The brain is a highly adaptable organ that is capable of converting sensory information into changes in neuronal function. This plasticity allows behavior to be accommodated to the environment, providing an important evolutionary advantage. Neurons convert environmental stimuli into long-lasting changes in their physiology in part through the synaptic activity-regulated transcription of new gene products. Since the neurotransmitter-dependent regulation of Fos transcription was first discovered nearly 25 years ago, a wealth of studies have enriched our understanding of the molecular pathways that mediate activity-regulated changes in gene transcription. These findings show that a broad range of signaling pathways and transcriptional regulators can be engaged by neuronal activity to sculpt complex programs of stimulus-regulated gene transcription. However, the shear scope of the transcriptional pathways engaged by neuronal activity raises the question of how specificity in the nature of the transcriptional response is achieved in order to encode physiologically relevant responses to divergent stimuli. Here we summarize the general paradigms by which neuronal activity regulates transcription while focusing on the molecular mechanisms that confer differential stimulus-, cell-type-, and developmental-specificity upon activity-regulated programs of neuronal gene transcription. In addition, we preview some of the new technologies that will advance our future understanding of the mechanisms and consequences of activity-regulated gene transcription in the brain. / Dissertation

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Le développement et l'homéostasie des os requièrent l'orchestration spatio-temporelle d'un grand nombre de signaux moléculaires. Ces signaux entraînent l'activation ou l'inhibition de différents facteurs de transcription, lesquels sont en mesure de contrôler la prolifération et la différenciation des ostéoblastes et des chondrocytes. L'intégrité de ces différents mécanismes se doit d'être maintenu tout au long de la vie. Ainsi, une anomalie dans l'un de ces mécanismes conduit à l'apparition de pathologies osseuses et métaboliques telles qu’une hypophosphatémie, l'ostéoporose ou l'ostéoarthrite (OA). Afin d'en apprendre davantage sur la biologie osseuse, le projet décrit dans cette thèse a pour objectif de caractériser de nouveaux mécanismes de régulation transcriptionnelle pour deux gènes importants dans le développement des os et le maintien de leur intégrité. Il s’agit du Paired-like Homeodomain Transcription Factor 1 (PITX1) et du Phosphate-regulating gene with homology to endopeptidase on the X chromosome (PHEX). Le premier mécanisme présenté dans cette thèse concerne la régulation transcriptionnelle du gène PITX1, un facteur de transcription à homéodomaine nécessaire, notamment, au développement des os des membres inférieurs et au maintien de l'intégrité du cartilage articulaire chez l'adulte. Ainsi, dans les chondrocytes articulaires, on note que l'expression de PITX1 est assurée par le recrutement du facteur de transcription E2F1 à deux éléments de réponse présents dans la région proximale du promoteur de PITX1. Aussi, dans les chondrocytes articulaires de patients souffrant d'OA, dans lesquels l'expression de PITX1 est fortement diminuée, un mécanisme de répression transcriptionnelle, lequel implique la protéine multifonctionnelle Prohibitin (PHB1), semble être activé. En effet, dans ces chondroytes, on note une forte accumulation nucléaire de PHB1 comparativement aux chondrocytes articulaires de sujets sains. Le second mécanisme présenté dans cette thèse concerne la répression transcriptionnelle de PHEX, la peptidase mutée dans le syndrome d'hypophosphatémie lié au chromosome X (X-Linked Hypophosphatemia, XLH), lequel se caractérise par une hypophosphatémie et une ostéomalacie. Le traitement d'ostéoblastes à la Parathyroid hormone-related protein (PTHrP) permet d’observer la répression de PHEX. Afin de caractériser le mécanisme responsable de cette répression, des expériences de gènes rapporteurs ont révélé la présence de deux éléments de réponse pour le répresseur transcriptionnel E4BP4 dans le promoteur de PHEX. La suppression de l'expression d'E4BP4 par l'utilisation d'ARN d'interférence a permis de valider que ce facteur de transcription est responsable de la répression de PHEX suite au traitement d'ostéoblastes à la PTHrP. En somme ces nouveaux mécanismes de régulation transcriptionnelle permettent de mieux comprendre la régulation de l'expression de PITX1 et de PHEX. Aussi, cette nouvelle implication de PHB1 dans la pathogenèse de l'OA offre de