Les tumeurs de la vessie sont le quatrième cancer en terme de fréquence chez l’homme dans les pays industrialisés. Elles peuvent schématiquement être séparées en deux sous-groupes principaux : les tumeurs basales, peu différenciées, et les tumeurs luminales, différenciées. PPARγ est un récepteur nucléaire fortement exprimé dans ce second groupe, qui agit en hétérodimère avec un co-récepteur partenaire, RXRα, et possède un rôle essentiel dans la différenciation des cellules de l’urothélium normal. Récemment, un rôle protumorigénique de PPARγ a été mis en évidence dans les tumeurs luminales de vessie, où son activité est augmentée par le biais d’amplifications de PPARγ, ainsi que des mutations activatrices de son partenaire, RXRα. Le premier axe de mon projet a consisté à mieux caractériser ce rôle protumorigénique de PPARγ. J’ai d’abord participé à la mise en évidence de mutations récurrentes activatrices de PPARγ dans les tumeurs luminales de la vessie renforçant le rôle protumorigénique du récepteur dans ces tumeurs. J’ai ensuite cherché à identifier les gènes cibles de l’hétérodimère PPARγ/RXRα pouvant médier cet effet protumorigénique. Grâce à des analyses transcriptomiques après extinction de l’expression PPARγ ou de RXRα et des expériences de ChIP-sequencing de PPARγ et RXRα, j’ai pu identifier 30 gènes candidats. L’étude de l’implication de ces gènes dans la progression tumorale des tumeurs luminales présentant des altérations de la voie PPARγ/RXRα est actuellement en cours. Parallèlement à ce rôle protumorigénique dans les tumeurs luminales, des résultats suggéraient que ce gène pourrait posséder un rôle suppresseur de tumeurs dans le sous-groupe basal. La deuxième partie de mon projet a consisté à explorer cette hypothèse. J’ai pu montrer que des délétions hétérozygotes de PPARγ sont associées à ce sous-groupe de tumeurs basales, qui présente également une diminution globale de l’expression de PPARγ. De plus, parmi les mutations non-récurrentes de PPARγ identifiées dans ces tumeurs, certaines sont des mutations inactivatrices, capables d’inhiber l’activité transcriptomique de l’hétérodimère PPARγ/RXRα en favorisant la fixation de co-répresseurs de l’hétérodimère. J’ai également pu montrer un rôle anti-tumoral de PPARG dans les tumeurs basales puisque l’expression de PPARγ dans des lignées cellulaires basales à la suite de leur transfection avec un plasmide codant pour PPARγ est capable d’inhiber leur viabilité. Ce projet a ainsi permis de mettre en évidence un rôle dual de PPARγ dans les tumeurs de vessie, avec un rôle protumorigénique dans les tumeurs luminales, où il est suractivé par des amplifications et des mutations activatrices, et un rôle suppresseur de tumeurs dans les tumeurs basales, où il est réprimé par des délétions et de mutations inactivatrices. / Bladder tumors are the fourth cancer in terms of frequency in men, in industrialized countries. Bladder cancers can be divided into two main subgroups: undifferentiated basal tumors and differentiated luminal tumors. The nuclear receptor PPARγ, which is highly expressed in the second subgroup, forms a heterodimer with its partner, the nuclear receptor RXRα, and plays a key role in normal urothelial differentiation. A protumorigenic role of PPARγ has been established in luminal bladder cancer, with an increased activity through PPARγ genomic amplification or activating mutations of its partner, RXRα. The first part of my project aimed to better characterize this protumorigenic effect. I first participated in the identification of recurrent activating mutations of PPARγ in the luminal subgroup, enhancing its protumorigenic role in those tumors. Then, I tried to identify the PPARγ/RXRα heterodimer target genes that drive its protumorigenic role. By analyzing transcriptomic data following down regulation of PPARγ and RXRα, as well as ChIP-sequencing data for each of them, I identified 30 candidate target genes. The implication of the candidate genes in tumor progression of luminal cancer carrying PPARγ/RXRα pathway alteration is in progress. As opposed to its protumorigenic role in luminal tumors, some results suggested that PPARγ could play a tumor suppressor role in the basal subgroup. The second part of my project explored this hypothesis. I characterized PPARγ deletions associated with the basal subgroup, which presents a global PPARγ downregulation. Moreover, some of the non-recurrent mutations identified in this subgroup are inactivating mutations, able to inhibit the transcriptomic activity of the PPARγ/RXRα heterodimer, by an enhanced affinity of the heterodimer for co-repressors. I also showed an antitumor effect of PPARγ in basal tumors: its expression in basal bladder cell lines after transfection with a plasmid coding for PPARγ was able to inhibit cell viability. This project highlighted the dual role of PPARγ in bladder tumors, with a protumorigenic effect in luminal tumors through amplifications and activating mutations, and a tumor suppressor effect in basal tumors through deletions and inactivating mutations.

