Vertebrate genomes are punctuated by CpG islands regions, which have an elevated frequency of CpG dinucleotides. CpG islands are associated with over 70% of mammalian promoters suggesting they may contribute to the regulation of transcription. However, despite being discovered over 30 years ago, the function of CpG islands is still not understood. Unlike the majority of the genome, CpG islands are resistant to DNA methylation. This provides a binding site for CFP1 which binds specifically to non-methylated DNA via its zinc-finger CXXC (zf-CXXC) domain. CFP1 is a subunit of the SET1 methyltransferase complex, and is thought to direct the activating histone modification H3K4me3 to CpG islands. Interestingly, CFP1 also contains a PHD domain which is proposed to bind the H3K4me3 mark, potentially producing a feedback loop between H3K4me3 and the SET1 complex. Although the structural basis for discrimination of non-methylated CpGs is known, it is not clear how zf-CXXC proteins distinguish CpG islands amongst the irregular nucleosomal landscape which exists within the nucleus. This thesis is focused on the role of CFP1 in the relationship between CpG islands, SET1 and H3K4me3. To address these questions, it was important to mechanistically dissect the contribution of the PHD and zf-CXXC domains. The proposal that the PHD domain of CFP1 binds selectively to H3K4me3 was confirmed by in vitro experiments, however this study demonstrates that the PHD domain is insufficient for stable interactions with chromatin. Using complementary genome-wide and live cell imaging approaches, the zf-CXXC domain shown to be required for PHD-dependent interactions. Genome-wide snapshots of binding interactions, together with spatial and temporal details, expose a surprising contribution of the SET1 complex to the nuclear mobility of CFP1, providing a new perspective on the role of CFP1 in H3K4 methylation.

Ce travail de thèse a porté sur l’étude d’activités enzymatiques virales impliquées dans la réplication de deux genres viraux : les Flavivirus et les Coronavirus. Dans un premier temps, nous avons étudié des activités enzymatiques impliquées dans la formation de la structure coiffe des ARNm viraux. En effet, du fait de leur cycle réplicatif cytoplasmique, ces virus n’ont pas accès à la machinerie de formation de la coiffe cellulaire et expriment donc une machinerie dédiée. Le processus canonique de formation de la coiffe fait appel à quatre activités enzymatiques, une ARN 5’-triphosphatase, une guanylyltransférase et deux méthyltransférases.Chez les flavivirus, nous avons développé des outils permettant d’identifier l’activité guanylyltransférase ainsi que des essais enzymatiques nécessaires à la caractérisation des activités méthyltransférases. Ces outils nous ont notamment permis d’évaluer l’effet inhibiteur de molécules choisies par des méthodes de criblages virtuels sur les deux activités méthyltransférases de la protéine NS5 nécessaires à la formation de la coiffe.Chez les coronavirus, nous nous sommes intéressés à une activité méthyltransférase impliquée dans la formation de la coiffe et notamment à sa régulation par un partenaire viral. Nous avons démontré que le processus de méthylation de la coiffe suit un ordre obligatoire, initié par la méthylation de la position N7 par la protéine nsp14. Dans une seconde étape, les structures coiffe-0 (7MeGpppA) sont converties en coiffe-1 (7MeGpppA2’OMe) par la protéine nsp16 en complexe avec nsp10. Nous avons démontré que l’activité 2’O-méthyltransférase portée par la protéine nsp16 nécessite une interaction spécifique avec la protéine nsp10 qui joue probablement un rôle d’échafaudage.Dans un second temps, nous avons démontré que l’activité exoribonucléase portée par la protéine nsp14 est également régulée par la protéine nsp10. La stimulation de l’activité passe par une interaction directe entre les deux protéines et il semble que les surfaces d’interaction de nsp10 avec nsp14 et nsp16 soient chevauchantes. Enfin, la caractérisation de l’activité exoribonucléase confirme la possibilité de son implication dans un mécanisme de réparation des erreurs incorporées lors de la synthèse d’ARN par la polymérase virale. / This work focused on enzymatic activities of two RNA virus genera, Flavivirus and Coronavirus.We first studied the mRNA cap synthesis machinery of these viruses. Indeed, as they replicate in the cytoplasm of the infected cell, these viruses encode their own mRNA cap-forming enzymes. The canonical mechanism of cap synthesis uses four enzymatic activities, a RNA 5’-triphosphatase, a guanylyltransferase and two methyltransferases.We tried to identify the guanylyltransferase activity involved in this process for flaviviruses and we developed enzymatic assays to characterize both guanylyltransferase and methyltransferase activities. We used the methyltransferase assay in order to test the inhibitor effect of molecules, selected by virtual screening, on the methyltransferase activities of the NS5 protein involved in the capping process.Concerning coronaviruses, we first focused on the methyltransferase activities of the nsp14 and nsp16 proteins. We have reconstituted the complete SARS-CoV mRNA cap methylation in vitro. We showed that mRNA cap methylation requires a third viral protein, nsp10, which acts as an essential trigger to complete RNA cap-1 formation. The obligate sequence of methylation events is initiated by nsp14, which first methylates capped RNA transcripts to generate cap-0 7MeGpppA-RNAs. The latter are then selectively 2′O-methylated by the 2′O-methyltransferase nsp16 in complex with its activator nsp10 to give rise to cap-1 7MeGpppA2′OMe-RNAs. Then, we took interest in the exoribonuclease activity of the nsp14 protein and found that this activity is also regulated by the same cofactor, the nsp10 protein. The interaction between the proteins is required to observe the stimulatory effect and it seems that the surface areas of nsp10 interacting with nsp14 and nsp16 overlap. The in vitro characterization of the nuclease activity of nsp14 is according with its potential implication in RNA proofreading mechanism.