nouvelles possibilités de traitement et pourrait servir pour le diagnostic précoce de cette pathologie. Enfin, la caractérisation d'E4BP4 en tant que médiateur pour la répression de PHEX par la PTHrP suggère que ce répresseur transcriptionnel pourrait être impliqué dans le contrôle de la minéralisation des os et des niveaux de phosphate sanguin. / Bone development and homeostasis need a large amount of molecular signals to be finely regulated in time and space. These signals lead to the activation or to the inhibition of different transcription factors, which are implicated in the control of osteoblast and chondrocyte proliferation and differentiation. The integrity of these mechanisms is required in order to have a healthy life. Indeed, if one of these mechanisms is dysfunctional, different diseases could develop such as hypophosphatemia, osteoporosis and osteoarthritis (OA). In order to contribute to the comprehension of bone biology, the present thesis describes new mechanisms for the transcriptional regulation of two genes implicated in bone development and regulation: PITX1 (Paired-like Homeodomain Transcription Factor 1) and PHEX (Phosphate-regulating gene with homology to endopeptidase on the X chromosome). The first mechanism described in this thesis relates to the transcriptional regulation of PITX1, a gene that encodes for a member of the homeobox family of transcription factors. PITX1 is required in bone development of inferior members and in the maintenance of the articular cartilage integrity in adults. Thereby, we showed that in articular chondrocytes, the expression of PITX1 is activated after the transcription factor E2F1 was recruited at two response elements in the proximal region of its promoter. Moreover, in articular chondrocytes from OA patients, we observed that the expression of PITX1 is strongly decreased. We proposed that the mechanism responsible for this repression requires the multitask protein Prohibitin (PHB1), which is strongly accumulated in OA chondrocyte nuclei, but not in chondrocyte nuclei from healthy individuals. The second mechanism described in this thesis reports a transcriptional mechanism by which PHEX, the gene that encodes for the peptidase mutated in the syndrome X-Linked Hypophosphatemia (XLH)and characterized by hypophosphatemia and osteomalecia, is repressed. We showed that the treatment of osteoblasts with the Parathyroid hormone-related protein (PTHrP) induced a decrease in PHEX expression. In order to characterize the mechanism responsible for this repression, we performed gene reporter experiments and identified two response elements for the transcription factor E4BP4 in the PHEX promoter. The downregulation of E4BP4 by siRNA led to the validation that this repressor decreased the expression of PHEX in osteoblasts after their treatment with PTHrP. In conclusion, the new transcriptional mechanisms presented in this thesis allow a better understanding of PITX1 and PHEX expression. Moreover, the potential role of PHB1 in the establishment of OA presents many interesting possibilities regarding the treatment and diagnosis of this disease. Finally, the characterization of E4BP4 as a mediator of PHEX repression by the PTHrP suggests that E4BP4 could be implicated in the control of bone mineralization and phosphate levels in the blood.

Niemann-Pick disease type C (NPC) is a rare, severe disease with autosomal recessive inheritance. Disease is caused by pathogenic mutations located in genes NPC1/NPC2. These genes encode lysosomal non enzymatic NPC1/NPC2 proteins that are part of lipid transport. As a result of malfunction of these proteins intracellular accumulation of lipids occurs, in particular free cholesterol and glycolipids. Causal therapy is currently still unsatisfactory therefore new therapies are evolved. However these therapies depend on whether the patient cells contain at least residual amount of transcript NPC1 gene. In a group of patiens, for which a fibroblast culture was available, I analyzed the effect of pathogenic mutations on the expression level of the transcript. Results showed that for all pathogenic mutations transcript level is low, but detectable. Moreover, I characterized the structure of the NPC1 gene promoter. By sequence analysis I found polymorphisms rs8099071, rs28403610, rs2981422, rs1652354, rs1788774, rs1788772 in promoter. On the basis of the composition of polymorphisms in individual patiens, I estimate six different haplotypes. I performed mutation analysis in DNA of recently diagnosed patient. I found only one pathogenic mutation p.I1061T (c.3182T> C) in the NPC1 gene. Therefore I tested...

