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Morey, Ramonell Lluís. "Chromatin alterations imposed by the oncogenic transcription factor PML-RAR." Doctoral thesis, Universitat Pompeu Fabra, 2008. http://hdl.handle.net/10803/7138.
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En mamíferos, así como en plantas, mutaciones en AND helicasas/ATPasas del la família SNF2, no solo afectan a la estructura de la cromatina, sino que también afectan al patrón global de la metilación del ADN. Sugiriendo una relación funcional entre la estructura de la cromatina y la epigenética. El complejo NuRD, el cual posee una ATPasa de la familía SNF2, está relacionado con la represión de la transcripción y en el remodelamiento de la cromatina. Nuestro laboratorio demostró que la proteína leucémica PML-RARα reprime la transcripción de sus genes diana por el reclutamiento de DNMTs y el complejo PRC2. En esta tesis, demostramos una relación directa del complejo NuRD en la represión génica y en los cambios epigenéticos en la leucemia promielocítica aguda (APL). Mostramos que PML-RARα se une y recluta NuRD a sus genes diana, incluyendo el gen supresor de tumores RAR2, facilitando que el complejo de Polycomb se reclute y metile la lisina 27 de la histona H3. Tratamiento con Acido Retinóico (RA), el qual se utiliza en pacientes, reduce la ocupación de NuRD en células leucémicas. Eliminando NuRD no solo provoca que las histonas no se deacetilen y que la cromatina no se compacte, sino que también provoca que tanto la metilación del ADN y de las histonas no se produzca, así como la represión génica del gen RAR2, favoreciendo la diferenciación celular. Nuestros resultados caracterizan un nuevo papel del complejo NuRD en el establecimiento de los patrones epigenéticos en APL, demostrando una relación esencial entre la estructura de la cromatina y epigenética durante el desarrollo de la leucemia, pudiéndose aplicar a la terapia de esta enfermedad.In mammals, as in plants, mutations in SNF2-like DNA helicases/ATPases were shown to affect not only chromatin structure but also global methylation patterns, suggesting a potential functional link between chromatin structure and epigentic marks. The SNF2-like containing NuRD complex is involved in gene transcriptional repression and chromatin remodeling. We have previously shown that the leukemogenic protein PMLRARα represses target genes through recruitment of DNMTs and Polycomb complex. In this thesis, we demonstrate a direct role of the NuRD complex in aberrant gene repression and transmission of epigenetic repressive marks in acute promyelocytic leucemia (APL). We show that PML-RARα binds and recruits NuRD to target genes, including to the tumor-suppressor gene RAR2. In turn, the NuRD complex facilitates Polycomb binding and histone methylation at lysine 27. Retinoic acid treatment reduced the promoter occupancy of the NuRD complex. Knock-down of the NuRD complex in leukemic cells not only prevented histone deacetylation and chromatin compaction, but also impaired DNA and histone methylation as well as stable silencing, thus favoring cellular differentiation. These results unveil an important role for NuRD in the establishment of altered epigenetic marks in APL, demonstrating an essential link between chromatin structure and epigenetics in leukemogenesis that could be exploited for therapeutic intervention.
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Ruiz, Emmanuelle. "Coopération entre les inducteurs de l’EMT (EMT-TF/miRNA) et les altérations oncogéniques dans la tumorigenèse mammaire." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10069.
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Les cellules cancéreuses sont capables de réactiver la transition Epithélio-Mésenchymateuse (EMT), mécanisme embryonnaire, pour acquérir une mobilité et une capacité de dédifférenciation. L'EMT conduit à une reprogrammation génétique avec la réactivation d'inducteurs de l'EMT, qui sont en majorité des facteurs de transcription (EMT-TF), et conduit à l'inhibition de miARN. Par ailleurs des stress oncogéniques sont essentiels à la progression tumorale. Le but de mon projet de thèse était de comprendre comment les événements de reprogrammation génétique survenant au cours de l'EMT coopèrent avec des stress oncogéniques dans la transformation tumorale mammaire.Premièrement, un criblage basé sur la coopération oncogénique en soft agar assay, entre les EMT-TFs et les stress oncogénique a été réalisé. Suite à une analyse bioinformatique, différentes signatures d'EMT-TF associés à un stress oncogénique ont été identifiées. Ainsi, par exemple, l'expression de l'EMT-TF Zeb1 et l'EMT-TF GSC sont associés à la délétion du gène suppresseur de tumeur PTEN pour transformer des cellules mammaires immortalisées. Une analyse en immuno-histochimie sur un set de 558 tumeurs du sein triple négatives a validé in vivo la présence d'une corrélation entre l'expression de GSC et l'expression de PTEN. Cependant cette association semble être plus complexe. En effet, l'expression de GSC est négativement associée à l'expression nucléaire de PTEN tandis qu'elle est positivement associée à l'expression de PTEN cytoplasmique. Enfin une analyse sur des métadonnées publiques de cancers telles que le TCGA ou le METABRIC est en cours pour valider ces signatures in vitro et plus largement pour déterminer comment l'EMT ou les signatures associées aux EMT-TF se corrèlent avec les voies oncogéniques classiques. Deuxièmement, une analyse in silico à partir d'algorithmes prédictifs de cibles de miARN, a été réalisée pour sélectionner les miARN capables d'inhiber l'expression de plusieurs EMT-TF. Deux miARN (miR-495 et 590-3p) ont été identifiés ciblant plusieurs membres des 4 principales familles d'EMT-TF (FoxC, Snail, bHLH et ZEB). Des tests in vitro ont été réalisés pour valider ces régulations identifiant Slug comme une cible de miR-590-3p. De plus, l'expression de ces miARN dans des lignées cellulaires mammaires est négativement associée à l'expression des EMT-TF et des marqueurs de l'EMT. Un traitement au TGF, inducteur de l'EMT, diminue leur expression, signifiant potentiellement que ces miARN peuvent négativement réguler l'EMT. En parallèle, plusieurs EMT-TF sont capables de réprimer l'expression de miR-590-3p, agissant directement sur son promoteur, créant ainsi des boucles de régulation. Des études fonctionnelles utilisant des vecteurs d'expression stable de miR-590-3p sembleraient montrer un rôle secondaire de ce miARN dans la régulation de l'EMT car mir-590-3p dérégule des marqueurs secondaires de l'EMT comme la N-cadhérine. Des études de restauration de fonctions sont envisagées pour déterminer quelle est l'importance de ces boucles de régulation dans la progression tumorale mammaire. Plus largement, l'expression des miARN identifiés va être corrélée avec les signatures associées aux EMT-TF et aux voies oncogéniques classiques pour déterminer le lien entre ces trois composants dans la tumorigenèse mammaire. Mes travaux de thèse ont montré qu'il existait un intéractome entre des inducteurs de l'EMT, des stress oncogéniques et des miARNs au cours de la transformation mammaire humaineCancer cells are able to reactivate the Epithelio-Mesenchymal Transition (EMT), an embryonic mechanism, to acquire mobility and dedifferentiation capacities. EMT leads to a genetic reprogramming with the reactivation of EMT inductors, mainly transcription factors (EMT-TF) and the inhibition of miRNA. Otherwise, oncogenic stresses are essentials to tumor progression. The aim of my thesis project was to have a better understanding about the cooperation between events of genetic reprogramming occurring during EMT and oncogenic stresses during mammary tumor transformation. First, a screening based on oncogenic cooperation in soft agar assay, between EMT-TFs and oncogenic stresses was performed. Following a bioinformatics analysis, different EMT-TFs signatures associated with an oncogenic stress were identified. Thus, for example, the expression of EMT-TF ZEB1 and GSC were associated with the deletion of tumor suppressor gene PTEN to transform immortalized mammary epithelial cells. An immunohistochemistry analysis on a set of 558 triple negative breast cancers validated in vivo the presence of a correlation between the expressions of GSC and PTEN. However, this association seems to be more complex. Indeed, the expression of GSC is negatively associated with the nuclear expression of PTEN while it’s positively associated with the cytoplasmic expression of PTEN. Finally, an analysis of public metadata on cancer samples as TCGA or METABRIC is ongoing to validate these in vitro signatures and wider to determine how EMT or EMT-TFs associated signatures correlate with classical oncogenic pathways.Secondly, an in silico analysis, from predictive algorithms of miRNA targets, was performed to select miRNA able to inhibit the expression of several EMT-TFs. Two miRNA (miR-495 and miR-590-3p) were identified targeting several members of four principal’s families of EMT-TFs (FOXC, Snail, bHLH and ZEB). In vitro tests were realized to validate these regulations identifying Slug as a target of miR-590-3p. Moreover, these miRNAs expression in mammary cell lines is negatively correlated with EMT-TFs expression and EMT markers. A treatment with TGF-, a major EMT inductor, decreases their expression, potentially meaning that these miRNA can negatively regulate EMT. In parallel, several EMT-TFs are able to repress the expression of miR-590-3p, acting directly on its promotor, thus creating feedback loops. Functional studies using stable expression vector of miR-590-3p suggest a secondary role of this miRNA in the regulation of EMT because miR-590-3p deregulates EMT secondary markers as N-Cadherin. Functions restauration studies are planned to determine how important these feedback loops in mammary tumor progression are. To open the project, expression of these identified miRNA will be correlated with EMT-TF associated signatures and with classical oncogenic pathways to determine the link between these three components in mammary tumorigenesis. My thesis works are shown that there is an interactome between EMT inductors, oncogenic stresses and miRNA during human mammary transformation
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McElwee, Joshua J. "A comparative analysis of transcriptional alterations in long-lived insulin/IGF-1-like signaling mutants in Caenorhabditis elegans and Drosophila melanogaster /." Thesis, Connect to this title online; UW restricted, 2004. http://hdl.handle.net/1773/4982.