Différents rôles de l'hélicase Pif1 ont été décrit dont le plus documenté est de décrocher la télomérase des télomères en déroulant les hybrides ARN/ADN formés entre l'ARN de la télomérase et l'ADN télomérique. Plus récemment, une nouvelle voie de signalisation des dommages à l'ADN a été mise en évidence, qui inhibe l'action de la télomérase au niveau d'une cassure de l'ADN via la phosphorylation de l'hélicase Pif1. Cette phosphorylation, dépendante de la kinase ATR (Mec1), inhibe la réparation aberrante de la cassure d'ADN par la télomérase. Nous étudions au sein de l’équipe la protéine RPA (Replication Protein A), affine de l'ADN simple-brin, qui recrute à la fois la protéine de recombinaison homologue Rad52 et la protéine Mec1 impliquée dans la cascade de signalisation des dommages de l'ADN. Lors de l'étude de différentes fonctions de l'hélicase Pif1, j'ai mis en évidence une interaction robuste entre Pif1 et RPA. J'ai identifié un allèle de RFA1, rfa1-D228Y, affectant l'interaction Pif1/RPA et montré, grâce à cet allèle, que cette interaction est impliquée dans le recrutement de Pif1 au niveau d'une cassure double-brins (CDB) induite de l'ADN. Enfin, il a été récemment mis en évidence un nouveau rôle de Pif1 dans la stabilité des G-Quadruplexes durant la réplication du brin avancé. En effet, les cellules pif1 présentent un taux d'instabilité du minisatellite CEB1 inséré sur le brin avancé d'environ 56%, correspondant à des réarrangements de l'ADN de type contractions ou expansions. Lors de l'étude de l'interaction Pif1/RPA, j'ai montré que la mutation rfa1-D228Y entraîne une instabilité du minisatellite CEB1 présent sur le brin avancé, similaire à celle observée avec la délétion pif1∆. Nous suggérons un modèle selon lequel RPA recruterait Pif1 au cours de différents processus cellulaires tels que la réponse des dommages à l'ADN ou la réplication des structures particulières de l'ADN telles que les G-Quadruplexes.En parallèle de cette étude, j’ai étudié le rôle de l'histone méthyltransférase Set1 spécifique de la lysine 4 de l'histone H3 dans la régulation de la taille des télomères. J’ai mis en évidence que le raccourcissement des télomères observé dans un mutant set1 est lié à l'absence de di- et tri-méthylation de H3K4 alors que la perte de monométhylation n'a aucun effet. Cependant, le défaut de la taille des télomères dans les cellules set1∆ n'est pas uniquement lié au défaut de méthylation de H3K4 mais semble impliquer une autre activité de Set1 qu’il reste à déterminer. Etonnamment, nous avons observé que la délétion de SET1 aggrave le raccourcissement des télomères des mutants dont les gènes sont impliqués dans la régulation positive de la taille des télomères et inversement, aggrave le rallongement des télomères de mutants dont les gènes sont impliqués dans la régulation négative des télomères. Nous postulons que l’inactivation de Set1 pourrait à la fois inhiber l’activation précoce des origines de réplication des régions subtélomériques et conduire à un sur-raccourcissement de la taille des télomères, à la fois affecter la synthèse du brin complémentaire dans un contexte où celle-ci est affectée (mutant rif1) et conduire à un sur-allongement des télomères. Une seconde hypothèse propose que Set1 régulerait la transcription deTERRA dans des cellules ayant les télomères déprotégés (mutant rif) entraînant le sur-allongement des télomères. / Different roles of Pif1 helicase have been described, the best documented being to remove telomerase from telomeres by unwinding the RNA/DNA hybrid between telomerase RNA and telomeric DNA. Recently, it was shown that the DNA damage signaling down-regulates telomerase action at a DNA break via Pif1 phosphorylation. Pif1 phosphorylation is dependent of the checkpoint kinase ATR (Mec1) and prevents the aberrant healing of broken DNA ends by telomerase. In our laboratory, we study RPA (Replication Protein A), a single-strand DNA binding protein which recruits the proteins involved in the DNA damage response and checkpoint regulation, such as the homologous recombination protein Rad52 and Mec1 involved in the DNA damage response. I have identified an allele of RFA1, rfa1-D228Y, that affects the Pif1/RPA interaction and showed using this allele that this interaction is implicated in the Pif1 recruitment at an induced double-strand break. Recently, a new role of Pif1 in the stability of G-quadruplex DNA during the leading strand replication has been described. pif1 cells show an instability about 56% of the human minisatellite CEB1 inserted on the leading strand. During my study of the Pif1/RPA interaction, I showed that the rfa1-D228Y mutant induced a similar instability of CEB1 minisatellite on the leading strand. We suggested that RPA would recruit Pif1 for many cellular processes such as DNA damage response or replication of secondary DNA structures such as G-Quadruplexes.In parallel, I have studied the role of the Set1 Histone methyltransferase which catalyse the methylation of the lysine 4 of histone H3, in the regulation of telomere length. I showed that the telomere shortening observed in set1 mutant is due to the loss of di- and tri-methylation of H3K4 while the loss of monomethylation has no effect. However, the short telomeres in set1∆ cells is not only due to the methylation defect shedding light on a new Set1 activity that remains to be fully characterized.. The SET1 deletion aggravates the telomere shortening of mutants which genes are involved in positive regulation of telomere length and conversely, aggravates the lengthening of mutants which genes are involved in negative regulation of telomere length. We postulated that inactivation of Set1 could affect at once activation of early-replication origins and leads to a telomere shortening, and affect synthesis of complementary strand in a context where this one is affected (mutant rif1) and leads to a telomere lengthening. A second hypothesis propose that Set1 would regulate TERRA transcription in cells with deprotected-telomere (rif mutant) leading to the lengthening of telomeres.