Das translationell kotrollierte Tumorprotein (TCTP) ist ein bei Eukaryonten vorkommendes hochkonserviertes Protein, das eine Rolle bei der Pathogenese allergischer Erkrankungen spielt. Bei atopischen Kindern vermittelt es eine IgE abhängige Histaminfreisetzung aus basophilen Granulozyten. Die zugrundeliegenden Mechanismen sind jedoch unklar. TCTP hat die Eigenschaft, an das Tubulin des Zytoskeletts der Zelle zu binden und besitzt eine hohe Affinität für Kalzium. Seine Synthese wird auf dem transkriptionellen und translationellen Niveau reguliert. Eine früher angenommene spezifische Funktion in Tumorzellen konnte nicht bestätigt werden. Das für TCTP kodierende Gen wird als TPT1 bezeichnet. Um die molekulare Basis für die Kontrolle der Synthese des TCTP zu verstehen, wurden in dieser Arbeit Struktur und Funktion des TPT1-Gens bei Mensch und Kaninchen untersucht. Erstmalig wurde die vollständige Struktur eines Säuger-TPT1-Gens durch Klonierung und Sequenzierung aufgeklärt und die funktionelle Rolle des Promotors analysiert. Das 3,8 kb große Kaninchengen wird durch fünf Introns unterbrochen, und kodiert für zwei mRNAs von 843 und 1163 nt, die sich in der Länge der 3' untranslatierten Region unterscheiden. Sie entstehen durch alternative Polyadenylierung. Vom Human-Gen wurden genomische Rekombinanten isoliert und seine vorläufige Struktur ermittelt. Es besitzt eine identische Intron/Exon Architektur und unterscheidet sich nur geringfügig in der Länge der Introns. Auch bei der Expression des Human-Gens entstehen zwei mRNAs. Hybridisierungsexperimente mit RNA aus 10 Kaninchen- und 50 Human-Geweben zeigten, daß beide TCTP mRNAs in allen untersuchten Geweben in ähnlichem Verhältnis zueinander exprimiert werden. Die Gesamtkonzentrationen der TCTP- mRNAs unterschied sich jedoch in verschiedenen Gewebegruppen bis zum Faktor 100. Dies deutet auf eine ausgeprägte Regulation der gewebsspezifischen Transkription hin. Die Promotorstrukturen von 1,2 kb 5'-flankierender Sequenzen des Kaninchen- Gens wurden mit Computerprogrammen auf Bindungsstellen für Transkriptionsfaktoren analysiert. Für funktionelle Aussagen wurden Promotorfragmente mit dem Chloramphenicol-Acetyltransferase-Gen (cat) gekoppelt und die Promotoraktivität durch Bestimmung der CAT-Enzymaktivität nach Zelltransfektionen ermittelt. Ein minimaler Promotor von 66 bp Länge, der eine TATA-Box enthält, konnte eingegrenzt werden. Die maximale Promotoraktivität, die 90% im Vergleich zum starken Thymidinkinase-Promotor betrug, war mit einem 290 bp langem Fragment assoziiert und enthielt eine SP-1, zwei AP-1/CREB und zwei ETS Bindungsstellen. Diese Konstellation ist ein häufiges Merkmal von Genen, die wie das TPT1-Gen durch Phorbolester und Lipopolysaccharide induzierbar sind. Im Sequenzbereich bis -160 sind die Promotoren des Human- und des Kaninchen-Gens sehr ähnlich (89% Homologie), alle Bindungsorte für Transkriptionsfaktoren sind hier konserviert. Weiterhin wurde im Kaninchengenom eine Vielzahl von prozessierten TPT1- Pseudogenen.gefunden. Sechs von ihnen und ihre genomisch-flankierenden Integrationsorte wurden sequenziert. Sie repräsentierten beide mRNA Typen und waren zu über 99% zu den korrespondierenden mRNAs homolog. Die Leserahmen aller Pseudogene waren intakt, bei zwei Pseudogenen war die Aminosäuresequenz sogar unverändert erhalten. Die durch CAT-Assays getestete Transkriptionsaktivität der 5'flankierenden Region eines Pseudogens zeigte eine Aktivität von über 15% gegenüber dem authentischen TPT1-Promotor. Dies ist ein Indiz für eine mögliche Expression von TPT1 Pseudogenen in vivo. / The translationally controlled tumor protein (TCTP) is a conserved eukaryotic protein, which is involved in the pathogenesis of allergic diseases. In atopic children it has been reported to mediate histamine release from basophilic leukocytes in an IgE dependent way. The underlying mechanism, however, is unknown. TCTP is characterized by an efficient binding to tubulin of cytoskeletal structures and by a high calcium affinity. Its synthesis is regulated at the transcriptional and translational level. A specific function in tumor cells, which was assumed initially, could not be confirmed. The gene coding for TCTP is called TPT1. To understand the molecular basis for the control of TCTP expression structure and function of the human and rabbit TPT1 genes were investigated including their promoter regions. The first mammalian TPT1 gene (rabbit) was cloned and sequenced. It consists of 3.8 kb and is interrupted by five introns. Two mRNAs of 843 and 1163 nt length are transcribed differing in their 3'untranslated regions. They are generated by alternative polyadenylation. Furthermore genomic recombinants were isolated containing the human TPT1 gene and a preliminary structure of the gene was established. The human gene has the same intron/exon architecture as the rabbit gene just differing in the length of its introns. Human multi-tissue dotblots revealed an identical transcription pattern for both mRNAs. The concentration of the TCTP mRNAs differed up to the factor 100 between different tissues, indicating distinct tissue specificity in transcriptional control. 