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Jamrog, Laura. "Impact des altérations génétiques de PAX5 sur le développement de la lignée lymphoïde B et dans la leucémogenèse des LAL-B." Electronic Thesis or Diss., Toulouse 3, 2021. http://www.theses.fr/2021TOU30306.
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Le gène PAX5 (Paired boX 5) code un facteur de transcription essentiel pour la différenciation lymphoïde B. Nous avons montré que les deux isoformes PAX5A et PAX5B étaient différentiellement régulées mais pouvaient exercer une fonction équivalente durant l'induction de la différenciation lymphoïde B et pourraient présenter des différences fonctionnelles à la suite de l'activation des lymphocytes B. Le contrôle précis de leur expression peut ainsi refléter un moyen d'ajuster finement le dosage de PAX5 pendant le processus de différenciation des cellules de la lignée lymphoïde B. PAX5 est la cible principale d'une large diversité d'altérations somatiques dans les LAL-B de l'enfant et de l'adulte. Cependant, le rôle des protéines de fusion impliquant PAX5 dans l'initiation et la transformation des LAL-B est encore méconnu. Nous avons précédemment décrit une nouvelle translocation chromosomique récurrente t(7;9)(q11;p13) dans les LAL-B qui juxtapose PAX5 à la séquence codante du gène de l'élastine (ELN). Pour étudier la fonction de la protéine de fusion résultante, PAX5-ELN, au cours du développement leucémique, nous avons créé un modèle murin dans lequel le transgène PAX5-ELN est exprimé spécifiquement dans le compartiment B. Les souris exprimant PAX5-ELN développent un phénotype de LAL-B avec une pénétrance de 80%. Leur transformation leucémique est associée à l'acquisition de mutations secondaires récurrentes des gènes Ptpn11, Kras, Pax5, et Jak3 affectant d'importantes voies de signalisation requises pour la prolifération cellulaire. Nos études fonctionnelles ont démontré que PAX5-ELN altérait in vitro et in vivo le développement lymphoïde B et pouvait induire une expansion aberrante du compartiment progéniteur B (pro-B) au stade préleucémique. Nos approches moléculaires et computationnelles ont identifié des gènes-candidats régulés par PAX5-ELN et pouvant être impliqués dans l'initiation leucémique. Nos données fournissent ainsi un nouveau modèle d'étude in vivo récapitulant la leucémogenèse multi-étapes des LAL-B décrites chez les patients et impliquent fortement les protéines de fusion engageant PAX5 en tant que puissantes oncoprotéines dans le développement leucémique. Par ailleurs, il existe de plus en plus de preuves d'une base génétique héréditaire de prédisposition aux LAL-B pédiatriques. Dans ce contexte, quatre cas de familles non-apparentées affectées par des LAL-B et exprimant des mutations ponctuelles germinales et hétérozygotes de PAX5 ont récemment été rapportés : la mutation PAX5 G183S altérant le domaine octapeptide de PAX5 a été décrite chez trois familles alors que la mutation PAX5 R38H altérant le domaine de liaison à l'ADN de PAX5 a été identifiée chez une autre. Nous avons renforcé l'hypothèse du caractère héréditaire des LAL-B familiales avec la description de trois nouveaux cas de LAL-B au sein d'une même famille exprimant la mutation germinale PAX5 R38H. Pour étudier l'effet intrinsèque de la protéine mutée PAX5 R38H dans le développement lymphoïde B, nous avons effectué des tests fonctionnels in vitro et in vivo combinés à une analyse d'expression génique, basés sur une approche de complémentation rétrovirale. Nos résultats ont indiqué que PAX5 R38H agissait comme un fort variant hypomorphique qui échouait à induire la différenciation lymphoïde B et n'exerçait pas d'effet dominant-négatif sur la forme sauvage de PAX5. Des transplantations syngéniques de cellules exprimant PAX5 R38H ont démontré qu'elles maintenaient une capacité de prise de greffe et menaient au développement leucémique chez la souris. Notre analyse transcriptomique a confirmé la perte de fonction de PAX5 sur ses gènes cibles et a révélé une signature moléculaire spécifique au mutant. Nos données mettent ainsi en évidence l'importance de la dérégulation transcriptionnelle dans la leucémogenèse des LAL-B familiales, en particulier des gènes impliqués dans la différenciation lymphoïde BThe PAX5 (Paired boX 5) gene encodes a key transcription factor crucial for B-cell differentiation. We showed that the two PAX5 isoforms are differentially regulated but have equivalent function during early B-cell differentiation. Indeed, PAX5A and PAX5B isoforms can both induce B-cell program but may have functional differences after B-cell activation. The tight control of their expression may thus reflect a way to finely tune PAX5 dosage during B-cell differentiation process. PAX5 is a well-known haploinsufficient tumor suppressor gene in human B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and is the main target of a wide diversity of somatic alterations in childhood and adult BCP-ALL, occurring in one third of sporadic cases. However, the role of PAX5 fusion proteins in BCP-ALL initiation and transformation is ill-known. We previously reported a new recurrent t(7;9)(q11;p13) chromosomal translocation in human BCP-ALL that juxtaposed PAX5 to the coding sequence of elastin (ELN). To study the function of the resulting PAX5-ELN fusion protein in BCP-ALL development, we generated a mouse model in which the PAX5-ELN transgene is expressed specifically in B cells. PAX5-ELN-expressing mice efficiently developed BCP-ALL phenotype with a penetrance of 80%. Leukemic transformation was associated with clonal Immunoglobulin gene rearrangement and recurrent secondary mutations in Ptpn11, Kras, Pax5, and Jak3 genes affecting key signaling pathways required for cell proliferation. Our functional studies demonstrated that PAX5-ELN impairs B-cell development in vitro and in vivo and induces an aberrant expansion of the pro-B cell compartment at the preleukemic stage. Our molecular and computational approaches identified PAX5-ELN-regulated candidate genes that establish the molecular bases of the preleukemic state to drive BCP-ALL initiation. In conclusion, our study provides a new in vivo model recapitulating the multistep leukemogenesis process of human BCP-ALL and strongly implicates PAX5 fusion proteins as potent oncoproteins in leukemia development. Furthermore, there is increasing evidence for an inherited genetic basis of susceptibility to childhood BCP-ALL. In this context, four unrelated families with childhood BCP-ALL expressing heterozygous PAX5 germline point mutations were recently reported: the recurrent mutation PAX5 G183S affecting the octapeptide domain of PAX5 has been described in three families while PAX5 R38H affecting its DNA-binding paired domain has been identified in another one. We strengthen the hypothesis of inherited character of familial BCP-ALL with the description of three novel familial BCP-ALL cases in related patients that express the germline PAX5 R38H mutation. To uncover the intrinsic effect of PAX5 R38H mutant in B-cell development, we performed in vitro, and in vivo functional assays combined with a gene expression analysis, based on a retroviral complementation approach. Our results indicated that PAX5 R38H mutant acts as a strong hypomorphic variant that fails to drive B-cell differentiation and does not exert a dominant-negative effect on wild-type PAX5. Syngeneic transplantation of PAX5 R38H-expressing cells demonstrated maintenance of engraftment capacity and led to development of BCP-ALL phenotype in mice. Our transcriptomic analysis of these PAX5 R38H-expressing cells showed that PAX5 R38H drastically alters the pattern of expression of PAX5 target genes but also revealed a distinct molecular signature specific to PAX5 R38H. Together with previous unrelated family study, our observations allow to establish the recurrence of the germline PAX5 R38H mutation associated with BCP-ALL. Our data also highlight the importance of transcriptional dysregulation in leukemogenesis of familial BCP-ALL, particularly of genes involved in B-cell differentiation
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Redondo, Monte Enric [Verfasser], and Philipp [Akademischer Betreuer] Greif. "Investigation of transcription factor alterations in core binding factor leukemia : implications in clonal expansion, cell metabolism and lineage fate decisions / Enric Redondo Monte ; Betreuer: Philipp Greif." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/122568269X/34.
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Borralleras, Fumaña Cristina 1988. "Correlation between cognitive phenotype, neural morphology and molecular alterations in mouse models of Williams-Beuren syndrome : new therapeutic approaches." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/388032.