Le virus de la dengue cause une maladie de type grippal qui peut dans certains cas évoluer vers des fièvreshémorragiques mortelles. Mon projet de thèse porte sur la réplication de ce virus. Je focalise sur la compréhension du mécanisme d'action de la protéine NS5 de ce virus. La protéine contient 2 domaines : 1) domaine méthyltransférase, essentiel pour la traduction des protéines virales, 2) domaine polymérase, synthétisant le génome ARN du virus. Premièrement, nous avons démontré que la polymérase joue un rôle principal dans la conservation de l'extrémité 3' et 5' du génome et de l'anti-génome. Puis, j'ai caractérisé l'influence du domaine méthyltransférase sur l'activité polymérase de la protéine NS5. J'ai développé un système d'études mécanistiques en utilisant des techniques biochimiques de cinétique pré-stationnaire pour la protéine NS5, et obtenu des paramètres cinétiques et thermodynamiques de cette protéine envers ses substrats. Avec ce même système, j'ai pu tester des activités de la polymérase NS5 avec des ARN coiffés et triphosphates de différente longueur, mimant les séquences à l'extrémité 5' du génome du virus de la dengue. L'activité polymérase de NS5 est influencée par la présence de la coiffe de l'ARN, ce qui m'a permis de proposer une distance physique correspondant à environ 13 nucléotides entre les sites actifs domaines méthyltransférase et polymérase. Mes travaux ouvrent la voie à la détermination de la structure 3D de NS5 avec ses ARN et des nucléotides 5'-triphosphate.Elucider son mécanisme d'action, c'est être capable d'inhiber son action et donc de pouvoir proposer des molécules capables d'arrêter la prolifération virale lors d'une infection. / Dengue virus causes dengue fever, which may evolve towards life-threatening hemorrhagic fever. My research projectfocuses on dengue replication, and more precisely on the mechanism of NS5 at the molecular/atomic level. NS5 is a bifunctionalenzyme containing two domains: 1) a methyltransferase domain essential for translation of viral proteins, 2) apolymerase domain synthesizing the viral RNA genome. First, we demonstrated the main role of the polymerase in theconservation of 5' and 3' ends of dengue genome and anti-genome RNAs. Next, I showed the influence of themethyltransferase domain on the activity of the polymerase domain. I also developed a system allowing mechanistic studiesusing pre-steady state kinetics to characterize NS5 in depth. I have made use of this system to determine the catalyticparameters of NS5 towards its substrates. Using the same pre-steady state system, I was able to test the polymerase activityof NS5 with capped and uncapped 5'-triphosphate RNAs of different lengths corresponding to the 5'-end of the dengue RNAgenome. The polymerase activity of NS5 is significantly affected by the presence of the 5'-cap, which allowed me to designan experimental set-up pointing to a minimal physical distance of around 13 nucleotides between the methyltransferase andpolymerase active sites. My work will be useful to characterize the biophysics of NS5 in complex with its RNA and NTPsubstrates, and then to determine the crystal structure of such complex at play during viral RNA synthesis. Knowing thedetailed NS5 mechanism paves the way to inhibit its action and thus design drugs aiming at stopping a viral infection.

