequence elements and mostly deviated from a nonanucleotide consensus derived previously for dicot mitochondrial promoters. Several promoters were detected that activate transcription of presumably non-functional sequences. Promoter architecture, distribution and utilization suggest a non-stringent control of transcription initiation in Arabidopsis mitochondria. An in vitro transcription system was set up to elucidate the roles of RpoTm and RpoTmp. Since RpoT enzymes possibly require auxiliary factors, the Arabidopsis genome was screened for potential cofactors of phage-type RNA polymerases. A mitochondrial protein (MetA) with similarity to mtTFB, an essential transcription factor in yeast mitochondria, was identified. In in vitro transcription studies, RpoTm recognized various promoters whereas RpoTmp displayed no significant promoter specificity. Promoter recognition by RpoTm depended on supercoiled DNA templates. Transcription initiation by RpoTm or RpoTmp was not affected by MetA, indicating that MetA is not functionally equivalent to mtTFB. Besides, MetA was found to be more closely related to non-mitochondrial rRNA dimethylases than to mtTFB. The present study establishes RpoTm to transcribe mitochondrial genes; RpoTmp may have a non-overlapping transcriptional role in mitochondria. The cofactor-independent promoter specificity of RpoTm and the apparently non-stringent control of transcription initiation in vivo imply that mitochondrial genes in Arabidopsis may not be regulated individually at the transcriptional level.
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Wiles, Natasha Shawn. "Identification of Regulatory Binding Sites and Corresponding Transcription Factors Involved in the Developmental Control of 5'-nucleotidase Expression in Dictyostelium discoideum." Diss., Virginia Tech, 2005. http://hdl.handle.net/10919/27810.
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Gene regulation is a critical aspect of normal development, energy conservation, metabolic control, and responses to environmental cues, diseases and pathogens in eukaryotic organisms. In order to appropriately respond to environmental changes and advance through the life cycle, an organism must manage the expression levels of a large number of genes by utilizing available gene regulation mechanisms. The developmental control of 5â -nucleotidase (5nt) expression in the model system Dictyostelium discoideum has provided a focal point for studies of gene regulation at the level of transcription.
In order to identify temporally-regulated control elements within the promoter of the 5nt gene, 5â and internal promoter deletions were designed and fused to the luciferase and lacZ reporter genes, and reporter enzyme activity was measured in cells from the slug stage of development. The results from these experiments enabled the identification of a 250 bp region of the promoter, which was used as a template for subsequent site-directed mutagenesis experiments. These experiments involved altering 6-12 bp regions of the promoter by substitution. Twelve mutagenized promoters were fused to the luciferase and lacZ reporter genes, and activity was measured at the slug stage of development to more precisely locate cis-acting temporally-regulated control elements. In addition, cAMP induction experiments were performed on amoebae transformed with the mutagenized promoters to identify control elements within the promoter influenced by the presence of cAMP. The regions between -530 and -560 bp and -440 and -460 bp from the ATG translation start site.
In order to evaluate the functions of the cis-acting promoter control elements, electromobility gel shift assays were performed to identify specific DNA-protein interactions on the 5nt promoter. These assays enabled the detection of a 0.13 Rf and 0.33 Rf binding activity to specific sites of the promoter. After characterization of these binding activities, both proteins were purified by a series of column chromatography techniques and characterized after mass spectrometry. The proteins purified were identified as formyltetrahydrofolate synthase and hydroxymethylpterin pyrophosphokinase. These enzymes function in the biosynthetic pathway of tetrahydrofolate and the production of folate coenzymes. The specific interactions of these enzymes with the 5nt promoter suggest these proteins may also function in regulating 5nt expression.Ph. D.
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Joyce, Bradley Ryan. "The Regulation of Alkaline Phosphatase during the Development of Dictyostelium." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/27646.
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Regulation of gene expression is known to be a critical factor involved in proper development, responses to environmental cues, metabolism, energy conservation, and disease. Gene expression is regulated at several levels including transcription, mRNA splicing, post translational modification, and the rate of protein degradation. The developmental control of alkaline phosphatase (alp) in Dicytostelium has provided a focal point for the study of gene regulation at the level of de novo synthesis.