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Williams-Beuren syndrome (WBS) is a rare neurodevelopmental disorder caused by a heterozygous deletion of 26-28 contiguous genes in the 7q11.23 region. So far, a great deal of attention has been focused on its unique and distinctive neurocognitive profile. Although important progress has been made with regards to clinical characterization or genotype-phenotype correlations, a much deeper insight into the neuropathological features of WBS would be of great interest. In this thesis project, we have used a WBS mouse model carrying a heterozygous deletion that mimics the most common deletion found in patients. We have characterized the cognitive and behavioral phenotype of these mice and we have indentified molecular and neuroanatomical alterations relevant for the disease. Moreover, we have attempted two novel therapeutic strategies: a gene therapy and a pharmacological approach. The results obtained highlight the utility of this animal model to study the mechanisms underlying the disease as well as to evaluate novel therapeutic strategies.La síndrome de Williams-Beuren (SWB) és una malaltia rara del neurodesenvolupament causada per una deleció heterozigota d’entre 26 i 28 gens contigus a la regió 7q11.23. Fins ara, una gran part de l’atenció s’ha centrat en el seu característic perfil neurocognitiu. Tot i que s’han fet progressos molt importants pel que fa a la caracterització clínica o a les correlacions genotip-fenotip, seria de gran interès aprofundir en les característiques neuropatològiques de la SWB. En aquesta tesi, hem utilitzat un model de ratolí del SWB amb una deleció heterozigota que mimetitza la deleció més comuna d’aquests pacients. Hem caracteritzat el fenotip cognitiu i comportamental d’aquests ratolins i hem identificat alteracions moleculars i neuroanatòmiques rellevants per a la malaltia. Per altra banda, hem dut a terme dues estratègies terapèutiques: una teràpia gènica i un tractament farmacològic. Els resultats obtinguts remarquen la utilitat d’aquest model animal per a l’estudi dels mecanismes subjacents a la malaltia així com també per a avaluar noves aproximacions terapèutiques.
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Chanapai, Seni. "Photocontrol of artificial transcription factors." Thesis, Cardiff University, 2013. http://orca.cf.ac.uk/58014/.
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The design of a photoswitchable homeodomain artificial transcription factor (PATF), modelled on an engrailed homeodomain, for the purpose of controlling DNA binding affinity and controlling the transcription process in cells using light has been investigated. This study was conducted using a 3,3’-bis(sulfo)- 4,4’bis(chloroacetamino)azobenzene crosslinker, alkylated between two cysteine residues with different spacings (i, i+4, i, i+7 and i, i+11) and either a rigid or flexible linker domain. In previous studies, basic leucine zipper transcription activators have been photocontrolled in living cells by incorporating a photoswitchable azobenzene crosslinker. Circular dichroism spectroscopy showed the conformation of crosslinked PATF (XLPATF) peptides (i, i+11 spacing) containing rigid and flexible linkers could be controlled reversibly by light. Fluorescence anisotropy experiments using labelled DNA confirmed the in vitro DNA binding affinity of PATF was considerably higher with the crosslinker in the trans (ground state) configuration than in the cis (photoexcited state) configuration. Further studies of peptides with i, i+4 and i, i+7 spacings with a semirigid and rigid linker domains showed increased binding affinity with the crosslinker in the cis configuration. Initiation of transcription was investigated by an in vitro transcription assay to measure the ability of PATF molecules to moderate the production of RNA by irradiation with UV light. PATF molecules with i, i+11 spacings showed increased transcriptional activation with the crosslinker in the ground state configuration and i, i+4 and i, i+7 spacings resulted in increased transcription activation with the crosslinker in the excited state conformation. Control of 50% of transcriptional activity was achieved for i, i+11 v spacings, and PATFs with a rigid linker domain were more effective switches than those with flexible linkers. Using i, i+4 and i, i+7 spacings in PATFs resulted in a lower degree of control but, as anticipated, transcriptional activation was increased after irradiation.
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Pinacho, Garcia Raquel. "SP Transcription factors in psychotic disorders." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/327025.
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Psychotic disorders including bipolar disorder and schizophrenia are a leading cause of disability across the world but the underlying pathophysiological mechanisms remain poorly understood. Available treatments are inadequate for some sets of symptoms as is the case for negative symptoms in schizophrenia. Alterations in brain connectivity, synaptic plasticity, N-methyl D aspartate receptor (NMDAR) signalling and calcium homeostasis have been suggested to contribute to these disorders. However, the particular transcriptional programmes altered in these disorders are not fully characterised. Previous data suggested that the transcription factors specificity protein 4 (SP4) and SP1 may be involved in the pathophysiology of psychotic disorders. We hypothesized that the expression and/or function of SP4 and SP1 may be altered in psychotic disorders through the regulation of transcriptional programmes involved in neuronal patterning, synaptic plasticity and glutamate signalling. In this doctoral Thesis we aimed to characterise the contribution of SP4 and SP1 transcription factors to the pathophysiology of psychotic disorders. By using real time quantitative RT-PCR and/or immunoblot techniques, we analysed the expression of SP factors, of SP4 S770 phosphorylation and/or of selected SP-regulated gene targets in at least one of the following substrates: (i) rat cerebellar granule neurons (CGNs), (ii) the postmortem brains of bipolar disorder, schizophrenia and control subjects, (iii) peripheral mononuclear blood cells (PMBC) of first-episode psychosis, and (iv) the rodent hippocampus after NMDAR blockade and antipsychotic treatment.
We found that membrane depolarisation regulates SP4 protein levels in CGNs by preventing SP4 degradation via the ubiquitin-proteasoma pathway and that lithium prevents SP4 degradation and increases SP1 gene expression in non-depolarising conditions. In postmortem human tissue, we found a reduction in protein but not mRNA expression of SP4 and SP1 in the cerebellum in subjects with bipolar disorder and in subjects with more severe negative symptoms in schizophrenia. We have also found reduced expression of protein and mRNA levels of SP4 in the prefrontal cortex in bipolar disorder and of SP1 in the same region in schizophrenia, suggesting a disorder-specific regulation in this area. In contrast, both SP4 and SP1 protein and mRNA levels were increased in the hippocampus in schizophrenia. Consistent with this, we also observed an increase of SP1 and SP4 protein levels in the hippocampus of a mouse model of psychosis, but not in the hippocampus of a rat model of chronic antipsychotic treatment, suggesting that this upregulation may be present from the early stages of psychosis.
We further characterised the phosphorylation of SP4 at serine 770 (S770), which is regulated by membrane depolarisation and NMDAR activity. We found an increase of SP4 S770 phosphorylation in conditions where SP4 protein levels are reduced, namely in the cerebellum of bipolar disorder and of schizophrenia patients with more severe negative symptoms, as well as in PMBC in first-episode psychotic patients. These results suggest that an imbalance in SP4 abundance may be regulated by NMDAR-dependent SP4 phosphorylation in the brain. Moreover, we found that reduced expression of NR2A and DRD2 in the cerebellum of schizophrenia patients correlated with more severe negative symptoms and SP protein levels. Additionally, we show here evidence for an imbalance in the SP4-NWK2-NR1 pathway in the cerebellum of patients with bipolar disorder. This pathway is involved in NR1 subunit availability on the cell surface, suggesting that SP4 could contribute to altered NR1 receptor trafficking in psychotic disorders.
Together, the results presented in this Thesis suggest an imbalance in SP4 and SP1 transcription factors in the brains of patients with bipolar disorder and schizophrenia that may contribute to alterations in NMDAR receptor signalling and thereby to the impaired synaptic plasticity and altered brain connectivity observed in psychotic disorders.
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Müller, Susanne. "Transcription factors regulating the Btk promoter /." Stockholm, 1997. http://diss.kib.ki.se/1997/91-628-2717-0.
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Paik, Elizabeth Jae-Eun. "Caudal Transcription Factors in Hematopoietic Development." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10254.
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During embryogenesis, hematopoietic cells arise from the lateral plate mesoderm (LPM) following gastrulation. The transcriptional program required for this LPM to blood switch is not fully understood. Previous work on a zebrafish mutant with a deletion in the cdx4 gene demonstrated the importance of this caudal transcription factor in the LPM to blood transition. To explain how cdx4 regulates embryonic hematopoiesis, two main approaches were taken in this thesis. The first part of the thesis describes a chemical genetics screen that identified cdx4 interacting pathways. To find small molecules that could rescue the loss of red blood cells caused by the cdx4 deletion, cdx4 mutant embryos were incubated with 2640 compounds from the beginning of the gastrula stage to the 10-somite stage. Two related psoralen compounds, Bergapten (Ber) and 8-methoxypsoralen (8-MOP), rescued the erythroid progenitors in the cdx4 mutants. This rescue is closely linked to the compounds' effects on anteriorposterior patterning, reminiscent of retinoic acid pathway compounds. The second part of my thesis identifies a Cdx4-Sall4 transcriptional module in the LPM. Chromatin-immunoprecipitation coupled to sequencing (ChIP-seq) and microarray analysis revealed that Cdx4 directly regulates cdx4 and a zinc finger transcription factor spalt-like 4 (sall4) transcription. Sall4 ChIP-seq showed that Sall4 also binds to its own locus and to the cdx4 locus, suggesting an auto- and cross-regulation between two transcription factors. In addition, Cdx4 and Sall4 bind to common genomic regions proximal to mesodermal progenitor (tbx16 and mespa) and hematopoietic genes (scl, gata2a, and ldb1a), indicating Cdx4 and Sall4 co-regulate key genes that are required for LPM and blood specification. sall4 knockdown in the cdx4 mutants demonstrated that Sall4 synergizes with Cdx4 in regulating embryonic hematopoiesis. These findings suggest that auto- and cross-regulation of Cdx4 and Sall4 establish a stable circuit in the LPM that facilitates the activation of blood-specific program as development proceeds. How undifferentiated germ layers transition into various tissues is a key question in developmental biology. My thesis establishes a model based on LPM to blood transition, which is also applicable to other studies on germ layer specification.