A cana-de-açúcar é uma monocotiledônea poliplóide, alógama que possui baixa taxa reprodutiva devido a dificuldade de florescimento. Devido estas características genéticas e fisiológicas os programas de melhoramento são longos e laboriosos. Alternativamente, modernas aplicações da biotecnologia visam contribuir com o desenvolvimento de novos cultivares. Neste trabalho estudou-se a metodologia de cultura de tecidos a partir de discos de folhas imaturas para o estabelecimento da cultura de calos embriogênicos e regeneração de plantas a partir dos calos embriogênicos e diretamente, a partir de folhas imaturas. O objetivo principal foi contribuir para o desenvolvimento de métodos eficientes para produção de plantas transgênicas a partir de calos e folhas imaturas, considerando-se a crescente necessidade de produção de novos cultivares com características agronômicas específicas. Diversas concentrações de 2,4-D e cinetina em meio MS foram testadas para o estabelecimento de calos altamente embriogênicos e para a indução da desdiferenciação celular nos discos foliares antecedendo a regeneração de plantas. Meios de cultura sem reguladores de crescimento (MS) e com a adição de BAP e ANA foram testados para a regeneração de plantas a partir de discos foliares. Calos embriogênicos com 12 a 20 semanas de cultivo produziram em média 3 a 5 plantas, em meio de regeneração MS. Folhas imaturas apresentaram elevado potencial de regeneração de plantas quando se utilizou 2,4-D em concentrações de 5 e 8 mg/L nos períodos de 5 e 8 dias no escuro. Houve indução a formação de embriões somáticos que resultaram em média 12 a 16 plantas por explante no período total de 7 a 10 semanas. Além disso, foi testado o pré-tratamento dos discos foliares em meio MS3K, contendo 2,4-D (3mg/L) e cinetina (0,1 mg/L), antes da transferência do discos para meio de regeneração MS. Os discos submetidos a este pré-tratamento durante 14, 21 e 28 dias apresentaram aumento significativo na eficiência de regeneração de plantas, variando em média de 41 a 50 plantas por disco foliar nas variedades RB835089 e RB855156. A redução no tempo para obtenção de plantas aliado ao aumento na média de plantas obtidas é a base para aumentar a eficiência de transformação genética de plantas. Experimentos de cotransformação dos genes neo e comt(AS), foram realizados por biolística. Em plantas regeneradas a partir de folhas imaturas da variedade RB835486, as análises de PCR confirmaram a incorporação do gene marcador neo em 57 e 90% das plantas em meio seletivo com geneticina (30 mg/L), sendo que a maior eficiência de regeneração de transgênicos (90%) foi obtida no pré-tratamento com o meio MS3K. Das plantas transgênicas para o gene neo, 7 e 38% também foram confirmadas para a incorporação do gene comt(AS). Nas plantas regeneradas a partir de calos embriogênicos em meio seletivo, as análises de PCR detectaram somente a incorporação do gene neo, o que ocorreu em 52% das plantas analisadas. Os resultados obtidos mostram que a cultura de discos de folhas imaturas para o processo de transformação genética por biolística é uma metodologia viável, rápida e menos onerosa, quando comparada com a cultura de calos embriogênicos. / Sugarcane is a polyploidy monocot and allogamous species that has low reproductive rate due to the difficulty of flowering. Because of these genetic and physiological characteristics breeding program takes long time and demand hard labor. Alternatively, modern biotechnology approaches contribute to the development of new cultivars. In this work we studied the methodology of plant tissue culture from immature leaf discs to establish callus culture and plant regeneration from those calli and from immature leaves, directly. The main objective was to contribute to the development of efficient methods to produce transgenic plants from callus and immature leaves, due to the growing need to produce new cultivars with specific agronomics traits. MS medium with different concentrations of 2,4-D and kinetin were tested to obtain highly embryogenic calli and to induce cellular dedifferentiation in the immature leaf discs prior to plant regeneration. Culture media without growth regulators (MS) and with the addition of BAP and NAA were tested for plant regeneration from leaf discs. Callus culture with 12 to 20 weeks resulted on average 3 to 5 plants on regeneration medium designed as MS. Immature leaves showed a high potential for plant regeneration when 2,4-D at concentrations of 5 and 8 mg/L in periods of 5 and 8 days in the dark. There were inducing of somatic embryos that resulted in average 12 to 16 plants per explant in the total period of 7 to 10 weeks. In addition, we tested the pre-treatment of leaf discs in MS3K medium which contain 2,4-D (3 mg/L) and kinetin (0.1 mg/L) before transfering to plant regeneration MS medium . The discs submitted to this pretreatment for 14, 21 and 28 days showed significant increase in the efficiency of plant regeneration, with on average of 41 to 50 plants per leaf disc in varieties RB835089 and RB855156. The reduction of time to obtain plants coupled with the increase of plants obtained is the basis for increasing the efficiency of plant genetic transformation. Co-transformation with genes neo and comt(AS), were performed by biolistics. Plants regenerated from immature leaves of the variety RB835486, PCR analysis confirmed the incorporation of the neo selection marker gene in 57 and 90% of the plants on selective medium with geneticin (30 mg/L), the higher efficiency of transgenic plants (90%) was obtained on pre-treatment in MS3K medium. Transgenic plants for the neo gene, 7 and 38% were also confirmed for the incorporation of comt (AS). PCR analysis of candidates transgenic plants from callus growing on selective medium, revelled only the insertion of the neo gene, which occurred in 52% of the analyzed plants. The results of this work showed that the approach of using immature leaf discs to obtain plant genetic transformation by biolistics methodology is a viable, cheaper and faster than using embryogenic callus.