The localization of alkaline phosphatase (alp) expression during development was characterized by fusing the 5' flanking sequence to the lacZ reporter and using an in situ β-galactosidase staining method. The localization of lacZ expression corresponds with that of the endogenous ALP enzyme suggesting that alp is regulated at the level of transcription. In order to identify temporal regulatory elements within the alp promoter a series of 5' and internal promoter deletions were generated and fused to the lacZ reporter. The data from these promoter deletion constructs indicated a regulatory element within the -683 to -468 bp sequence that is required for normal expression of alp during development. A series of small internal and 5' promoter deletions were designed within the -683 to -468 bp regulatory sequence. The results from these promoter deletion-reporter gene fusions suggested a DNA regulatory element is located within a 26-bp sequence beginning at the -620 bp site.
The function of cis-acting regulatory elements were evaluated using the electromobility shift assay (EMSA) to identify sequence specific DNA-protein interactions on the alp promoter. We report the characterization of three DNA-binding activities with the 20% ammonium sulfate (AS) slug nuclear fraction. These DNA-binding activities appear to be related as they all require magnesium or calcium for effective binding to the alp promoter. Interestingly, the DNA-binding proteins appeared to interact with a GT-rich sequence that contained a G-box binding factor (GBF) consensus element.
Additionally, a DNA-binding activity observed in the 80% AS slug nuclear extract was characterized and sequentially purified using conventional and affinity chromatography techniques. The DNA-binding protein was identified as TFII, a protein that was previously identified during the investigation of glycogen phosphorylase-2 (gp2) regulation. A comparison of the alp and gp2 probes used to identify TFII suggests a DNA-binding site, ACAATGN₈₋₁₂CACTA. The ability of TFII to bind specifically with the promoter of two functionally different genes suggests that it may regulate the temporal and/or spatial expression of several Dictyostelium genes.Ph. D.
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Vickers, Claudia Estelle. "Functional analysis of the endosperm - specific AsGlo1 promoter in barley /." St. Lucia, Qld, 2003. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17515.pdf.
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Wang, Fang. "DNA methylation and promoter sequence analysis of colon cancer genes." Connect to this title online, 2008. http://etd.lib.clemson.edu/documents/1211398606/.
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Thesis (M.S.) -- Clemson University, 2008.Title from first page of PDF file. Document formatted into pages; contains ix, 68 p. ; also includes graphics (some col.). Contains additional supplemental files.
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Klan, Niko [Verfasser]. "Functional analysis of the human 5-LO promoter / Niko Klan." Aachen : Shaker, 2003. http://d-nb.info/1179024540/34.
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McDonald, Bernadette Catherine. "Characterisation and analysis of the prostate-specific membrane antigen promoter." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369325.
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Gardella, Thomas James. "A Genetic Analysis of RNA Polymerase-Promoter Interactions: A Thesis." eScholarship@UMMS, 1988. http://escholarship.umassmed.edu/gsbs_diss/200.
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Transcription initiation is a key step at which gene expression can be regulated. The sigma subunit of RNA polymerase provides the enzyme with the ability to recognize promoter sequences and initiate transcription at specific sites on the chromosome. The molecular basis of sigma function is not well known. It has been suggested that sigma factors confer promoter specificty by making direct contacts to the promoter DNA (Losick and Pero, 1981). To test this idea, suppressors of promoter down mutations were sought that affected the promoter recogniton properties of the σ70 subunit of E. coli RNA polymerase. Four such sigma mutants were obtained, two of which are allele-specific. One of these mutants has a change at a position in the predicted helix-turn-helix DNA binding structure which lies in a conserved region of the protein (region 4). This mutant specifically suppresses promoter down mutations in the -35 region of the promoter. The other mutant has a change at a residue that lies in a predicted α-helix of conserved region 2. This mutant specifically suppresses promoter mutations in the -10 region of the promoter. These data support the idea that regions 2 and 4 of sigma interact with the -10 and -35 regions of the promoter, respectively.
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Jain, Nishant Rajkumar. "Characterization and functional analysis of the P2Y₂R gene promoter." Diss., Columbia, Mo. : University of Missouri-Columbia, 2006. http://hdl.handle.net/10355/4629.