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Costanzo, Federico. "Role of NER factors in transcription." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ099.
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Les mutations dans les gènes codant pour les facteurs NER donnent lieu à des maladies autosomiques récessives telles que Xeroderma pigmentosum (XP), le syndrome de Cockayne (CS) et la trichothiodystrophie (TTD). Les phénotypes associés à ces syndromes génétiques se caractérisent par une sensibilité extrême à la lumière UV, avec prédisposition accrue à certains cancers (pour XP et XP / CS combiné, principalement), ainsi qu’un retard mental et des signes de progeria (pour CS et XP / CS combiné). Si on peut admettre une corrélation entre réparation de l'ADN endommagé et sensibilité aux UV / cancer, celle avec les symptômes neurologiques/progéroïdes est encore sujet à débat. Une explication pourrait provenir du rôle des facteurs NER dans la régulation de la transcription. Nous proposons une vue d’ensemble des roles de XPG et XPC dans la régulation de la transcription en absence des stress exogènes et comment CSA et CSB orchestrent l’arret de la transcription après une attaque génotoxique. XPC était capable d’interagir stablement avec la methyltransferase NSD3. Des mutations dans XPC altèrent le transcriptôme et la distribution des H3K36me3. Les mutations dans XPG dérégulent l’expression génique et XPG est capable d’etre recruté sur l’ensemble du genôme avec TFIIH. CSA et CSB faisant partie de la machinerie ubiquitin/proteasôme, régulent le recrutement de facteurs fixant l’ADN et contrôlant le programme transcriptionnel après irradiation aux UV. Nos donnés mettent en évidence le rôle des facteurs NER dans la transcription et leur défaut d’action provoque les maladies XP et XP/CS. En plus, nos données fournissent des explications sur le méchanisme d’arrêt de la transcription après un stress genotoxique et pose la question de l’origine du phenotype CSMutations in genes coding for NER factors give rise to autosomal recessive diseases such as Xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The phenotypes associated with these genetic syndromes spans from extreme sensitivity to UV light, with increased predisposition to cancer (for XP and combined XP/CS, mostly), mental retardation and progeria (for CS and combined XP/CS). Whether the correlation between defective DNA repair reactions and UV-sensitivity/cancer may be more intuitive, a link with neurological/progeroid symptoms is still a matter of debate. As a possible explanation, it has been proposed a connection between NER and transcription regulation. We propose additional insights on XPG and XPC roles in transcription regulation in absence of exogenous stress and how CSA and CSB orchestrate transcription arrest due to genotoxic attack. XPC was able to stably interact with NSD3 methyltransferase. Mutations in XPC also disturbed the transcriptome and the H3K36me3 distribution. Mutations in XPG deregulate gene expression and XPG is able to be recruited genome wide together with TFIIH. CSA and CSB can, as part of the ubiquitin/proteasome machinery, regulate the recruitment timing of DNA binding factors and control transcriptional program after UV irradiation. Hence, our data shed more light in NER factors role in transcription and their defective action as a cause of XP and XP/CS disorders. Additionally, our data provide explanations on the mechanism of transcription arrest following genotoxic stress and pose questions about the origins of CS phenotype
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Grossman, Sharon R. (Sharon Rachel). "Combinatorial gene regulation by transcription factors." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/128406.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019Cataloged from PDF of thesis. "The Table of Contents does not accurately represent the page numbering"--Disclaimer page.
Includes bibliographical references.
Combinatorial gene regulation is encoded in enhancers and promoters in the form of binding sites for transcription factors (TFs), which collaboratively recruit the transcriptional machinery and drive gene expression. Using high-throughput and quantitative technologies developed by our lab and others, we studied TF binding sites in enhancers from numerous different cell types and regulatory systems, shedding light general principles of motif composition and organization in typical cellular regulatory elements. We find extensive synergy between TF binding sites, some with organizational constraints and some with flexible positioning. We demonstrate that different TFs bind at distinct positions within regulatory elements, suggesting a new type of architectural constraint in enhancers. Importantly, our analysis of both TF organization and cooperativity revealed distinctive patterns that separates TFs into potential functional classes. Together, our results suggest a structure of the regulatory code at the level of TF function and generate new hypotheses about regiospecific binding patterns and functions of TF classes within enhancers.
by Sharon R. Grossman.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Greberg, Maria Hellqvist. "Cloning and characterization of FREACs, human forkhead transcription factors." Göteborg : Dept. of Cell and Molecular Biology, Göteborg University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39751934.html.
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Patel, Vyoma. "Monocyte subset functional alterations with increased cardiovascular risk factors." Thesis, The University of Sydney, 2019. http://hdl.handle.net/2123/20501.
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Atherogenesis is dependent upon monocyte influx into the vessel wall. In humans, three monocyte subsets exist, classical, intermediate and non-classical. Of these monocyte subsets, clinically, the intermediate monocytes are considered to be a potential treatment target in cardiovascular disease (CVD), due their significant elevation and inflammatory nature. However, whether their elevation in CVD would translate to a functional contribution to atherogenesis is currently unknown. In addition, intermediates are also known to adhere more to endothelium than the classical subset as described in murine models. However, adhesion does not necessarily equate to migration as classical subset migrates at a greater rate to the plaque (in response to chemokines such as CCL2/MCP-1) than other subsets. Further research in understanding the contribution of each monocyte subset in CVD is needed. Here we aimed to determine the phenotype of monocyte subsets in individuals (who were generally healthy) relative to their lipid levels, as monocytes displaying an atherogenic phenotype in those with perturbed lipid levels would indicate whether the monocyte functional changes are occurring in the circulation, prior to entry into the vessel wall. First, we determined the inflammatory nature of monocyte subsets by assessing the monocyte subset cytokine production and expression of inflammatory/anti-inflammatory markers (Chapter 4). The findings from cytokine production (upon LPS stimulation) and surface marker expression combined suggest that intermediates and non-classicals are more inflammatory than the classical subset. This is consistent with the literature but we extend the understanding to show that this remains the case even when including individuals with an altered lipid profile. However, for the intermediates and non-classicals, being more inflammatory than classicals does not mean that they will have the greatest contribution to atherosclerotic plaque development as their level of recruitment into the plaque is also a factor. Recruitment depends on two key steps, adhesion and migration – that are regulated by adhesion molecules and chemokine receptors. Therefore, we next assessed monocyte subset adhesive and migratory nature by the expression of various adhesion molecules and chemokine receptors. From assessment of expression of adhesion molecules (Chapter 5) and chemokine receptors (Chapter 6) on monocyte subsets, we found that they differentially express various adhesion molecules and chemokine receptors which ultimately, would result in their distinct trafficking patterns and thus differential functional consequences. This suggests that all monocyte subsets possess a potential to adhere or migrate into the plaque and thus, raises a question whether targeting intermediates alone would sufficiently reduce CVD risk. Further, we assessed whether the changes in cytokine production and surface marker (inflammatory, adhesion molecule and chemokine receptor) expression occurs in a gradual or distinct manner at the subset level by flow cytometry. Our findings indicate that the changes in cytokine production and surface marker expression levels varied incrementally from one subset to another. We also assessed monocytes at the cellular level by flow cytometry, where we suggest that the monocytes in some individuals are likely to be entering the circulation in a pro-atherogenic state as differences were evident in the classical monocytes of one individual compared to another. This finding adds to the growing body of evidence that challenges the paradigm that monocytes are just precursors to macrophages and dendritic cells. Importantly, we found that monocyte expression of pro-atherogenic markers varies between the participants with the degree of spread (coefficient of variance) for the monocytes being comparable. This suggests that no one particular monocyte subset displays an increased proatherogenic phenotype but instead, all do, and this acquisition of a pro-atherogenic phenotype by monocytes occurs even before they differentiate into the intermediate subset. We further explored the relationship between the pro-atherogenic marker expression by the monocyte subsets and we found that participants’ pro-atherogenic marker expression by one subset correlated with that of the next. This indicates that the pro-atherogenic state acquired throughout differentiation (from classical to non-classical) is dictated by the pro-atherogenic profile of the emerging classical subset. This finding suggests that no particular subset is proatherogenic but rather all, as they recapitulate the pro- therogenic phenotype of a precursor, the classical subset or perhaps, bone marrow cells. The monocyte subset pro-atherogenic state (increased monocyte inflammation, adhesion or migration) was related to the participants’ lipid levels. The key result was that not only the cytokines, but also the expression of most of the pro-atherogenic markers (M1 markers, adhesion molecules, chemokine receptors) on monocyte subsets, were inversely associated with participants’ Apo A1 (or HDL-C) levels and, importantly, this was evident for all monocyte subsets. This finding suggests that altered lipid levels may be a key factor promoting monocyte pro-atherogenic changes. Lastly, we assessed whether the relationship between the monocyte pro-atherogenic state (chemokine receptor expression) and participants’ lipid levels could be seen functionally by in vitro static migration assay in response to chemokines, as a preliminary study (Chapter 6). Interestingly, we observed an inverse relationship (trend only) with monocyte subset migration and participants’ cholesterol and LDL-C levels suggesting that the higher levels of cholesterol and LDL-C negatively impact on the degree of monocyte migration in these participants. Thus, overall it is noteworthy that the changes in expression of chemokine receptors on monocyte subsets may not necessarily translate to direct changes in theirmigration in vitro. Taken together, the findings from the present study provide a fundamental change in the understanding of the importance of monocytes in atherosclerosis (particularly, their role and functional contribution i.e. adoption of pro-atherogenic phenotype) as we have shifted the paradigm from the need to target the intermediate monocyte subset, to targeting specific functions of monocytes overall. Importantly, with the changes evident in individuals that have perturbed lipids, but no diagnosed CVD, this study has drawn attention to proatherogenic changes that are occurring quite early sub-clinically in association with an altered lipid profile. This could be contributing to plaque development as monocytes would enter the vessel wall primed to become pro-atherogenic macrophages.