1.2 kb 5'flanking promoter structures were analyzed for transcription factor binding sites. For functional studies TPT1 promoter fragments were fused to the chloramphenicol acetyltransferase (CAT) reportergene and assayed by cell transfection and CAT enzyme activity. A basic promoter of 66 bp length containing a TATA box could be defined. Maximal promoter activity of 90% compared to the strong thymidine kinase promoter was associated with a fragment of 290 bp containing a SP-1, two AP-1/CREB and two ETS binding sites. This is a common feature of genes like TPT1, which are inducible by phorbolesters and lipopolysaccharides. Furthermore, numerous processed TPT1 pseudogenes were found spread through the rabbit genome. Six pseudogenes and their flanking genomic integration sites were sequenced. They represented both mRNA types and were at least 99% homologous to the corresponding mRNAs. In all pseudogenes the open reading frames were retained and in two of them the original amino acid sequence was even conserved completely. The 5'flanking region of one pseudogene was tested for transcriptional activity by CAT assays and revealed an activity of about 15% of the authentical TPT1 promoter. This could suggest a possible expression of TPT1 pseudogenes in vivo.

<p>Prostate cancer is one leading cause of cancer-related death among men in Western countries. The standard therapies for localized prostate cancer include radical prostatectomy and radiation therapy. Such measures are relatively effective in the short term, but many patients ultimately relapse. These patients may benefit from a combination of standard therapy and oncolytic virus therapy. My work aimed to develop viruses for this purpose.</p><p>TARP is a protein that in males is specifically expressed in prostate epithelial and cancer cells. In my thesis, I characterized the TARP promoter and showed that TARP expression is regulated at the transcriptional level by testosterone through binding of the androgen receptor in the proximal TARP promoter. I further developed TARP promoter-based regulatory sequences for prostate-specific gene expression. A sequence comprising a PSA enhancer, a PSMA enhancer and the TARP promoter was constructed and designated PPT. An adenoviral vector containing the PPT sequence shielded from transcriptional interference by an H19 insulator showed high prostate-specific transcriptional activity in human cells both in the presence and absence of testosterone. However, in experimental murine prostate cancer the PPT sequence is not active. Therefore, a two-step transcriptional amplification (TSTA) system was used together with the PPT sequence to develop an adenovirus that confers prostate-specific transgene expression also in murine cells.</p><p>I constructed a conditionally replicating adenovirus where the E1A gene expression is controlled by an H19 insulator-shielded PPT regulatory sequence, Ad[I/PPT-E1A]. This virus exhibited absolute prostate specificity in terms of E1A expression, viral replication and cytolysis <i>in vitro</i> and <i>in vivo</i>. Importantly, our virus is active both in the presence and absence of testosterone, which may prove beneficial for patients treated by hormonal withdrawal. </p><p>Hopefully, my work will improve existing gene therapy strategies for prostate cancer and in the long term improve the prognosis for patients with prostate cancer.</p>