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Thesis (M.S.)--University of Missouri-Columbia, 2006.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on April 21, 2009) Includes bibliographical references.
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Karanam, Suresh Kumar. "Automation of comparative genomic promoter analysis of DNA microarray datasets." Thesis, Available online, Georgia Institute of Technology, 2004:, 2003. http://etd.gatech.edu/theses/available/etd-04062004-164658/unrestricted/karanam%5Fsuresh%5Fk%5F200312%5Fms.pdf.
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Crespo, Marion. "Analyse multi-omique des acylations de lysines d'histones pendant la gamétogénèse." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV066.
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L’aspect novateur de ce projet réside dans l’étude des acylations au niveau de la lysine K27 de l’histone H3, classiquement étudiée sous forme méthylée ou acétylée. Nous avons réalisé ce travail sur des cellules germinales méiotiques et post-méiotiques de souris. La spermiogénèse, qui implique un programme d’expression spécifique ainsi qu’une régulation fine de la transcription, est un processus particulièrement adapté à la compréhension du rôle des nouvelles modifications d’histones. Ces travaux regroupent l’utilisation de quatre approches omiques différentes, à savoir la protéomique, la métabolomique, la transcriptomique et le séquençage ChIP-seq afin de décrypter la régulation des acylations sur H3K27.Dans la première partie de ce projet, nous avons exploré la dynamique d’acétylation et de crotonylation sur les lysines d’histones au cours des processus de sporulation de la levure et de spermatogénèse de la souris, ce qui nous a permis de mettre en évidence un site d’intérêt H3K27 crotonylé. Son accumulation sur le variant d’histone H3.3 et sa stoechiométrie importante par rapport à la forme acétylée H3K27ac dans les cellules germinales post-méiotiques de souris nous ont conduits à étudier la distribution génomique de cette marque, par des analyses de ChIP-seq. L’analyse comparative de H3K27ac et H3K27cr a révélé une synergie entre la présence de ces deux marques à la fois au niveau des promoteurs et des enhancers distants, ce qui suggére une possible alternance des deux marques afin de réguler la transcription. Au niveau des promoteurs, nous avons observé une augmentation de ces modifications entre les stades méiotiques et post-méiotiques en amont des gènes caractéristiques de la spermiogénèse. D’autre part, la présence simultanée des deux marques coïncide avec la co-localisation de plusieurs régulateurs de la transcription spécifiques de ce processus (SLY, SOX30) et de protéines de liaison à la chromatine (BRD4, BORIS et CTCF), tandis qu’une sélectivité de fixation est observée lorsque H3K27ac et H3K27cr sont identifiées seules aux promoteurs. De façon intéressante, nous observons des résultats similaires au niveau des enhancers ainsi que des super-enhancers, confirmant que la régulation de la transcription est modulée par la présence alternative de ces deux acylations.La deuxième partie de ma thèse a porté sur l’étude de la propionylation et de la butyrylation de H3K27 au cours de la sporulation de la levure et de la spermatogénèse de la souris. Cependant, cette partie s’est avérée pleine de surprises car les analyses MS/MS en cellules HCD et la comparaison avec les peptides synthétiques correspondants n’ont pas permis de valider une propionylation et une butyrylation sur H3K27. Il s’est avéré qu’il s’agissait de structures strictement isobares avec ces modifications connues, mais de nature différente, puisque plus hydrophile que ces acylations. Plusieurs hypothèses ont été testées afin de déterminer la composition de ces modifications, mais au moment de la finalisation de ce manuscrit, nous n’avons pas encore trouvé le fin mot de l’histoire.Mes travaux de thèse rappellent les obervations de Goudarzi et al., à savoir une dynamique entre acétylation et acylation sur les résidus lysines à l’origine de la fixation différentielle de facteurs de régulation ou de protéines se liant à la chromatine et responsables de la régulation de la transcription. Ils ont également mis en lumière un rôle importante de H3K27cr, au niveau des enhancers en combinaison avec H3K27ac, lesquels ne sont classiquement pas étudiés dans les études fonctionnelles portant sur la compréhension du rôle de nouvelles acylationsThe innovative aspect of this project lies in the study of acylations at lysine 27 from histone H3 (H3K27), conventionally studied in a methylated or an acetylated form. We performed this work on meiotic and post-meiotic mouse germ cells. Spermiogenesis, which involves a specific expression program as well as a fine regulation of transcription, is a process that is particularly well suited to understanding the roles of