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Zhang, Mei. "Molecular alterations induced by dysregulated PKA activity in bone development and homeostasis." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397578707.
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Koo, Sonya Janet. "Downstream targets of motor neuron transcription factors /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2005. http://wwwlib.umi.com/cr/ucsd/fullcit?p3190171.
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Kinyanjui, Margaret. "Targeting Th2 transcription factors in experimental asthma." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=18717.
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Antigen specific CD4+ T cells adoptively transfer airway inflammation comprised mainly of lymphocytes and eosinophils. The ability of these transferred T cells to induce inflammation is dependent on the cytokines they express particularly Th2 cytokines. In order to better understand the mechanism by which adoptively transferred T cells induce airway inflammation, we chose to modulate the expression (GATA-3) and activity (STAT-6) of two key regulators of Th2 cytokine production. To modify expression of GATA-3, we used a bicistronic retroviral vector encoding GATA-3 and enhanced green fluorescent protein (EGFP). As a control, we used a retrovector encoding EGFP alone. By coupling in vitro antigen stimulation with retroviral transduction we generated antigen specific CD4+ T cells expressing EGFP alone or GATA-3 and EGFP. When transferred into naïve recipients that were subsequently challenged, these transduced CD4+ T cells induced lung inflammatory responses with an increase in both CD4+ lymphocytes and eosinophils. This antigen specific inflammatory response was enhanced in animals receiving T cells overexpressing GATA-3. Analysis of the infiltrating cells also revealed that the EGFP+ T cells were present in the lung following antigen challenge, comprising only a small fraction of the CD4+ T cells recruited to the lung during the antigen response. Thus, GATA-3 amplifies antigen-specific inflammatory responses in the airways by augmenting the ability of antigen specific T cells to recruit inflammatory cells to the lung following antigen challenge. To modify the activity of STAT-6 we used chimeric cell penetrating peptides containing a poly-arginine protein transduction domain (PTD) coupled to a sequence predicted to bind and inhibit STAT-6 activity (SIP-1). Using fluorescein-tagged SIP-1, we demonstrate that the poly-arginine PTD efficiently translocates to the cytoplasm within an hour. In vitro, antigen-induced IL-4 production was inhibited in SIP-1-treated splenoLes cellules CD4+ T à antigènes spécifiques transfèrent par adoption l'inflammation pulmonaire constituées principalement de lymphocytes et d'éosinophiles. L'habileté de celles-ci à transférer des cellules T pour induire l'inflammation est dépendante de leur expression de cytokines Th2. De manière à mieux comprendre le mécanisme par lequel les cellules T transmises par adoption induisent l'inflammation pulmonaire, nous avons choisi de moduler l'expression de GATA-3) ou l'activité de (STAT-6) des deux régulateurs-clés de production de cytokine Th2. Afin de modifier l'expression de GATA-3 dans les cellules T destinées au transfert par adoption, nous avons utilisé un rétrovirus recombinant concentré avec une filtration par centrifugeuse. Ce procédé a dramatiquement augmenté leurs titres et ainsi leur habileté à transduire les cellules CD4+ T en culture primaire. Nous avons utilisé un rétrovirus recombinant qui encode la GATA-3 et / ou la protéine fluorescente verte (EGFP). En couplant in vitro la stimulation d'antigènes avec la transduction par vecteur viral, nous avons généré des cellules CD4+ T à antigènes spécifiques exprimant de l'EGFP seul ou bien de la GATA-3 et de l'EGFP. Lorsque transféré dans un rat qui avait subséquemment été provoqué avec des antigènes, ces cellules CD4+ T induisent une réaction aux inflammations pulmonaires avec une augmentation des lymphocytes et éosinophiles. Cette réaction inflammatoire fut accrue chez les animaux recevant les cellules T surexprimant la GATA-3. L'analyse des cellules infiltrantes a aussi révélé que bien que les cellules EGFP+ étaient présentes dans les poumons suivant la provocation par antigènes, elles étaient constituées seulement d'une petite fraction de cellules CD4+ T recrutées dans les poumons. Ainsi, la GATA-3 amplifie la réaction inflammatoire des poumons induite par antigènes en augmentant l'habileté des cellules T à antigènes spécifiques à recruter
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Ali, Asif. "Transcription factors in parathyroid development and embryology." Thesis, Open University, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.489906.
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The roles of two transcription factors, GATA3 and PARAFIBROMIN, that are involved in parathyroid function have been studied. Thus, loss of function mutations of the dual zinc finger transcription factor GATA3 result in hypoparathyroidism-deafness-renal dysplasia (HDR) syndrome; whilst loss of function mutations of PARAFIBROMIN which is a nuclear protein with a likely role in the RNA polymerase complex, lead to the hyperparathyroidism-jaw tumour (HPT-JT) syndrome.
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Young, Neville Jonathan. "The role of transcription factors in odontogenesis." Thesis, King's College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.393692.
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Bidon, Baptiste. "Mediator and NER factors in transcription initiation." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ093/document.
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La synthèse d’ARN messagers résulte d’une cascade d’évènements temporellement et spatialement orchestrée. Au moment de l’initiation de la transcription, divers facteurs tels que les facteurs généraux de transcription, le complexe Médiateur, des co-activateurs, des facteurs de remodelage de la chromatine ainsi que l’ARN polymérase II sont recrutés au niveau de la région promotrice du gène. Certains facteurs de la voie NER de réparation de l’ADN sont également recrutés. En utilisant des cellules de patients porteurs de mutations dans les gènes MED12 (sous-unité du Médiateur) ou XPC (facteur initiant la voie NER), nous avons pu étudier le rôle de ces protéines dans la transcription. Les patients MED12 sont notamment caractérisés par une lourde déficience intellectuelle et des malformations congénitales. Nous avons montré que MED12 est impliqué dans le contrôle de certains gènes de réponse immédiate comme JUN, qui contribue notamment au développent et à la plasticité cérébrale. L’expression de ce dernier est affectée par les mutations de MED12, mais différemment en fonction de la position de la mutation, apportant une possible indication sur l’origine des variations phénotypiques observées chez les patients. En parallèle, les patients XPC se caractérisent par une forte photosensibilité. Nous avons montré que la protéine XPC, en collaboration avec le facteur E2F1, est impliquée dans le recrutement de l’histone acetyl-transférase GCN5 au niveau du promoteur d’un certain nombre de gènes. Cette dernière permet notamment l’a modification de l’environnement chromatinien, en coopération avec le facteur général de transcription TFIIH et participe ainsi à l’initiation de la transcription. En plus d’approfondir la compréhension des mécanismes régissant la transcription, ces résultats ont permis de mieux comprendre l’étiologie des maladies associées aux mutationsThe synthesis of messenger RNA is a highly regulated process. During transcription initiation, a large number of proteins are recruited to gene promoter, including the RNA polymerase II, general transcription factors, co-activators, chromatin remodellers and the Mediator complex. Some DNA repair factors from the NER pathway are also recruited. Using cells derived from patients bearing mutations in either MED12 gene or XPC gene, we studied the roles of such proteins in transcription. MED12 patients are mostly characterised by intellectual disability and developmental delay. We showed that MED12 is implicated in the transcription regulation of immediate early genes like JUN, known for its role in neurological development and neuronal plasticity. JUN expression is markedly altered by MED12 mutations. We also showed that the position of the mutation influences this alteration, bringing possible explanation for inter-patients symptom variability. Meanwhile, XPC patients are mostly characterized by photosensitivity. We showed that XPC protein, which engages one of the NER pathways, is implicated in chromatin post-translational modification. Together with E2F1, it helps the recruitment of GCN5 acetyl-transferase to promoter of a certain set of genes. On the promoter, GCN5 notably cooperates with TFIIH to modify the chromatin environment during transcription initiation. In addition to help the comprehension of the transcription mechanisms, these results bring knew insight into the aetiology of mutations associated diseases
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Friedrich, Dhana. "Oscillatory transcription factors and stochastic gene expression." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/22053.