Charles University, Faculty of Pharmacy in Hradec Králové Department of Pharmacology and Toxicology Candidate Mgr. Jan Dušek Supervisor Prof. PharmDr. Petr Pávek, Ph.D. Title of Doctoral Thesis Development of novel Constitutive androstane receptor (CAR) ligands Constitutive androstane receptor is nowadays known as the established nuclear receptor that regulates the expression of several key cytochrome P450 enzymes, predominantly CYP3A4 and CYP2B6. Recently it has been shown that CAR has also essential role in the regulation of endogenous metabolism of glucose, lipids, cholesterole or bile acids. Simultaneously, this receptor is considered to have proliferative effect on human hepatocytes and protective effects against toxic and dietary damage of liver parenchyme. Given the possible therapeutic utilization of CAR, its therapeutic options are being intensively studied. Unfortunately, currently known ligands of human or mouse CAR are either poorly selective or indirect. The aim of my doctoral thesis was to find new ligands of mouse and human CAR, that would enable more detailed study of the receptor.

Transcriptional regulation of gene expression in eukaryotes has evolved over millions of years. The regulatory pathways of nuclear receptors represent an evolutionarily ancient, but conserved mechanism with associated accessory proteins, many of them forming a functional nexus known as the Mediator complex involved in transcription. Despite the versatility of the pathway, e.g. through the adoption of new regulatory functions in phylogenetically more recent Metazoa, we hypothesise that the intrinsic potential of the NR-Mediator axis to directly translate a stimulus to a biological response is conserved across species, and additional regulation could also be achieved through secondary functions of its essential members. To support the hypothesis, we assessed the ligand-binding capability of retinoic X receptor in Trichoplax adhaerens and provided evidence to support the concept that this capability was already present at the base of metazoan evolution. With regards to the potential secondary functions, we took inspiration from previous research and identified the Mediator subunit 28 (MED28) as the only known member having documented nuclear and cytoplasmic dual roles, and thus possessing the potential to transmit signals from the cellular structural states to the nucleus. Due to the lack of...

Le récepteur X des farnésoïdes (FXR) fait partie de la superfamille des récepteurs nucléaires et agit comme un facteur de transcription suite à la liaison d’un ligand spécifique. Le récepteur FXR, activé par les acides biliaires, joue un rôle essentiel dans le métabolisme des lipides et du glucose en plus de réguler l’homéostasie des acides biliaires. Notre laboratoire a récemment mis en évidence une nouvelle voie de régulation du récepteur PPARγ en réponse au récepteur de la ghréline. En effet, la ghréline induit l’activation transcriptionnelle de PPARγ via une cascade de signalisation impliquant les kinases Erk1/2 et Akt, supportant un rôle périphérique de la ghréline dans les pathologies associées au syndrome métabolique. Il est de plus en plus reconnu que la cascade métabolique impliquant PPARγ fait également intervenir un autre récepteur nucléaire, FXR. Dans ce travail, nous montrons que la ghréline induit l’activation transcriptionnelle de FXR de manière dose-dépendante et induit également la phosphorylation du récepteur sur ses résidus sérine. En utilisant des constructions tronquées ABC et CDEF de FXR, nous avons démontré que la ghréline régule l’activité de FXR via les domaines d’activation AF-1 et AF-2. L’effet de la ghréline et du ligand sélectif GW4064 sur l’induction de FXR est additif. De plus, nous avons démontré que FXR est la cible d’une autre modification post-traductionnelle, soit la sumoylation. En effet, FXR est un substrat cellulaire des protéines SUMO-1 et SUMO-3 et la sumoylation du récepteur est ligand-indépendante. SUMO-1 et SUMO-3 induisent l’activation transcriptionnelle de FXR de façon dose-dépendante. Nos résultats indiquent que la lysine 122 est le site prédominant de sumoylation par SUMO-1, quoiqu’un mécanisme de coopération semble exister entre les différents sites de sumoylation de FXR. Avec son rôle émergeant dans plusieurs voies du métabolisme lipidique, l’identification de modulateurs de FXR s’avère être une approche fort prometteuse pour faire face à plusieurs pathologies associées au syndrome métabolique et au diabète de type 2. / The farnesoid X receptor (FXR) is a ligand-activated transcription factor within the nuclear receptor superfamily. FXR is activated by bile acids and plays a crucial role in the regulation of glucose and lipid metabolism and in bile acid homeostasis. Our group has recently identified the contribution of the ghrelin receptor in the regulation of the nuclear receptor PPARγ. Indeed, ghrelin triggers transcriptional activation of PPARγ through a concerted signaling cascade involving Erk1/2 and Akt kinases. These results support the peripheral actions of ghrelin in diseases associated with the metabolic syndrome. It is recognized that there is