new histone modifications. This work combines the use of four different omics approaches, namely proteomics, metabolomics, transcriptomics and ChIP- sequencing to decipher the regulation of acylations on H3K27.In the first part of this project, we explored the dynamics of acetylation and crotonylation on histone lysines during the processes of yeast sporulation and mouse spermatogenesis, which allowed us to highlight in particular crotonylated H3K27. Its accumulation on the histone variant H3.3 and its important stoichiometry compared to the acetylated form H3K27ac in mouse post-meiotic germ cells led us to study the genomic distribution of this mark by ChIP-seq analysis. The comparative analysis of H3K27ac and H3K27cr revealed a synergy between the presence of these acylations at both promoters and distal enhancers, suggesting a possible alternation of the two marks to regulate transcription. At the promoter level, we observed an increase of these modifications between the meiotic and post-meiotic stages upstream of the genes characteristic of spermiogenesis. In addition, the simultaneous presence of the two marks coincides with the co-localization of several transcriptional regulators specific for this process (SLY, SOX30) and of chromatin-binding proteins (BRD4, BORIS and CTCF), whereas a binding selectivity is observed when H3K27ac and H3K27cr are identified alone at promoters. Interestingly, we observe similar results at enhancers as well as super-enhancers, confirming that the regulation of transcription is modulated by the alternative presence of these two acylations.The second part of my thesis focused on the study of the possible propionylation and butyrylation of H3K27 during yeast sporulation and mouse spermatogenesis. However, this part proved to be full of surprises because the MS/MS analyses and the comparison with the corresponding synthetic peptides did not make it possible to validate a propionylation and a butyrylation on H3K27. It turned out that the modifications observed on H3K27 from mouse histones were strictly isobaric with these known modifications, but of a different nature, since they are more hydrophilic. Several hypotheses were tested in order to determine the structure of these modifications, but at the time of finalizing this manuscript, we have not found out what it is all about.My PhD work contributes further to the idea of a dynamics between acetylation and acylations on lysine residues at the origin of the differential binding of chromatin-binding proteins responsible for regulating transcription. It also highlighted an important role of H3K27crat enhancers which are not classically considered in studies aiming at understanding the roles of new acylations
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Srinivasan, Venkataraghavan. "A Biclustering Approach to Combinatorial Transcription Control." Thesis, Virginia Tech, 2005. http://hdl.handle.net/10919/43915.
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Combinatorial control of transcription is a well established phenomenon in the cell. Multiple transcription factors often bind to the same transcriptional control region of a gene and interact with each other to control the expression of the gene. It is thus necessary to consider the joint conservation of sequence pairs in order to identify combinations of binding sites to which the transcription factors bind. Conventional motif finding algorithms fail to address this issue. We propose a novel biclustering algorithm based on random sampling to identify candidate binding site combinations. We establish bounds on the various parameters to the algorithm and study the conditions under which the algorithm is guaranteed to identify candidate binding sites. We analyzed a yeast cell cycle gene expression data set using our algorithm and recovered certain novel combinations of binding sites, besides those already reported in the literature.Master of Science
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Barrera, Leah Ortiz-Luis. "Genome-wide mapping and analysis of mammalian promoters." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3258393.
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Thesis (Ph. D.)--University of California, San Diego, 2007.Title from first page of PDF file (viewed June 1, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 151-169).
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Boulay, Thomas M. "Analysis of the downstream promoter element in Drosophila melanogaster and humans /." Diss., Connect to a 24 p. preview or request complete full text in PDF formate. Access restricted to UC campuses, 2005. http://wwwlib.umi.com/cr/ucsd/fullcit?p3191995.
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Staudt, Michelle Ruth. "Analysis of the principle latent promoter of Kaposi's sarcoma-associated herpesvirus." Oklahoma City : [s.n.], 2006.