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Transkriptionsfaktoren (TFs) empfangen Signale in Signaltransduktionskaskaden und übersetzen diese in eine zelluläre Antwort. Dadurch ermöglichen sie es Zellen, Organen und Organismen sich an verändernde Umgebungsbedingungen anzupassen. In früheren Studien wurde gezeigt, dass viele TFs nach Aktivierung Oszillationen im Zellkern aufweisen. Ein Beispiel dafür ist p53. Als zentrales Protein im Rahmen der zellulären Stressantwort reguliert es nach DNA Schaden die Expression hunderter Zielgene die das Zellschicksal steuern. Anomalien in der Aktivität von p53 stehen im Zusammenhang mit schwerwiegenden Erkrankungen wie der Krebsentstehung. Die Dynamik der Akkumulation von p53 im Zellkern ist abhängig von der Art des DNA Schadens und korreliert mit der resultierenden zellulären Antwort. Obwohl dieser Zusammenhang mehrfach gezeigt wurde, sind die zugrundeliegenden molekularen Mechanismen jedoch weitgehend unerforscht.
Mit der vorliegenden Arbeit soll ein Beitrag zum Verständnis dazu geleistet werden, wie p53 Oszillationen im Zellkern die Transkription von Zielgenen auf Einzelzellebene modulieren. Dazu wurden sieben Zielgene ausgewählt und mittels Einzelmolekül-Fluoreszenz in situ Hybridisierung und mathematischer Analyse charakterisiert. Es werden Ergebnisse der quantitativen, zeitaufgelösten mRNA Expression und der bursting Aktivität von Zielgenpromotoren mit Einzelzell- und Einzelmolekülauflösung dargestellt. Diese Analyse weist darauf hin, dass die Aktivierung von p53 nach DNA Doppelstrangbrüchen primär die Frequenz des stochastischen bursting der untersuchten Zielgene reguliert. Diese können anhand ihrer Promotoraktivität in drei Archetypen eingeteilt werden: anhaltend, transient und pulsierend, die jedoch nicht ausschließlich durch veränderte p53 Menge im Zellkern erklärt werden können. Stattdessen weisen die Ergebnisse darauf hin, dass Veränderungen im Acetylierungszustand der C-terminalen Lysinreste von p53 entscheidend für diese Gen-spezifische Regulation sind.Transcription factors (TFs) are receiver and compiler of cell signaling, transmitting incoming inputs into cellular responses that enable cells, organs and organisms to respond and adapt to a changing environment. In the past, it has been shown that many TFs exhibit oscillations of nuclear abundance over time when activated. One of these TFs is the tumor suppressor p53, a central hub in the signaling network regulating the cellular stress response, controlling cell fate decisions by changing the expression of hundreds of target genes. Aberrations in p53’s activity are related to severe human malignancies such as cancer. The dynamics of its nuclear accumulation are stimulus dependent and enable the p53 pathway to mediate distinct responses to cellular stress. However, the molecular mechanisms translating such dynamics to altered gene expression remain elusive. In this thesis, I analyzed how oscillations of p53 affect the transcriptional regulation of target genes in single-cells and at individual promoters. I chose a panel of seven targets and employed a combinatorial approach of single-molecule fluorescence in-situ hybridization and mathematical analysis. I present quantitative, time-resolved measurements of target gene mRNA expression and transcriptional bursting activity with single-cell and single-molecule resolution. The resulting data show characteristic principles how p53 nuclear accumulation increases transcriptional bursting upon stimulation and reveal gene-specific modulations. P53 target promoters are regulated by changing the fraction of active promoters, indicating burst frequency regulation. Based on this, genes can be grouped along three archetypes of promoter activity: sustained, transient and pulsatile. These archetypes cannot solely be explained by nuclear p53 levels or promoter binding of total p53. Instead, I provide evidence that the time-varying acetylation state of p53’s C-terminal lysine residues is critical for this gene-specific regulation.
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Gillis, William Joseph. "The evolution of metazoan GATA transcription factors /." Connect to title online (Scholars' Bank) Connect to title online (ProQuest), 2008. http://hdl.handle.net/1794/8568.
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Thesis (Ph. D.)--University of Oregon, 2008.Typescript. Includes vita and abstract. "This dissertation includes both ... previously published and unpublished co-authored material"--P. v. Includes bibliographical references (leaves 120-135). Also available online in Scholars' Bank; and in ProQuest, free to University of Oregon users.
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Gillis, William Joseph 1981. "The evolution of metazoan GATA transcription factors." Thesis, University of Oregon, 2008. http://hdl.handle.net/1794/8568.
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xiii, 135 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number.This thesis explores the origin and evolution of animal germ layers via evolutionary-developmental analyses of the GATA family of transcription factors. GATA factors identified via a conserved dual zinc-finger domain direct early germ layer specification across a wide variety of animals. However, most of these developmental roles are characterized in invertebrate models, whose rapidly evolved sequences make it difficult to reconstruct evolutionary relationships. This study reconstructs the stepwise evolution of metazoan GATA transcription factors, defining homologous developmental roles based upon clear orthology assignments. We identified two GATA transcription factors ( PdGATA123 and PdGATA456 ) from the marine annelid Platynereis dumerilii to aid comparison of protostome and deuterostome GATA factors. Our phylogenetic analyses defined these as protostome orthologs of GATA1/2/3 and GATA4/5/6 vertebrate subfamilies, while the mRNA localization of the Platynereis GATAs showed ectodermal versus endomesodermal germ layer restrictions, similar to their vertebrate orthologs. To define the phylogenetic relationships of more divergent genes in the invertebrate models, we identified GATA homologs from recently sequenced protostome genomes. Molecular phylogenetic analyses, comparisons of intron/exon structure, and conserved synteny confirm all protostome GATA transcription factor genes are members of either the GATA123 or GATA456 class. These data allowed us to identify multiple protostome-specific duplications of GATA456 homologs and reconstruct the origin and relationships of all arthropod GATA genes. To probe GATA transcription factor evolution in deuterostomes, including vertebrates, we identified GATA factors in basal deuterostomes, including the cephalochordate Branchiostoma floridae and the hemichordate Saccoglossus kowalevskii. Phylogenetic analyses of these data independently confirmed that the ancestral deuterostome and chordate--like the bilaterian ancestor--possessed only two GATA transcription factors. This work was facilitated by a bioinformatics platform we are developing to identify gene families from preassembled genomic sequence. We generated anti- PdGATA antibodies to further explore the role of Platynereis GATAs in germ layer formation. We identified multiple presumptive endomesodermal cells in which nuclear localization of PdGATA456 protein first occurs and utilized PdGATA456 protein localization to follow endomesodermal cell populations throughout development. These analyses represent some of the first cellular and molecular analyses of Platynereis germ layer formation. This dissertation includes both my previously published and unpublished co-authored material.
Adviser: Stephan Q. Schneider
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Matthews, Chris. "Economic and social factors behind housing alterations in Windsor, Ontario." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ30967.pdf.
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Roberts, Karen. "Regulation of melanocyte-specific transcription by the transcription factors BRN-2 and microphthalmia." Thesis, Institute of Cancer Research (University Of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286144.
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Li, Yuxin. "The DEC1 transcription factor : oncogenic involvement and molecular mechanisms on transcription regulation /." View online ; access limited to URI, 2003. http://0-wwwlib.umi.com.helin.uri.edu/dissertations/dlnow/3115632.
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Jadlowsky, Julie Kendal. "Dual control of HIV transcription elongation virus-specific negative control by NELF-E is counterbalanced by positive transcription factor P-TEFb /." Cleveland, Ohio : Case Western Reserve University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1228234927.
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Eustis, Robyn Lynn. "The Role of Pyrococcus furiosus Transcription Factor E in Transcription Iniitiation." PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2522.
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All sequenced archaeal genomes encode a general transcription factor, TFE, which is highly conserved and homologous to the alpha subunit of the eukaryotic transcription factor TFIIE. TFE functions to increase promoter opening efficiency during transcription initiation, although the mechanism for this is unclear. The N-terminus of TFE contains a common DNA binding motif, a winged helix. At the tip of this winged helix is a highly conserved region of aromatic amino acids that is close to DNA during initiation. TFE activation can compensate for mutations in another transcription factor, TFB2, which is homologous to TFIIB. P. furiosus encodes two paralogs of the eukaryotic RNA polymerase II transcription factor TFIIB: TFB1 and TFB2. TFB2 lacks a portion of the highly conserved N-terminus, and functions in transcription complexes at a lower efficiency than TFB1. It has been demonstrated that the presence of TFE is able to assist in transcription with TFB2 in vitro bringing its efficiency to almost TFB1 levels. Thus, TFB2 provides a unique opportunity to evaluate the function of the TFE winged helix in transcription. In this study the aromatic patch of the TFE winged helix was mutated to test its role in activation of TFB1 and TFB2-containing transcription complexes, because this aromatic patch is required for full TFE activity especially when NTP concentrations are low.