Fine temporal regulation of dopamine transmission is critical to its effects on behaviour. Dopamine can be cleared from the synapse either by recycling via the dopamine transporter (DAT) or by enzymatic degradation involving catechol-O-methyltransferase (COMT). DAT recycling predominates in striatum and contributes to dopaminergic regulation of reward-guided behaviour, while COMT degradation predominates in cortex and modulates executive functions. However, human functional imaging studies demonstrate interactive effects of DAT and COMT genotype, suggesting that the traditional division between DAT and COMT is not so clear-cut. Given the interdependence of mesolimbic and mesocortical circuitry and the presence of COMT in the striatum, it is possible that DAT and COMT interact to a greater extent than previously thought. We investigated the contributions of DAT and COMT to regulation of dopamine transmission and reward-guided behaviour by combining in vivo electrochemical recording, pharmacology, and behavioural testing in mice. Using fast scan cyclic voltammetry to record evoked dopamine release in anaesthetised animals, we found that systemic DAT blockade increased the size of dopamine transients in the nucleus accumbens (NAc) but not in the medial frontal cortex (MFC), demonstrating that DAT regulates phasic striatal dopamine release and confirming that DAT makes little contribution to regulation of cortical dopamine transmission. Unexpectedly, COMT inhibition did not affect evoked dopamine transients in either the NAc or the MFC. In agreement with these findings, systemic administration of a DAT blocker, but not of a COMT inhibitor, increased motivation to work for reward in a progressive ratio paradigm. COMT inhibition also had little effect on reinforcement learning (RL) strategies during reward-guided decision making. Intriguingly, however, we found that DAT blockade both decreased the influence of model-free RL and increased the influence of model-based RL on behaviour. Our study confirms that DAT regulates dopamine transmission in striatum but not in cortex and indicates that sub-second changes in dopamine transmission in both regions are largely insensitive to COMT. However, our behavioural data reveal the importance of striatal dopamine in multiple components of reward-guided behaviour, including both motivational aspects traditionally associated with striatum as well as cognitive aspects heretofore mainly associated with cortical function. Together, these findings emphasise that reward processing occurs across corticostriatal circuits and contribute to our understanding of how striatal dopamine transmission regulates reward-guided behaviours.

La lysyl oxydase-like 1 (LOXL1) est une enzyme nécessaire à la maturation des fibres élastiques dans matrice extra-cellulaire lors des processus de réparation tissulaire à l'âge adulte. Chez l'Homme, le niveau d'expression de LOXL1 dans les fibroblastes dermiques diminue avec l'âge contribuant ainsi au relâchement cutané. Dans la pathologie génétique cutis laxa, pouvant être considérée comme un modèle de vieillissement accéléré, le promoteur du gène loxl1 est la cible de méthylation au niveau de sites riches en cytosines et guanosines, appelés îlots CpG, ce qui empêche l'initiation de la transcription. Dans ce travail de thèse, d'une part, nous avons voulu savoir si le déficit en fibres élastiques au cours du vieillissement du derme humain pouvait être la conséquence de l'hyperméthylation de loxl1 ; et d'autre part, nous avons recherché des actifs végétaux capables de contrer ce mécanisme. Pour cela, nous avons testé des modèles de vieillissement in vitro afin de corréler la perte en fibres élastiques et l'hyperméthylation de loxl1. Une méthode d'analyse de la méthylation nous a permis de déceler l'hyperméthylation spécifique de loxl1 au cours du vieillissement chronologique. Des analyses transcriptomiques en PCR en temps réel, des expériences de précipitation de la chromatine ainsi que des analyses d'activités de promoteurs ont permis de mettre en évidence l'importance de l'ADN méthyltransférase 3a (DNMT3a) dans la régulation du promoteur loxl1. Cette enzyme a été clonée en système eucaryote et deux nouveaux partenaires ont été identifiés: la protein arginin methyltransferase 5 (PRMT5) et la methylosome protein 50 (MEP50). Enfin, ce mécanisme de régulation a été testé lors d'un criblage d'actifs végétaux à des fins cosmétiques. Nous avons trouvé deux actifs ayant la capacité de contrer de façon directe ou indirecte l'activité de la DNMT3a et de supprimer la méthylation de loxl1 dans des fibroblastes âgés / Lysyl oxidase-like 1 (LOXL1) is an enzyme required for the maturation of elastic fibres in the extracellular matrix during tissue repair process at adulthood. In human dermal fibroblasts, LOXL1 expression decreases with age, thus contributing to sagging skin. In the genetic disease cutis laxa, which can be regarded as a model of accelerated ageing, the loxl1 gene promoter has been shown to undergo DNA methylations in a cytosine-guanine rich region, known as CpG Island, which prevented the initiation of transcription. In this thesis, firstly, we wanted to know whether the deficit in elastic fibres in the dermis of human during ageing could be the result of loxl1 hypermethylation; and secondly, we sought plant extracts capable of counteracting this mechanism. Different in vitro ageing models were assessed to correlate the loss of elastic fibres and hypermethylation of loxl1. A particular methylation analysis method allowed us to identify specific hypermethylation of loxl1 during chronological ageing. Transcriptomic analyses by real-time PCR, precipitation of chromatin experiments and analysis of promoter activity led to highlight the importance of DNA methyltransferase 3a (DNMT3a) in the regulation of loxl1 promoter. This enzyme has been cloned in an eukaryotic system and two new partners have been identified: protein arginine methyltransferase 5 (PRMT5) and methylosome protein 50 (MEP50). Finally, this regulatory mechanism has been tested as a screening tool for cosmetic purposes. We selected two plant extracts with the ability to counteract, directly or indirectly, the activity of DNMT3a and remove methylation from loxl1 promoter in aged fibroblasts