interplay between PPARγ metabolic cascade and FXR. Here, we demonstrate that ghrelin promotes FXR transcriptional activity in a dose-dependent manner and also promotes its phosphorylation on serine residues. By using truncated ABC and CDEF constructs of FXR, we found that ghrelin induces FXR activity through the AF-1 and AF-2 activation domains. The ghrelin-induced FXR activity is additive to the induction by the selective agonist GW4064. Also, we demonstrate that FXR is the target of sumoylation, another post-translational modification. In particular, FXR is modified by SUMO-1 and SUMO-3 in a ligand-independent manner. SUMO-1 and SUMO-3 promote dose-dependent transcriptional activity of FXR. Our results show that lysine 122 is the prevalent site of sumoylation by SUMO-1, though a compensation mechanism seems to exist between the various sumoylation sites of FXR. With its emerging role in several metabolic cascades, identification of FXR modulators represents a promising approach for the treatment of the metabolic syndrome and type 2 diabetes.

Les récepteurs nucléaires (RN) sont des facteurs de transcription ligand dépendants qui contrôlent une grande variété de processus biologiques de la physiologie humaine, ce qui a fait d'eux des cibles pharmacologiques privilégiées pour de nombreuses maladies. L'un de ces récepteurs, le récepteur de l’œstrogène alpha (ERα), peut activer la prolifération cellulaire dans certaines sections de l'épithélium mammaire tandis qu’un autre, le récepteur de l'acide rétinoïque alpha (RARα), peut provoquer un arrêt de la croissance et la différenciation cellulaire. La signalisation de ces deux récepteurs peut être altérée dans le cancer du sein, contribuant à la tumorigénèse mammaire. L’activité d’ERα peut être bloquée par les anti-oestrogènes (AE) pour inhiber la prolifération des cellules tumorales mammaires. Par contre, l’activation des voies de RARα avec des rétinoïdes dans un contexte clinique a rencontré peu de succès. Ceci pourrait résulter du manque de spécificité des ligands testés pour RARα et/ou de leur activité seulement dans certains sous-types de tumeurs mammaires. Puisque les récepteurs nucléaires forment des homo- et hétéro-dimères, nous avons cherché à développer de nouveaux essais pharmacologiques pour étudier l'activité de complexes dimériques spécifiques, leur dynamique d’association et la structure quaternaire des récepteurs des œstrogènes. Nous décrivons ici une nouvelle technique FRET, surnommée BRET avec renforcement de fluorescence par transferts combinés (BRETFect), qui permet de détecter la formation de complexes de récepteurs nucléaires ternaires. Le BRETFect peut suivre l'activation des hétérodimères ERα-ERβ et met en évidence un mécanisme allostérique d'activation que chaque récepteur exerce sur son partenaire de dimérisation. L'utilisation de BRETFect en combinaison avec le PCA nous a permis d'observer la formation de multimères d’ERα fonctionnels dans des cellules vivantes pour la première fois. La formation de multimères est favorisée par les AE induisant la dégradation du récepteur des oestrogènes, ce qui pourrait contribuer à leurs propriétés spécifiques. Ces essais de BRET apportent une nette amélioration par rapport aux tests de vecteurs rapporteur luciférase classique, en fournissant des informations spécifiques aux récepteurs en temps réel sans aucune interférence par d'autres processus tels que la transcription et de la traduction. L'utilisation de ces tests nous a permis de caractériser les propriétés de modulation de l’activité des récepteurs nucléaires d’une nouvelle classe de molécules hybrides qui peuvent à la fois lier ERa ou RAR et inhiber les HDACs, conduisant au développement de nouvelles molécules prometteuses bifonctionnelles telles que la molécule hybride RAR-agoniste/HDACi TTNN-HA. / Nuclear receptors (NRs) are ligand-dependent transcription factors that control a wide variety of biological processes in human physiology, which has made them preferred pharmacological targets for many diseases. One such receptor, the estrogen receptor alpha (ERα), can activate cell proliferation in some sections of the mammary epithelium while another, the retinoic acid receptor alpha (RARα), can cause growth arrest and cellular differentiation. Signalling by these receptors can be altered in breast cancer, contributing to tumorigenesis. ERα can be blocked by antiestrogens (AEs) in the clinical setting to inhibit tumor cell proliferation. However, attempts to activate the RARα pathway with retinoids have not proven beneficial in clinical trials. This may result from the lack of specificity of the tested ligands for RARa and/or from their activity only in a subset of breast tumors. Since nuclear receptors form homo- and heterodimers, we sought to develop novel pharmacological assays to study the activity of specific receptor-dimer complexes, their dynamics and quaternary structure. We report here a new FRET technique dubbed BRET with fluorescence enhanced by combined transfers (BRETFect) that can detect the formation of ternary nuclear receptor complexes. BRETFect can monitor the activation of ERα-ERβ heterodimers and highlights an