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Bielecka, Monika. "Analysis of transcription factors under sulphur deficiency stress." Phd thesis, kostenfrei, 2007. http://opus.kobv.de/ubp/volltexte/2007/1481/.
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Montelius, Andreas. "Role of transcription factors in sensory neuron specification /." Stockholm, 2007. http://diss.kib.ki.se/2007/978-91-7357-115-9/.
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Andersson, Tove. "Transcription factors regulating the immunoglobulin heavy chain locus /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3559-9/.
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Li, Yifan. "Gene regulation by WT1 and related transcription factors." Thesis, University of Bristol, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.509772.
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Jahangiri, Leila. "Combinatorial gene regulation by T-domain transcription factors." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610328.
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Jager, S. M. de. "Isolation and characterisation of Arabidopsis E2F transcription factors." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.605016.
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The present work shows that the maize Rb homologue, ZmRb, interacts with human E2F1, Drosophila dE2F and the Drosophila dE2F/dDP heterodimer, while this activity is absent from a ZmRb mutant. Genomic and cDNA sequences with the potential to encode Arabidopsis E2F homologues were identified in the Arabidopsis thaliana database. Amplification of Arabidopsis sequences by PCR with degenerated primers, based on the database sequence information, followed by DNA hybridisation library screening led to the isolation of cDNA sequences for three Arabidopsis E2F clones-AtE2F1, AtE2F2 and AtE2F3. Phylogenetic analysis of the AtE2F sequences indicated that the AtE2Fs are related to human E2Fs (30% - 44% identity), but form a distinct group. The structural domain organisation of the AtE2Fs is the same as for other E2Fs, with the DNA-binding domain, leucine zipper and marked box conserved. A putative Rb-binding domain was identified in the C-termini of the AtE2Fs. Preliminary characterisation of AtE2F1 has revealed that AtE2F1 activated transcription in yeast cells and that ZmRb repressed AtE2F1-mediated transactivation. Direct interaction of AtE2F1 with ZmRb, but not a ZmRb mutant, was shown. As a heterodimer with the human DP1 protein, AtE2F1 bound to the E2F-binding sites in the promoters of a putative Arabidopsis CDC6 homologue and the human dihydrofolate reductase gene. The expression of the three AtE2Fs was followed in a partially synchronised Arabidopsis cell suspension culture re-entering the cell cycle, and was found to be cell cycle-dependent, with peak expression during S phase. The isolation of three Arabidopsis E2F homologues which share characteristics with mammalian E2Fs, indicates that this aspect of cell cycle regulation has been conserved between plants and mammals.
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Andersen, K. G. "Immune modulation using inducible lineage-specific transcription factors." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.595497.
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The launch of an immune response is regulated on several different levels. Whilst responses against foreign antigens proceed relatively unrestricted, CD4+CD25+ regulatory T cells suppress potential immune attacks directed against self. During their development in the thymus these cells start to express the lineage-specific transcription factor Foxp3, which is both required and sufficient for their development and function. I have identified functional domains of Foxp3 that were differentially required for its function as a master regulator of gene expression. I extended these studies by generating a series of reporter constructs, which were used to measure some of the cellular consequences of Foxp3 expression in vivo and in vitro. I have also showed that ectopic expression of Foxp3 in CD4+CD25- T cells leads to a significant downregulation of the homing factor CD62L. This appeared to result in these cells being excluded from the peripheral lymph nodes, with a subsequent failure to expand ‘appropriately’ upon immunological challenge. By utilising a genetically engineered inducible version of Foxp3 (iFoxp3), I circumvented these problems and showed that cells expressing iFoxp3 both homed ‘correctly’ into lymph nodes and partook in immune responses. In two different animal models of autoimmune disease, I showed that T cells transduced with iFoxp3, but not Foxp3, could be used to control and treat such disorders. Finally, I went on to show that the iFoxp3-mediated suppression was specific to the antigen(s) the cells partook in prior to the induction of iFoxp3.
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West, Adam Geoffrey. "Molecular interactions of the MADS-box transcription factors." Thesis, University of Newcastle Upon Tyne, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362415.
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Brown, A. Louise. "Molecular characterisation of zebrafish ETS-domain transcription factors." Thesis, University of Newcastle Upon Tyne, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362472.
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Gay, Robert Daniel. "Neuronal gene regulation by POU family transcription factors." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267026.
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Wrighton, N. C. "Transcription factors regulating the human beta-globin genes." Thesis, University College London (University of London), 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382204.
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Miles, Anna Louise. "V-ATPase regulation of Hypoxia Inducible transcription Factors." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/283217.
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Metazoans have evolved conserved mechanisms to promote cell survival under low oxygen tensions by initiating a transcriptional cascade centered on the action of Hypoxia Inducible transcription Factors (HIFs). In aerobic conditions, HIFs are inactivated by ubiquitin-proteasome-mediated degradation of their a subunit, which is dependent on prolyl hydroxylation by 2-oxoglutarate (2-OG) and Fe(II)-dependent prolyl hydroxylases (PHDs). In hypoxia, HIF-$\alpha$ is no longer hydroxylated and is therefore stabilised, activating a global transcriptional response to ensure cell survival. Interestingly, HIFs can also be activated in aerobic conditions, however the mechanisms of this oxygen-independent regulation are poorly understood. Here, I have explored the role of the vacuolar H+-ATPase (V-ATPase), the major proton pump for acidifying intracellular vesicles and facilitating lysosomal degradation, in regulating HIF-$\alpha$ turnover. Unbiased forward genetic screens in near-haploid human cells identified that disruption of the V-ATPase leads to activation of HIFs in aerobic conditions. Rather than preventing the lysosomal degradation of HIF-$\alpha$, I found that V-ATPase inhibition indirectly affects the canonical proteasome-mediated degradation of HIF-$\alpha$ isoforms by altering the intracellular iron pool and preventing HIF-$\alpha$ prolyl hydroxylation. In parallel, I characterised two putative mammalian V-ATPase assembly proteins, TMEM199 and CCDC115, identified by the forward genetic screen and subsequent mass spectrometry analysis. I confirmed that both TMEM199 and CCDC115 are required for V-ATPase function, and established assays to determine how TMEM199 and CCDC115 associate with components of the core V-ATPase complex. Lastly, to measure how V-ATPase activity leads to changes in the labile iron pool, I developed an endogenous iron reporter using CRISPR-Cas9 knock-in technology. This approach confirmed that iron homeostasis is impaired during V-ATPase inhibition, and demonstrated that exogenous ferric iron can restore the labile iron pool in a transferrin-independent manner. Together my studies highlight a crucial link between V-ATPase activity, iron homeostasis, and the hypoxic response pathway.
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Iazzetti, Paul Christopher. "High-throughput binding characterization of bacterial transcription factors." Thesis, Boston University, 2014. https://hdl.handle.net/2144/11020.
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Thesis (Ph.D.)--Boston UniversityTuberculosis (TB) is a global pandemic responsible for the deaths of 1.5 million people annually. A third of the world's population is thought to harbor the latent form of the disease, and a disproportionate majority of TB cases are reported in Asia and Africa where poor infrastructure impedes proper treatment. Non-adherence to drug regimens has helped foster the rise of multi drug-resistant tuberculosis, with implications for those in the developed world. Treatment of the disease is hindered by an inadequate understanding of its causative agent, the pathogen Mycobacterium tuberculosis (MTB). Decreases in thecost of gene sequencing have heralded a new era of genomic technologies such as chromatin immunoprecipitation sequencing (ChiP-Seq), which can generate comprehensive in-vivo genomic binding data for transcription factors and help elucidate the workings of bacterial regulatory networks. In this work we explore the in vitro binding behavior of MTB transcription factors important to disease pathogenesis using electrophoretic mobility shift assays (EMSAs) and High-Throughput Sequencing- Fluorescent Ligand Interaction Profiling (HiTS-FLIP). We compare this data to high-throughput in vivo binding data generated by ChiP-Seq to assessing binding patterns across in vitro and in vivo conditions, and demonstrate the use of HiTS-FLIP as a powerful complement to ChiP-Seq for accurately characterizing transcription factor binding affinity. The results of this work lay the foundation for an integrated experimental workflow combining high-throughput in vitro and in vivo transcription factor binding data to better understand transcription factor behavior in vivo.
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Sangwung, Panjamaporn. "Kruppel-Like Transcription Factors: Master Regulators of VascularEndothelium." Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1499426148493334.
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Chen, Xi. "The DNA-binding specificity of forkhead transcription factors." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/the-dnabinding-specificity-of-forkhead-transcription-factors(bc02fd29-30d0-47da-9b4f-448687504463).html.