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Macleod, Donald T. "A molecular analysis of a promoter trap in embryonic stem systems." Thesis, University of Edinburgh, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.280628.
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Fasani, Elisa. "Identification of regulatory elements responsible for metal hyperaccumulation in the Brassicaceae family. Functional analysis of the Arabidopsis thaliana MYB48 and MYB59 transcription factors." Doctoral thesis, 2014. http://hdl.handle.net/11562/671558.
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Capitolo 1: Identificazione di elementi regolatori responsabili per l’iperaccumulo di metalli nella famiglia delle Brassicaceae.
Il ruolo del trasportatore MTP1 nella tolleranza ai metalli pesanti è stato studiato approfonditamente, in quanto esso ha un ruolo molto importante nell’iperaccumulo. MTP1 è presente in più copie nella specie iperaccumulatrice Arabidopsis halleri; inoltre sono state osservate possibili differenze nella regolazione della trascrizione tra iperaccumulatori e non accumulatori. Questo lavoro è incentrato sull’analisi del promotore di MTP1. Il pattern e il livello di espressione indotti dai promotori di Arabidopsis thaliana e A. halleri sono molto diversi, in accordo con la differente capacità di accumulo dimostrata dalle due specie. Entrambe le specie esprimono MTP1 nelle radici: questo è associato alla presenza in entrambi i promotori di elementi regolatori per l’espressione specifica nelle radici. Inoltre, i promotori di A. thaliana e A. halleri inducono entrambi espressione a livello delle cellule di guardia, dovuta alla presenza di motivi di legame a fattori di trascrizione di tipo Dof. Il promotore di MTP1 di A. halleri è responsabile invece dell’espressione specifica nei ticomi. Questa localizzazione è probabilmente associata alla presenza di una coppia di siti di legame di MYB nella 5’UTR del gene. L’accumulo di metalli nei tricomi è una caratteristica interessante di A. halleri ed è probabilmente coinvolta nella tolleranza a breve termine.
Capitolo 2: Analisi di funzione dei fattori di trascrizione MYB48 e MYB59 di Arabidopsis thaliana.
I fattori di trascrizione di tipo MYB sono coinvolti in molti eventi della vita delle piante, come la differenziazione e il metabolismo cellulare, lo sviluppo della pianta, la risposta agli ormoni e agli stimoli ambientali. Si è ipotizzato che MYB48 e MYB59 di Arabidopsis thaliana partecipino allo sviluppo della struttura secondaria, al controllo del ciclo cellulare e alla risposta agli stress abiotici. In questo lavoro si è scelto di usare un doppio mutante myb48myb59, poiché i due fattori di trascrizione sono probabilmente ridondanti. Le piante myb48myb59 hanno foglie più piccole, forse a causa della ridotta distensione cellulare, e radici più lunghe; mostrano inoltre un ritardo nella fioritura e senescenza anticipata, come confermato dall’espressione del marcatore di senescenza SAG12. Il fenotipo può essere attribuito ad un ridotto contenuto di citochinine; quest’ipotesi è confermata dalla maggiore sensibilità dei doppi mutanti alla somministrazione esogena di citochinine e dai geni modulati identificati tramite analisi trascrittomica.Chapter 1: Identification of regulatory elements responsible for metal hyperaccumulation in the Brassicaceae family. The role of the metal transporter MTP1 in metal tolerance and accumulation has been extensively studied, due also to its great importance in the hypertolerance trait. MTP1 is known to have undergone copy number expansion in hyperaccumulator Arabidopsis halleri; moreover, possible differences in cis-regulation between hyperaccumulators and non-accumulators have been proposed. This work focuses on the analysis of the MTP1 promoter. The expression pattern and levels driven by the Arabidopsis thaliana and A. halleri promoter sequences are markedly different, coherently with the different accumulation ability and metal storage tissues displayed by the two species. MTP1 expression in roots was found in both species and is associated with the presence of root-specific cis elements in both promoters. Similarly, guard cell-specific expression was observed for both A. thaliana and A. halleri sequences and is associated with the presence of Dof-binding sites. In addition, the MTP1 promoter of A. halleri drives expression in trichomes. This interesting localization is likely associated to a couple of MYB-binding sites in the 5’UTR of the gene. Metal accumulation in trichomes is an intriguing feature in A. halleri and is possibly involved in short-term tolerance to metals. Chapter 2: Functional analysis of the Arabidopsis thaliana MYB48 and MYB59 transcription factors. MYB transcription factors are involved in many events of plant life, as cell differentiation and metabolism, plant development, response to hormones and to environmental stimuli. Among the others, MYB48 and MYB59 have been proposed to participate in secondary development, cell cycle regulation and response to abiotic stress in Arabidopsis thaliana. In this work, a myb48myb59 double mutant was used due to probable functional redundancy of the two transcription factors. myb48myb59 plants show smaller rosette leaves, likely due to reduced cell distension, delayed flowering and longer roots in comparison to wt; early senescence was also considered and confirmed by the higher SAG12 expression levels. The phenotype is consistent with a reduced cytokinin content: this observation was confirmed by the increased sensitivity to exogenous cytokinins and by the modulated genes resulting from the microarray experiment.