INTRODUÇÃO: O caráter familial do transtorno obsessivo-compulsivo (TOC) já é bem estabelecido. O gene da catecol O-metiltransferase (COMT) vem sendo objeto de estudo na genética de transtornos mentais, como o TOC. No caso deste transtorno, os resultados de estudos de associação com o gene da COMT são, em sua maioria, contraditórios. Meta-análises prévias, todas elas conduzidas com limitações metodológicas, encontraram achados também divergentes. Nesta tese, foram realizadas: uma revisão sistemática da literatura sobre estudos de associação baseados em famílias envolvendo o polimorfismo Val158Met do gene da COMT e o TOC e duas meta-análises, uma convencional e outra bayesiana, a fim de sintetizar os achados sobre este tema. MÉTODOS: Este trabalho seguiu o protocolo para revisão sistemática e meta-análise da Rede de Epidemiologia Genética Humana (HuGE). A busca por estudos de associação baseados em famílias foi feita em cinco bases de dados eletrônicas, assim como foram pesquisados estudos não publicados, dentre os quais um estudo ainda inédito, liderado pela autora desta tese. A meta-análise convencional foi calculada com o auxílio do programa STATA V. 11 e a bayesiana a partir da média das verossimilhanças. Foram investigados os viéses de publicação, heterogeneidade, além de análise de sensibilidade e metarregressão. RESULTADOS: O estudo original, que contou com 83 trios, conduzido pela autora desta tese, não encontrou associação entre COMT e TOC. Este estudo, em conjunto com mais oito estudos (seis estudos publicados e dois não publicados), foram incluídos na meta-análise. As meta-análises com método convencional e bayesiano não encontraram associação entre o polimorfismo Val158Met do COMT e o TOC na amostra total, nem nas amostras separadas por gênero. CONCLUSÕES: Contrariando meta-análises prévias, os achados deste estudo não demonstraram associação entre COMT e TOC. No entanto, a participação do gene da COMT em subgrupos específicos do TOC e em seus endofenótipos de risco ainda merece ser investigada / BACKGROUND: Obsessive-compulsive disorder (OCD) has long been considered a familial disorder. The catechol-O-methyltransferase gene has been studied in several mental disorders, including OCD. Particularly in this disorder, the findings of an association between COMT and OCD are inconclusive. Previous meta-analyses, which were conducted with several methodological limitations, found conflicting results. This work comprises: a systematic literature review regarding family-based association studies involving the COMT Val158Met polymorphism and OCD, and two metaanalyses, a conventional and a Bayesian meta-analysis, to summarize the findings on this subject. METHODS: This study was performed according to the Human Genome Epidemiology network (HuGE) guidelines for systematic review and meta-analysis. The search for family-based association studies were conducted in five electronic databases and in sources from unpublished studies. An original unpublished study, led by the author of this thesis, was included in the meta-analysis. The conventional meta-analysis was calculated with the STATA V.11 software and the Bayesian meta-analysis through the likelihood mean. Publication bias and heterogeneity were investigated. Sensitivity analysis and meta-regression were also performed. RESULTS: The original study with 83 OCD trios, conducted by the author of this thesis, found no association between COMT and OCD. This study, together with eight other studies (six studies being published and two unpublished), were included in the meta-analysis. Meta-analyses with the conventional and Bayesian method found no association between the COMT Val158Met polymorphism and OCD in the total, female-only or male-only samples. CONCLUSIONS: Different from previous meta-analyses, this study does not support the association between COMT and OCD. However, the involvement of the COMT gene in specific subgroups of OCD or endophenotypes associated with a risk for OCD should be further investigated

INTRODUÇÃO: O caráter familial do transtorno obsessivo-compulsivo (TOC) já é bem estabelecido. O gene da catecol O-metiltransferase (COMT) vem sendo objeto de estudo na genética de transtornos mentais, como o TOC. No caso deste transtorno, os resultados de estudos de associação com o gene da COMT são, em sua maioria, contraditórios. Meta-análises prévias, todas elas conduzidas com limitações metodológicas, encontraram achados também divergentes. Nesta tese, foram realizadas: uma revisão sistemática da literatura sobre estudos de associação baseados em famílias envolvendo o polimorfismo Val158Met do gene da COMT e o TOC e duas meta-análises, uma convencional e outra bayesiana, a fim de sintetizar os achados sobre este tema. MÉTODOS: Este trabalho seguiu o protocolo para revisão sistemática e meta-análise da Rede de Epidemiologia Genética Humana (HuGE). A busca por estudos de associação baseados em famílias foi feita em cinco bases de dados eletrônicas, assim como foram pesquisados estudos não publicados, dentre os quais um estudo ainda inédito, liderado pela autora desta tese. A meta-análise convencional foi calculada com o auxílio do programa STATA V. 11 e a bayesiana a partir da média das verossimilhanças. Foram