allosteric mechanism of activation that each receptor exerts on its dimer partner. Use of BRETFect in combination with PCA-BRET has allowed us to observe the formation of functional ERα multimers in live cells for the first time. The formation of multimers is favored by AEs which induce receptor degradation, and may underlie their specific properties. These assays are a net improvement over the classical luciferase-reporter experiment as they deliver real-time receptor specific information with no interference by other process such as transcription and translation. Using these BRET assays we developed a new class of NR hybrid ligands that can modulate ER or RAR activity and inhibit HDACs. This has allowed for the development of promising new bifunctional molecules such as the RAR-agonist/HDACi hybrid molecule TTNN-HA. In conclusion, the work presented here brings new insight in NR dynamics and quaternary structure and offers novel tools to study their mechanism of action or design new modulators of NR activity such as hybrid AE-HDACis and Retinoid-HDACis.

Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Lenka Linhartová Supervisor: Prof. PharmDr. Petr Pávek, Ph.D. Title of diploma thesis: Molecular mechanisms of intractions - interactions of constitutive androstane receptor with selected stilbene compounds Constitutive androstane receptor (CAR), member of nuclear receptors family, is a major regulator of gene expression of phase I and II enzymes metabolizing endobiotics and xenobiotics. Changes in its activity can lead to pharmacokinetic drug interactions, ineffective treatment or higher toxicity of drugs simultaneously administered with CAR ligands. Recently another effects of this receptor, especially in homeostasis of bile acids, lipids and glucose have been discovered and CAR is now considered as a potential drug target for the treatment of metabolic diseases. Stilbenes represent a small group of plant polyphenols with typical 1,2-diphenylethylene nucleus. The most famous member is resveratrol, which has attracted great attention thanks to its antioxidant, anti-inflammatory, antiproliferative and cardioprotective effects. Others stilbene compounds such as pterostilben, piceatannol or pinosylvin have shown similar health beneficial effects as well. The aim of this diploma thesis was...

Les acides gras polyinsaturés à longue chaîne (AGPI-LC) de la série n-3 jouent un rôle essentiel dans le fonctionnement cérébral, notamment dans le maintien des processus de plasticité synaptique et de mémoire au cours du vieillissement. Il est maintenant bien admis que ces acides gras peuvent moduler la transcription de gènes impliqués dans les processus de plasticité synaptique sous-tendant les performances mnésiques via leur liaison à des récepteurs nucléaires tels que les PPAR (peroxisome proliferator-activated receptor) et les RXR (retinoid X receptor). Les RXR sont les partenaires communs d’hétérodimérisation de nombreux autres récepteurs, dont le récepteur nucléaire de l’acide rétinoïque (AR), RAR (retinoic acid receptor), métabolite actif de la vitamine A. Ainsi, les RXR jouent un rôle majeur dans la régulation des voies de signalisation des AGPI n-3 et des rétinoïdes.Dans ce contexte, l’objectif de notre travail était de mieux comprendre les mécanismes mis en jeu dans l’action des AGPI-LC n-3 sur les processus neurobiologiques qui sous-tendent les performances mnésiques au cours du vieillissement, notamment en abordant de manière spécifique les mécanismes mis en jeu dans les interactions entre les voies de signalisation des AGPI-LC n-3 et des rétinoïdes. Les approches expérimentales mises en place ont consisté notamment à évaluer chez le rat âgé les effets de supplémentations nutritionnelles en AGPI-LC n-3 et/ou vitamine A sur les performances de mémoire, ainsi que l’action du DHA administré seul sur différents types de mémoire dépendants de l’hippocampe.Nos principaux résultats montrent une altération du métabolisme des acides gras et de la vitamine A au cours du vieillissement. Ces changements métaboliques sont associés à une hypoexpression des voies de signalisation des AGPI n-3 et des rétinoïdes, accompagnée de déficits mnésiques. Nous montrons par ailleurs un effet synergique d’une supplémentation nutritionnelle en AGPI-LC n-3 et en vitamine A sur le maintien des performances de mémoire chez l’animal âgé. De plus, cette supplémentation permet de prévenir, dans l’hippocampe, les changements de composition en AGPI n-3 ainsi que l’hypoexpression des ARNm de RXRγ et de kinases régulées par l’AR et les AGPI n-3.Ces résultats plaident en faveur d’une action synergique des AGPI-LC n-3 et de la vitamine A sur le maintien des performances mnésiques au cours du vieillissement, via une action combinée sur leurs voies de signalisation, lesquelles participeraient ainsi au maintien de certains processus de plasticité synaptique sous-tendant la mémoire et qui se trouvent être altérés avec l’âge. / N-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFAs) play a critical role in brain functioning, notably in the maintenance of synaptic plasticity and memory processes during aging. It is now well accepted