Prostate cancer is one leading cause of cancer-related death among men in Western countries. The standard therapies for localized prostate cancer include radical prostatectomy and radiation therapy. Such measures are relatively effective in the short term, but many patients ultimately relapse. These patients may benefit from a combination of standard therapy and oncolytic virus therapy. My work aimed to develop viruses for this purpose. TARP is a protein that in males is specifically expressed in prostate epithelial and cancer cells. In my thesis, I characterized the TARP promoter and showed that TARP expression is regulated at the transcriptional level by testosterone through binding of the androgen receptor in the proximal TARP promoter. I further developed TARP promoter-based regulatory sequences for prostate-specific gene expression. A sequence comprising a PSA enhancer, a PSMA enhancer and the TARP promoter was constructed and designated PPT. An adenoviral vector containing the PPT sequence shielded from transcriptional interference by an H19 insulator showed high prostate-specific transcriptional activity in human cells both in the presence and absence of testosterone. However, in experimental murine prostate cancer the PPT sequence is not active. Therefore, a two-step transcriptional amplification (TSTA) system was used together with the PPT sequence to develop an adenovirus that confers prostate-specific transgene expression also in murine cells. I constructed a conditionally replicating adenovirus where the E1A gene expression is controlled by an H19 insulator-shielded PPT regulatory sequence, Ad[I/PPT-E1A]. This virus exhibited absolute prostate specificity in terms of E1A expression, viral replication and cytolysis in vitro and in vivo. Importantly, our virus is active both in the presence and absence of testosterone, which may prove beneficial for patients treated by hormonal withdrawal. Hopefully, my work will improve existing gene therapy strategies for prostate cancer and in the long term improve the prognosis for patients with prostate cancer.

The first chapter will provide an introduction to the physiology, pathogenesis and biology of mycobacteria. Host-pathogen interactions, different modes of resistance of the bacteria, adaptations for survival under nutrient and oxygen depleted conditions has been discussed. This is followed by a general discussion on gene expression and regulation in the microbe. The physiology of bacteria under stresses from the view of the transcriptional regulation of specific genes has also been discussed. The scope and objective of the present study in M. smegmatis covered in the thesis has been considered at the end. The next chapter discusses the characterization of msdps promoter in vivo with the help of reporter gene assay technologies. With the advent of promoterless E. coli-mycobacterium shuttle vectors, activity assays can be easily performed to characterize unknown upstream putative promoter sequences of genes. Both the 1 kb upstream as well as a 200bp upstream region of msdps gene has been characterized by. Primer extension analysis and subsequent site directed mutagenesis studies reveal +1 transcription start site and the promoter consensus sequence for the msdps gene respectively. Next chapter comprises of the method of constructing heterologous in vitro transcription machinery in mycobacteria. It is followed by characterization of transcription initiation at two dps promoters of M. smegmatis. A novel pull-down assay has been designed which enabled us to identify the sigma factors in the reconstituted RNA polymerases to be associated with the respective dps promoters and to compare the regulation of the two genes at transcription level. Further characterization through single round in vitro transcription at mycobacterial promoters has been attempted. The following two chapters provide some newer insights into the structure-function relationship of the first Dps molecule, MsDps (MsDps1) with respect to its DNA binding activity. The DNA binding activity is associated with the higher oligomeric form only. With the help of time resolved anisotropy and Förster Resonance Energy Transfer (FRET) experiments, we have monitored the nature of Dps dodecamer-DNA complex and mapped the distance between the N and C169 position in the absence and the presence of DNA. A new computational programme, Maximum Entropy Method (MEM) has been applied successfully to analyze data obtained from phase-modulation (Phi-M) lifetime experiments in order to get distribution of lifetime. In the last chapter a new method is adopted to predict amino acids important for stabilizing the interface in a trimeric structure. Subsequently, single and double amino acid mutants of the native MsDps protein has been constructed through site directed mutagenesis and are scored for the ability of the mutants to oligomerize under conditions similar to that of the native protein. This helped us to propose a hypothetical model of the overall mechanism of the protein oligomerization process in solution.