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Francis, Zachary T. "ANALYSIS OF THE CRYPTIC PROMOTER IN THE 5’-UTR OF P27." Thesis, 2012. http://hdl.handle.net/1805/2760.
Full textAbstract:
Indiana University-Purdue University Indianapolis (IUPUI)Cyclin Dependent Kinase regulation is often manipulated by cancer cells to promote unlimited proliferation. P27 is an important regulator of Cyclin E/CDK 2, which has been found in low amounts in many types of malignant cancers. Lovastatin has been shown to cause cell cycle arrest in the G1 phase of the cell cycle by increasing the P27 protein. There has been some question, however, if lovastatin regulates P27 at the transcriptional or translational level. Although it has been claimed that P27 expression regulation is due to an IRES located in its 5’UTR, other studies suggested that P27 expression is regulated at the level of transcription. To further investigate the regulation mechanism of P27 expression, the 5’-UTR of P27 and its deletion mutants were examined using a luciferase reporter gene in HeLa cells following exposure to lovastatin. It was found that lovastatin stimulated a significant 1.4 fold increase in its promoter activity of the full length 5’UTR (575). Deletion of 35 nucleotides from the 5’ end of the UTR eliminated the lovastatin-induced increase in promoter activity. Further mapping analyses of the first 35 bases showed that two regions, M1 (575-559) and M3 (543-527), were less sensitive to lovastatin than the other mutated constructs. Since M1 and M3 still showed some activity, a construct was created with deletions in both the M1 and M3 regions. This showed no increase in luciferase activity when exposed to lovastatin. Looking at RNA levels, there was a 1.5 fold increase in RNA when the full length 5’UTR was inserted into HeLa cells and exposed to 81 µM of lovastatin. In contrast, there was no increase in RNA when M1/M3 (575-559; 543-527) was inserted into HeLa cells and exposed to 81 µM of lovastatin. In addition, there was a 1.6 fold increase in endogenous P27 RNA levels after HeLa cells were exposed to 81 µM of lovastatin. In all of these experiments, there seems to be two promoters that work cooperatively: M1 (575-559) and M3 (543-527).
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Huang, Yi-Chien, and 黃怡倩. "Promoter analysis of rice embryogenesis." Thesis, 2002. http://ndltd.ncl.edu.tw/handle/42245248845701782564.