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The healthy development of a living cell requires precise spatial-temporal gene expression. The code that dictates when and where genes are expressed is stored in a pattern of specific sequence motifs, which can be recognised by transcription factors. Understanding the interaction between these DNA sequence motifs and transcription factors will help to elucidate how genomic sequences build transcriptional control networks. However, the DNA-binding specificities of ~1400 human transcription factors are largely unknown. The in vivo DNA-binding events of transcription factors involve great subtlety, because most transcription factors recognise degenerate sequence motifs and related transcription factors often prefer similar or even identical sequences. Forkhead transcription factors exemplify these challenges. To understand how members within the Forkhead transcription factor family gain their binding and functional specificities, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) to interrogate the genome-wide chromatin binding events of three Forkhead transcription factors: FOXM1, FOXO3 and FOXK2. We find that FOXM1 specifically binds to the promoters of a large array of genes whose activities peak at the G2 and M phases of the cell cycle. The canonical Forkhead consensus GTAAACA is not enriched within the FOXM1 cistrome. It gains its own specific binding events and biological functions by interacting and cooperating with the MMB complex. FOXO3 and FOXK2 are recruited to chromatin by the canonical Forkhead consensus GTAAACA, and they bind both shared and specific regions in the genome. FOXO3 mostly binds to the regions which are also bound by FOXK2, but no competitive or assisted binding between FOXO3 and FOXK2 is detected within those regions. Overall, these results help explain how individual members of the Forkhead transcription factor family gain binding specificity within the genome yet raises new questions of how functional specificity is achieved by other family members.
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Pomeranz, Karen M. "Regulation of FoxO transcription factors in breast cancer." Thesis, Imperial College London, 2008. http://hdl.handle.net/10044/1/4253.
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Breast cancer is the world's most prevalent cancer. Although several drugs and chemotherapeutic strategies have been developed to tackle breast cancer, to date most patients eventually acquire resistance to these anticancer therapies. Therefore, identifying ways to increase the efficiency of currently used chemotherapeutic drugs and the development of new drugs for breast cancer treatment is essential. One way to achieve this goal is by identifying cellular targets which play a pivotal role in tumourigenesis and tumour progression. Paclitaxel belongs to a class of naturally occurring anti microtubule agents used for the treatment of malignancies such as breast cancer. Previous work has shown that FoxO3a, a transcription factor downstream of the phosphotidylinsitol-3-kinase/Akt signalling pathway, mediates apoptosis and cell cycle arrest in breast cancer cells in response to paclitaxel treatment. In order to elucidate the significance of FoxO expression and activation in response to paclitaxel treatment and oxidative stress (which is caused by paclitaxel treatment), I investigated the regulation of FoxO in endometrial and breast cancer cells. Both paclitaxel and oxidative stress were found to upregulate FoxO expression at the protein, mRNA and gene-promoter levels. Moreover, treatment with paclitaxel and hydrogen peroxide were shown to increase FoxO3a protein stability. Paclitaxel treatment resulted in JNK mediated nuclear accumulation of FoxO3a with a corresponding reduction in Akt activity. JNK was also shown to induce FoxO3a gene-promoter activity and to phosphorylate FoxO3a at two sites. These phosphorylation events may be important in the regulation of FoxO3a stability and activity. I also investigated the function of FoxO3a, by studying the role of BTG1, a downstream target of FoxO3a. I found that BTG1 expression was induced at the gene-promoter level by FoxO3a in MCF-7 cells. The use of a BTG1 inducible MCF-7 cell line revealed that over-expression of BTG1 results in changes in the expression levels of cell cycle regulators, reduction in cell growth and accumulation of cells in the G2/M phase of the cell cycle. Taken together, these results show that FoxO expression and activity are upregulated following paclitaxel treatment and demonstrate that the PI3K/Akt/FoxO and JNK signalling pathways cross-talk at least at two levels. Furthermore, these results indicate that FoxO expression levels may serve as bio-marker for determining the effectiveness of paclitaxel treatment of breast cancer patients and that FoxOs may serve as a potential target for anti-cancer chemotherapeutic intervention.
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Bermudez, Vladimir Paredes. "Role of transcription factors in eukaryotic DNA replication /." free to MU campus, to others for purchase, 1998. http://wwwlib.umi.com/cr/mo/fullcit?p9924864.
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Ketola, Ilkka. "GATA transcription factors during testicular development and disease." Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/laa/kliin/vk/ketola/.
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Hopwood, Blair. "Towards characterisation of histone H1 gene transcription factors /." Title page, contents and summary only, 1993. http://web4.library.adelaide.edu.au/theses/09PH/09phh799.pdf.
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SALA, TEA. "Functional analysis of MYB transcription factors in Arabidopsis." Doctoral thesis, Università degli Studi di Milano, 2005. http://hdl.handle.net/2434/59749.
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MYB proteins are a class of transcription factors with a characteristic DNA-binding domain. In vertebrates MYB proteins form a small family with a central role in controlling cellular proliferation, cell cycle progression and differentiation.The information available on the function of plant MYB proteins suggested a role in plant-specific processes. The aim of Ph.D project has beeen the functional characterization of AtMYB41 and AtMYB60. AtMYB41 is not expressed in wild type plants grown in normal conditions. Its transcript is accumulated in response to drought, NaCl and PEG treatments, but not after ABA supply. The overexpression of AtMYB41 in transgenic plants results in severe growth inhibition and in the deposition of a discontinue cuticle. AtMYB60 is specifically expressed in stomata guard cells and the transcript is accumulated under conditions promoting stomatal aperture whereas its abundance is reduced by stimuli triggering stomatal closure.Loss-of-function atmyb60-1 mutation resulted in the impairment of stomatal opening and in reduced wilting during water stress.
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Cominelli, E. "PLANT TOLERANCE TO DROUGHT: MODULATION OF TRANSCRIPTION FACTORS." Doctoral thesis, Università degli Studi di Milano, 2011. http://hdl.handle.net/2434/150909.
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Water scarcity is a serious problem that will be exacerbated by global climate change. Massive quantities of water are used in agriculture, and abiotic stresses, especially drought and increased salinity, are primary causes of crop loss worldwide. Various approaches may be adopted to consume less water in agriculture, one of them being the development of plants that use less water yet maintain high yields in conditions of water scarcity. In recent years several molecular networks concerned with stress perception, signal transduction and stress responses in plants have been elucidated.
In this PhD thesis the various approaches used so far to produce transgenic plants having improved tolerance to abiotic stresses, and criteria for choosing which genes and promoters have been used to obtain successful results are discussed.
Then research results on the promoter of the Arabidopsis AtMYB60 gene, specifically expressed in guard cells and on the promoter of the Arabidopsis AtMYB41 gene, specifically expressed in response to abiotic stresses, are presented. The AtMYB60 promoter was characterised through serial deletion and mutagenesis analysis and some DOF-binding sites, fundamental cis-elements for the specific activity of this promoter in guard cells were identified. Through analysis of transegnic plants carrying the AtMYB41 promoter fused to a reporter gene specific response to drought stress was confirmed.
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Bhattarai, Arati. "The orientation of the Pyrococcus furiosus transcription factor TFB2 in the transcription initiation complex." PDXScholar, 2014. https://pdxscholar.library.pdx.edu/open_access_etds/1938.
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The hyperthermophile archaeon, Pyrococcus furiosus encodes two eukaryotic TFIIB family proteins, TFB1 and TFB2. TFB1 is very similar to TFIIB in terms of sequence homology and function, whereas TFB2 is unusual as it is missing highly conserved sequences in its N-terminal domain that are present in TFIIB and TFB1. Despite this, TFB2 is effective in transcription process, albeit with lower efficiency compared to TFB1. Other archaea also contain multiple TFBs, but unlike Pyrococcus furiosus TFB2, these multiple TFBs have higher sequence homology to each other and have similar transcription efficiencies. Photochemical cross-linking experiments have shown that the B-reader of TFB in archaea and TFIIB in eukaryotes is close to transcription start site and is very important in RNAP recruitment to promoter DNA and transcription start site selection. Thus the lack of the highly conserved B reader region in P. furiosus TFB2 presents the opportunity to further study the functional importance of this region.
In this study several amino acids in N-terminal domain of TFB2 were mutated with photoactivable unnatural amino acid p-benzoyl L- phenylalanine (pBpa) and the proximity of TFB2 relative to DNA was determined by photochemical cross-linking experiments. The results showed that TFB2 interacts with DNA near the TATA box via its C-terminal domain, and interacts with both strands of DNA near the transcription start site via its divergent B-reader and the B-linker sequences. The B-reader loop region is close to transcription start site and interacts with the transcribed strand of promoter DNA while the B-linker strand cross-links with the non-transcribed strand. Some of the amino acids in between the B-reader loop and the B-linker strand region in TFB2 are seen to cross-link both the transcribed and the non-transcribed strand. Thus, despite the absence of strong homology to conserved B-reader and B-linker sequences, TFB2 is likely to interact with DNA in the transcription bubble and facilitate in transcription initiation.