that n-3 PUFAs can modulate transcription of genes involved in synaptic plasticity processes underlying the memory performances through binding and activating nuclear receptors such as PPARs (peroxisome proliferator-activated receptors), and RXRs (retinoid X receptors). RXRs are the common heterodimerization partner of numerous nuclear receptors, among them the retinoic acid receptor (RAR), which binds retinoic acid (RA), the active metabolite of vitamin A. Thus, RXRs play a key role in the regulation of n-3 PUFA and retinoid signaling pathways.In this context, the aim of this work was to study the mechanisms involved in the action of n-3 PUFAs on neurobiological processes underlying the memory performances during aging, and more particularly by assessing specifically the molecular mechanisms involved in interactions between n-3 PUFA and retinoid signaling pathways. For this purpose, we studied the effects of dietary supplementations in n-3 PUFAs and/or vitamin A on memory performances in aged rats. We also studied the specific effect of unesterified DHA pharmacological treatments on different hippocampal-dependent memory tasks.Our main results showed impairments in fatty acid and vitamin A metabolism during aging. These modifications were associated with an hypoexpression of n-3 PUFA and retinoid signaling pathways, and memory deficits. Furthermore, we demonstrated a synergetic effect of the joint n-3 LC-PUFA and vitamin A dietary supplementation on the maintenance of memory performances in aged rats. Moreover, in the hippocampus, this supplementation prevented the n-3 PUFA compositional changes, and also the mRNA hypoexpression of RXRγ and of several kinases regulated by RA and n-3 PUFAs which were observed during aging.These results suggest a beneficial synergetic effect of n-3 LC-PUFAs and vitamin A on the maintenance of memory performances during aging, through a combined action on their signaling pathways, which could be involved in the maintenance of synaptic plasticity processes underlying memory performances impaired during aging.

Os projetos genoma têm fornecido uma grande quantidade de informação sobre a arquitetura gênica e sobre a configuração física de suas respectivas regiões flanqueadoras (RF). Estas RF contêm informações com o potencial de auxiliar na elucidação de vários processos biológicos, como os mecanismos de expressão gênica e de sua regulação. Estes mecanismos são de extrema importância para a compreensão do correto funcionamento dos organismos e das patologias que os afetam. Uma parte significativa dos mecanismos de controle de expressão gênica atuam na fase transcricional. Na base destes mecanismos está o recrutamento de proteínas que se ligam às regiões promotoras da transcrição, as quais são segmentos específicos de DNA que podem estar localizados tanto próximos à região de início da transcrição (TSS) quanto a centenas ou até a milhares de pares de bases dela. Essas proteínas compõem a maquinaria transcricional e podem ativar ou inibir o processo de transcrição. Experimentalmente, os segmentos regulatórios podem ser identificadas utilizando métodos complexos de biologia molecular, tais como SELEX, ChiP-ChiP, ChIP-Seq, dentre outros. Uma estratégia alternativa aos métodos experimentais é a utilização de metodologias computacionais. Análises computacionais tendem a ser mais rápidas, baratas e flexíveis do que protocolos experimentais, além de poderem ser utilizadas em larga escala. Atualmente, os métodos computacionais disponíveis necessitam de informações experimentais para a definição de padrões globais de preferências de sequências de DNA para a ligação de fatores de transcrição (TFBS, em inglês transcription factor binding sites). Entretanto, esses métodos apresentam uma elevada taxa de falso positivos e, por vezes, apresentam também taxas significativas de falso negativos, além de serem limitados ao estudo de fatores de transcrição de espécies bem conhecidas, o que diminui a área de aplicação dos mesmos. Diante deste cenário, o uso de métodos computacionais que não necessitem da informação referente aos sítios de ligação, bem como os que utilizem parâmetros mais robustos de detecção dos resultados, em detrimento dos escores de pontuação provindos de alinhamentos, podem acrescentar uma sensível melhoria ao processos de predição de regiões regulatórias. Neste projeto, foi desenvolvido um novo modelo computacional (TFBSAnalyzer) para análise e identificação de TFBS em elementos regulatórios, que utiliza técnicas de modelagem molecular para a construção de complexos entre um fator de transcrição ancorado a estruturas de DNA com sequências variáveis de bases e, através de cálculos termodinâmicos de entalpia de ligação, determina uma função de pontuação baseada na energia de ligação e realiza a predição de sítios de ligação ao DNA para o fator de transcrição em análise. Esta abordagem foi testada com três fatores de transcrição como sistemas-modelo, pertencentes à família dos receptores nucleares, a saber: o receptor de estrógeno ER-alfa (Estrogen Receptor Alpha), o receptor de ácido retinoico RAR-beta (Retinoid Acid Receptor Beta) e o receptor X retinóico RXR (Retinoid X Receptor). Os modelos previstos computacionalmente foram comparados aos dados experimentais disponíveis para estes receptores nucleares, os quais apresentaram as seguintes taxas de FP/FN: 10%/0 para RAR-beta e RXR, 21%/6% para ER-alfa. Também simulamos um experimento de ChIP-seq do ER-alfa no genoma humano, cujos genes selecionados foram submetidos a uma análise de enriquecimento de fatores de transcrição curados experimentalmente, que fazem sua regulação, revelando que o receptor de estrógeno está realmente envolvido no processo. Para mostrar a aplicabilidade geral de nosso método, nós modelamos a distribuição de energia de ligação para o receptor NHR-28 isoforma a de Caenorhabditis elegans com DNA . Obtivemos distribuições de energia semelhantes àquelas encontradas para os NRs modelos, portanto seria possível aplicar o método para buscar possíveis TFBSs para este receptor no genoma de C. elegans. Os dados gerados e as metodologias desenvolvidas neste projeto devem acrescentar uma sensível melhoria aos processos de predição de regiões regulatórias e consequentemente auxiliar no entendimento dos mecanismos envolvidos no processo de expressão gênica e de sua regulação. / The genome projects have provided a lot of information about the genetic architecture, as well as on the physical configuration of their flanking regions (FR). These FR have the potential to aid in the elucidation of many biological processes, such as the mechanisms involved in gene expression and its regulation. These mechanisms are extremely important for undeerstanfind the correct functioning of organisms as well as the pathologies that affect them. A significant part of the control mechanisms of gene expression act during transcription. On the basis of this mechanisms is the recruitment of proteins that bind to promoter regions of transcription, which are specific segments of DNA that can be located either near the transcription start site or at hundreds or even thousands of base pairs away. These proteins form the transcription machinery, which can activate or inhibit the transcription process. The regulatory segments can be identified experimentally using complex methods of molecular biology, such as SELEX, ChIP-chip, ChIP-seq, among others. An alternative strategy to these experimental methods is the use of computational methodologies for predicting regulatory regions. Computational analysis tend to be faster, cheaper and more flexible than the experimental protocols, and can be used on a larger scale. Currently, the available computational methods require information previously obtained from experiments in order to define global standards of preference of DNA-Binding sequences for transcription factors (TFBS - Transcription Factor Binding Sites). However, these methods have a high rate of false positives and sometimes also have significant rates of false negatives, besides being limited to the study of transcription factors of well-known species, which decreases their application area. In this scenario, the use of computational methods that do not require previous information concerning the binding sites and use more robust parameters of results detection, instead of alignment scores, may add significant improvement to the processes of predicting regulatory regions. In this project, we developed a new computational model TFBSAnalyzer) for analysis and identification of regulatory elements using molecular modeling techniques for the construction of complexes between a transcription factor bound to specific DNA structures with variable sequences of bases and, by means of thermodynamic calculations of bond enthalpy, provides a scoring function based on the binding energy and predicts the DNA binding sites for the transcription factor in analysis. This approach was tested initially with three transcription factors as models, belonging to the nuclear receptor family, namely estrogen receptor ER-alpha (Estrogen Receptor Alpha), the retinoic acid receptor RAR-beta (Retinoid Acid Receptor Beta) and the retinoic X receptor RXR (Retinoid X Receptor). The computationally predicted models were compared to experimental data available for these nuclear receptors, and presented the following rates of FP/FN: 10%/0 for RAR-beta and RXR, 21%/6% for ER-alpha. We also simulated an experiment of ChIP-seq with ER-alpha with the human genome, where the selected genes were subjected to a transcription factor enrichment analysis, with curated information, revealing that the estrogen receptor is indeed involved in their regulation. To show that our method has a general applicability, we modeled the binding energy distribution for the NHR-28 receptor, isoform a, from Caenorhabditis elegans. The energy distributions obtained were similar to the ones obtained for the model NR, so it would be possible to use the method and search for possible TFBS in the C. elegans genome. The data generated and the methodologies developed in this project should add a significant improvement to the prediction processes of regulatory regions and, consequently, help to understand the mechanisms involved in the gene expression process and its regulation.