Full textAbstract:
碩士國立中興大學
分子生物學研究所
90
The purpose of this study is to set up a transient assay system to analyze the important DNA sequences involved in promoter activity of rice embryo-specific genes. Two rice embryo-specific genes, Ose705 and Ose730, were used in this study. Neither the function nor the sequence of Ose705 gene has been reported in GenBank. The Ose730 gene has been identified tentatively to be a Late Embryogenesis Abundant (LEA) protein, but how these genes being regulated were still unknown. In order to understand their regulation, the upstream DNA sequences of Ose705 and Ose730 genes were deleted serially with exonuclease III to get various lengths of promoter. These promoters were then fused to a reporter GUS gene for activity assay. Rice coleoptiles and embryo-derived calli were used as materials in this transient assay. In addition to the transient assay, some deletion constructs were selected for stable transformation to further investigate their tissue-specific expression in transgenic plants. All the tested Ose705 deletion constructs including promoter length ranged from -1659 to -119 bp showed GUS activities in transient assay. The highest GUS activity was observed in the -497 bp construct suggesting the existence of a negative regulation region between -1297 and -497 bp, and possibly some positive sequence domains between -497 and -218 bp. The preliminary observations for Ose705 gene in transgenic study suggested that the sequences between -1659 and -1585 bp might contain an embryo-specific element. Another transient assay for Ose730 gene showed that the -907 bp construct had a much higher GUS activity than -2315 and all other tested constructs --- an observation consistent with the previous result obtained in transgenic assay. On the contrary, the observation that -1248 had a better GUS activity than that of -989 was not consistent with the result obtained in transgenic study. This inconsistency required further verification. However, the transient assay set-up using embryo-derived calli is reproducible and this study represents one step further in studying the regulation of embryo-specific gene in terms of the DNA sequence elements involved in regulation.
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Chen, Feng-Wei, and 陳逢維. "Promoter analysis of Interleukin 19." Thesis, 2002. http://ndltd.ncl.edu.tw/handle/y6v75h.
Full textAbstract:
碩士國立成功大學
生物化學研究所
90
Cytokines are important molecules of hormones. Most of the cytokines are small to medium sized proteins which mediate potent biological effects on most cell types. Originally they are identified as being important in inflammatory processes, the development and maintenance of immune respones and haematopoiesis. A family of interleukin-10 (IL-10)-related cytokines has been emerged which include IL-19, IL-20, IL-22 [IL-10-related T-cell-derived inducible factor (IL-TIF)], IL-24 [melanoma differentiation-associated antigen 7 (MDA-7)] and IL-26 (AK155). Whereas IL-10 is a well-studied pleiotropic immunosuppressive and immun-stimulatory cytokine. It inhibits the production of IL-1, IL-6 and TNF-α. IL-22/IL-TIF can mediate acute-phase response signals in hepatocytes and IL-20 induces the hyperproliferation of keratinocytes. IL-24 is related to the suppression of tumor cell growth. But the function of IL-19 and IL-26 are still unclear. The genes for IL-10, IL-19, IL-20 and IL-24 are found within a 200kb region of chromosome 1 and the two other family members IL-22 and IL-26 are found on chromosome 12. IL-19 was first discoveried in year 2000. It shares 21% amino acid identity with the amino acid sequence of IL-10. In the previous study, it was reported that IL-10 functions as an inhibitor in immune system especial on monocyte、T cell and B cell and the production of cytokines ,such as IFN-γ. The expression of IL-19 mRNA could be induced by LPS and GM-CSF treatment in monocytes. The exon/intron structure of IL-19 is similar to that of the human IL-10 gene, comprising five exons and four introns within the coding region of the IL-19 cDNA. There are at least two distinct IL-19 mRNA species that differ in their 5'-sequences. By 5’RACE experiment, we identified the transcription start site and constructed 5 potential promoter fragments of different length upstream of exon1. We termed these five constructs to PSA、PSB、PSC、PSD、PSE and transfected these plasmid into MDCK and 293 cell lines. The results of luciferase activity showed that the PSE region expressed highest promoter activity in both MDCK and 293 cells. To find the binding protein and binding region of IL-19 promoter, we used EMSA experiment to define the binding sequence between promoter region and transcription factor. The EMSA data proved that a specific region of PSE can bind to some transcription factors contained in the nuclear extract and control the luciferase activity. In the region of nt.-141~-146 and nt.-42~-51, the HNF-5 and TFIID-MBP may bind to the DNA sequence. Furthermore, we mutated the six nucleotide of -141~-146 region in reporter vector. We found the luciferase activity of this mutant decreased 70％ activity compared to the wild type control. When we treated cells with several reagents:LPS､TGF-β､IFN-γ､IL-6､GM-CSF. We found that GM-CSF could enhance the IL-19 promoter activity in 293 cell line.