In marine teleosts that spawn pelagic eggs (pelagophils), the process of oocyte hydration that occurs during meiosis resumption is a key physiological process for the survival of the eggs in the ocean. Previous studies have discovered the role of a teleost-specific aquaporin water channel (Aqp1b) during fish oocyte hydration, but direct experimental evidence for the function of Aqp1b in oocytes is still lacking. In addition, the molecular regulation of the Aqp1b-mediated mechanism remains poorly understood. In this context, the main objectives of the present thesis were to investigate the evolutionary origin of aqp1ab in teleosts, to provide functional evidence of the role of Aqp1b during oocyte hydration, and to begin to dissect the molecular mechanisms involved in the transcriptional regulation of aqp1b in the oocyte of marine teleosts. By integrating the molecular phylogeny with synteny and structural analyses we show that the teleost aqp1aa and -1ab paralogs (previously annotated as aqp1a and -1b, respectively) arose by tandem duplication, and that the Aqp1ab C-terminus is the most rapidly evolving subdomain within the vertebrate aquaporin superfamily. The functional role of Aqp1ab was investigated in Atlantic halibut (Hippoglossus hippoglossus), a marine acanthomorph teleost that spawns one of the largest pelagic eggs known. Using immunological inhibition of Aqp1ab in halibut oocytes and artificial expression of the halibut paralog Aqp1aa, we demonstrate that Aqp1ab is required for full hydration of oocytes undergoing meiotic maturation. To investigate the aqp1ab transcriptional regulation in oocytes, we isolated the 5’-flanking region of the gilthead seabream (Sparus aurata) aqp1ab gene which contains regulatory cis-elements for the nuclear progestin receptor (Pgr) and SOX transcription factors. The Pgr, as well as sox3 and -8b transcripts, are co-expressed in seabream oo-gonia, whereas in primary growth oocytes, when aqp1ab mRNA and protein are synthesized, the Pgr is translocated into the nucleus. In contrast, sox9b is highly expressed in more advanced oocytes showing the depletion of aqp1ab transcripts. In the seabream, four different pgr transcript variants are expressed in primary growth ovaries which are generated by alternative pre-mRNA splicing. Seabream wild-type Pgr shows the highest transactivation response to progestins such as 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-P) and 17α,20β,21-trihydroxy-4-pregnen-3-one (17,20β,21-P), whereas two of the N-terminally truncated Pgr isoforms regulate novel nuclear and cytosolic mechanisms of dominant-negative repression of Pgr-mediated transcription. Transactivation assays on the aqp1ab promoter demonstrated that aqp1ab transcription is dependent on wild-type Pgr, with Sox3 and -8b acting synergistically, while Sox9b acts as a repressor. Incubation of primary ovarian explants in vitro with 17,20β-P, followed by chromatin immunoprecipitation, confirmed that 17,20β-P-activated Pgr enhanced aqp1ab promoter activation. The production of 17,20β-P in seabream primary growth ovaries in vivo was consistent with the expression of P450c17-II (Cyp17a2) and 20β-hydroxysteroid dehydrogenase (Cbr1), enzymes needed for progestins synthesis, in granulosa cells associated with primary growth oocytes, and with a high concentration of 17,20β-P. Incubation of primary ovarian explants with recombinant piscine follicle-stimulating hormone (rFsh) in vitro stimulated 17,20β-P synthesis, which was reduced in the presence of Cbr1 inhibitors. The rFsh-mediated production of 17,20β-P correlated with the up-regulation of cyp17a2 and cbr1 transcription, as well as of wild-type pgr mRNA and protein levels. Altogether, these data suggest that aqp1ab transcription in seabream primary growth oocytes is under Fsh regulation through the synthesis of progestins. The results of this thesis show that the Aqp1ab mediated mechanism for oocyte hy-dration is likely conserved in marine teleosts. In addition, the tight transcriptional reg-ulation of Aqp1ab during oogenesis highlights the essential physiological role of this water channel and opens new research avenues for understanding the molecular basis of egg formation in marine fish. / La hidratación de los oocitos de teleósteos marinos que producen huevos pelágicos es clave para la supervivencia de los embriones en el océano. Estudios previos han descu-bierto el papel de una acuaporina específica de teleósteos (Aqp1b) durante este proceso, pero se carece todavía de evidencias experimentales directas, así como información sobre la regulación molecular de la Aqp1ab. En la presente tesis, estudios iniciales con el fletan Atlántico (Hippoglossus hippoglossus) confirman que los parálogos aqp1aa y -1ab de teleósteos han surgido probablemente por duplicación génica en tándem, y han demostrado el papel esencial de la Aqp1ab durante la hidratación del oocito. Para investigar el control transcripcional del gen aqp1ab en los oocitos de la dorada (Sparus aurata) se ha aislado su región promotora, la cual contiene elementos cis-reguladores de unión al receptor nuclear de progestinas (Pgr), como la 17α,20β-dihidroxi-4-pregnen-3-ona (17,20β-P), y factores de transcripción Sox. Estudios de localización subcelular indican que el Pgr aparece en el citoplasma de las oogonias, así como en el núcleo de oocitos en crecimiento primario (pre-vitelogénicos) coincidiendo con la activación de la expresión de aqp1ab. En este estadio también se expresan cuatro isoformas diferentes del Pgr, dos de las cuales pueden inhibir la transcripción mediada por el Pgr de forma dominante negativa. Las oogonias también expresan sox3 y -8b, mientras que el sox9b aparece en el estadio de alveolo cortical, cuando se reduce la expresión de aqp1ab. Ex-perimentos de transactivación indican que el Pgr activa la transcripción de aqp1ab, con Sox3 y -8b actuando de forma sinérgica, mientras que el Sox9b reprime este mecanismo. El papel del Pgr se ha investigado sobre explantes ováricos pre-vitelogénicos incubados in vitro, lo cual ha demostrado que la 17,20β-P, producida en las células de la granulosa en respuesta a la hormona folículo estimulante, activa el promotor de aqp1ab en el oocito induciendo la síntesis de Aqp1ab. Los resultados de esta tesis revelan por primera vez una estricta regulación transcripcional del gen aqp1ab durante la oogénesis de teleósteos marinos, lo cual remarca la función fisiológica esencial de este canal de agua durante la formación de los huevos pelágicos.

Creating receptors for control of transcription with arbitrary small molecules has widespread applications including gene therapy, biosensors, and enzyme engineering. Using the combination of high throughput docking, codon randomization, and chemical complementation, we have created new receptors to control transcription with small molecules. Chemical complementation, a new method of protein engineering, was used to discover retinoid X receptors (RXR) variants that are activated by compounds that do not activate wild-type RXR. A first library of 32,768 RXR variants was designed for the synthetic retinoid-like compound LG335. The library produced ligand-receptor pairs with LG335 that have a variety of EC50s and efficacies. One engineered variant has essentially the reverse ligand specificity of wild-type RXR and is transcriptionally active at 10 and #64979;fold lower LG335 concentration than wild-type RXR with 9cRA in yeast. The activity of this variant in mammalian cells correlates with its activity in yeast. A second library of 262,144 RXR variants was designed for two purposes: (i) to develop a high-throughput chemical complementation method to select variants that have high efficacies and low EC50s; and (ii) to find variants which are activated by small molecules not known to bind RXR variants. Selection conditions were manipulated to find only variants with high efficacies and low EC50s. This library was also selected for variants that activate transcription specifically in response to gamma-oxo-1-pyrenebutyric acid (OPBA), which is different from any known RXR ligand. OPBA was chosen as a potential ligand using high-throughput docking with the software program FlexX. Two variants are activated by OPBA with an EC50 of 5 mM. This is only ten-fold greater than the EC50 of wild type RXR with its ligand 9cRA (500 nM) in yeast. An improved method synthesizing LG335 and a method for quantifying intracellular ligand concentrations were developed. Although the LG335 synthetic method has an additional step, the overall yield was improved to 8% from 4% in the original publication. Liquid chromatography and mass spectrometry was used to quantify the intracellular concentration of LG335, which was found to be within four fold of the LG335 concentration in the media.