investigados os viéses de publicação, heterogeneidade, além de análise de sensibilidade e metarregressão. RESULTADOS: O estudo original, que contou com 83 trios, conduzido pela autora desta tese, não encontrou associação entre COMT e TOC. Este estudo, em conjunto com mais oito estudos (seis estudos publicados e dois não publicados), foram incluídos na meta-análise. As meta-análises com método convencional e bayesiano não encontraram associação entre o polimorfismo Val158Met do COMT e o TOC na amostra total, nem nas amostras separadas por gênero. CONCLUSÕES: Contrariando meta-análises prévias, os achados deste estudo não demonstraram associação entre COMT e TOC. No entanto, a participação do gene da COMT em subgrupos específicos do TOC e em seus endofenótipos de risco ainda merece ser investigada / BACKGROUND: Obsessive-compulsive disorder (OCD) has long been considered a familial disorder. The catechol-O-methyltransferase gene has been studied in several mental disorders, including OCD. Particularly in this disorder, the findings of an association between COMT and OCD are inconclusive. Previous meta-analyses, which were conducted with several methodological limitations, found conflicting results. This work comprises: a systematic literature review regarding family-based association studies involving the COMT Val158Met polymorphism and OCD, and two metaanalyses, a conventional and a Bayesian meta-analysis, to summarize the findings on this subject. METHODS: This study was performed according to the Human Genome Epidemiology network (HuGE) guidelines for systematic review and meta-analysis. The search for family-based association studies were conducted in five electronic databases and in sources from unpublished studies. An original unpublished study, led by the author of this thesis, was included in the meta-analysis. The conventional meta-analysis was calculated with the STATA V.11 software and the Bayesian meta-analysis through the likelihood mean. Publication bias and heterogeneity were investigated. Sensitivity analysis and meta-regression were also performed. RESULTS: The original study with 83 OCD trios, conducted by the author of this thesis, found no association between COMT and OCD. This study, together with eight other studies (six studies being published and two unpublished), were included in the meta-analysis. Meta-analyses with the conventional and Bayesian method found no association between the COMT Val158Met polymorphism and OCD in the total, female-only or male-only samples. CONCLUSIONS: Different from previous meta-analyses, this study does not support the association between COMT and OCD. However, the involvement of the COMT gene in specific subgroups of OCD or endophenotypes associated with a risk for OCD should be further investigated

Restriction endonucleases occur ubiquitously among bacteria, archaea and in viruses of certain unicellular algae, and they are usually accompanied by a modification enzyme of identical specificity; together, the two activities form a restriction-modification (R-M) system- the prokaryotic equivalent of an immune system. More than 3,800 R-M enzymes have been characterized so far and they manifest 262 unique recognition specificities. These enzymes represent the largest family of functionally related enzymes. Based on the number and organization of subunits, cofactor requirements, catalytic mechanism, and sequence specificity, restriction enzymes have been classified into different types, Types I, II, III, and IV. R-M systems are important model systems for studying highly specific DNA-Protein interactions and serve as excellent systems for investigating structure-function relationship and for understanding the evolution of functionally similar enzymes with highly dissimilar sequence. In bacteria, DNA methyltransferases (MTases) associated with R-M systems protects the host DNA from cleavage by the cognate restriction endonuclease recognizing the same sequence and provides the integrity of host cell genome against foreign DNA invasion. The modification MTases catalyses the addition of a methyl group to one nucleotide in each strand of the recognition sequence using S-adenosyl-L-methionine (AdoMet) as the methyl group donor. Based on the chemistry of the methylation reaction catalyzed, DNA MTases are classified as C5 enzymes (endocyclic MTases), which transfer the methyl group to C5 position of cytosine, and N6 and N4 enzymes (exocyclic amino MTases), which transfer the methyl group to the exocyclic amino group of adenine or cytosine, respectively. DNA MTases of all three types contain conserved regions, which are responsible for catalysis and AdoMet binding, and variable regions known as target recognition domains (TRD), which determine the substrate specificity of a particular enzyme. Ten conserved amino acid motifs (I–X) are found in C5 MTases. Exocyclic DNA MTases are subdivided further into six groups (namely α, β, γ, ζ, δ and ε), according to the linear arrangements of three conserved motifs, the AdoMet-binding domain (FXGXG), the TRD (target recognition domain) and the catalytic domain (D/N/S)PP(Y/F). Base flipping has been proposed as a general mechanism used by all MTases in which the target base to be methylated is rotated 180º out of the DNA into a catalytic domain (motif IV). EcoP15I restriction enzyme (R.EcoP15I) belongs to the Type III restriction-modification (R-M) family. These enzymes are composed of two subunits, Res (Restriction) and Mod (Modification). The Mod subunit alone functions as a DNA methyltransferase in presence of AdoMet and magnesium and determines the specificity for restriction and methylation, whereas restriction activity requires the cooperation of both the Res and Mod subunits. EcoP15I methyltransferase (M.EcoP15I), a homodimeric enzyme catalyzes the transfer of a methyl group from AdoMet to the second adenine residue in the recognition sequence, 5’-CAGCAG-3’, in presence of magnesium ions. M.EcoP15I belongs to the β-subfamily of N6-adenine methyltransferases. In addition to the two highly conserved sequence motifs, FXGXG (motif 1) involved in AdoMet binding and DPPY (motif IV) involved in catalysis, the amino acid residues of the region 355-377 contains a PD(X)n(D/E)XK-like motif involved in metal binding. A Mutation in the Mod Subunit of EcoP15I Restriction Enzyme Converts the DNA Methyltransferase to a Site-Specific Endonuclease An interesting aspect of M.EcoP15I is that the methylation requires magnesium and magnesium binding to the PD(X)n(D/E)XK-like motif participates in base flipping. The PD-(D/E)XK superfamily of Mg2+-dependent nucleases were initially identified in structurally characterized Type II REases and later found in many enzymes involved in DNA replication, recombination and repair. The charged residues from the catalytic triads are implicated in metal ion mediated DNA cleavage. In EcoP15I DNA methyltransferase, a PD(X)n(D/E)XK like motif is present in which the partially conserved proline is replaced by methionine (MD(X)18(D/E)XK). Using site-directed mutagenesis methionine at 357 was changed to proline (M357P), which resulted in the formation of a Mg2+ binding/catalytic motif similar to several Mg2+-dependent endonucleases. Substitution of methionine at position 357 by proline converts EcoP15I DNA methyltransferase to a site-specific endonuclease. The mutant protein specifically binds to the recognition sequence 5’-CAGCAG-3’ and cleaves DNA in presence of Mg2+. The engineered EcoP15I-M357P is an active, sequence-dependent restriction endonuclease that cleaves DNA 10/1 nucleotide away from its recognition sequence in the presence of Mg2+. Unlike the holoenzyme, R.EcoP15I, the engineered endonuclease neither requires AdoMet or ATP nor requires two sites in the inverted orientation for DNA cleavage. It is of potential interest to use such an engineered enzyme as a genetic manipulation tool. Dimerisation of EcoP15I DNA Methyltransferase is Required for Sequence Recognition and Catalysis In the cell, after each round of replication, substrate for any DNA MTase is hemimethylated DNA and therefore, only a single methylation event restores the fully methylated state. This is in agreement with the fact that most of the DNA MTases studied exist as monomers in solution. The peculiar feature of M.EcoP15I is that it methylates only one strand of the DNA, at the N6-position of the adenine residue. Earlier studies using gel filtration and glutaraldehyde cross-linking demonstrated that M.EcoP15I exists as dimer in solution. However, the significance of dimerisation in the reaction mechanism of EcoP15I MTase is not clear. Therefore, experiments have been performed to determine whether M.EcoP15I could function as a monomer and the significance of dimerisation, if any, in catalysis. Towards this a homology model of the M.EcoP15I was generated by “FRankenstein monster” approach. Residues D223, V225, and V392, the side chains of which are present in the putative dimerisation interface in the model were targeted for site-directed mutagenesis. These residues were mutated to lysine and their importance was studied. Methylation and in vitro restriction assays showed that the triple mutant was catalytically inactive. Interestingly, the mutations resulted in weakening of the interaction between the monomers leading to both monomeric and dimeric species. M.EcoP15I was inactive in the monomeric form and therefore, dimerisation might be the initial step in its function. This must be required for positioning of the target base of the DNA in the active-site pocket of the M.EcoP15I. A part of this interface may be involved in site-specific DNA binding. Dimerisation of M.EcoP15I is, therefore, a prerequisite for the high-affinity substrate binding needed for efficient catalysis. Understanding the role(s) of Amino and Carboxyl-terminal Domains of EcoP15I DNA Methyltransferase in DNA Recognition and Catalysis N-terminal and C- terminal domains (NTD and CTD) of proteins are known to play many important roles such as folding, stability, dimerisation, regulation of gene expression, enzyme activity and substrate binding. From the modeled dimeric structure of M.EcoP15I, it was hypothesized that N- and C-termini are in close proximity with each other. In addition, it was predicted that each monomer can bind to AdoMet and DNA. Towards understanding the role(s) of the N- and C-terminal domains of M.EcoP15I in its structure and function, N-, and C-terminal deletions were created. Interestingly, deletion of N-terminal 53 amino acids and C-terminal 127 amino acids from of EcoP15I MTase converted the dimeric enzyme to a stable, monomeric protein that was structurally stable but enzymatically inactive. Each monomer could bind single-stranded DNA but dimerisation was required for double-stranded DNA binding and methylation. This indicated that amino acids at the N- and C-termini are important for maintaining a proper dimeric structure for M.EcoP15I functions. Therefore, it can be proposed that in a complex three-dimensional structure, the NTD and CTD should be properly maintained in order to execute its function, including dimerisation and DNA binding. However, since the 3D structure of M.EcoP15I has not yet been determined, the biochemical, biophysical and bioinformatics approaches may serve to provide useful information on the relative contributions of the electrostatic forces and hydrophobic contacts to the structural stability. Understanding the structural organization and folding of M.EcoP15I is crucial to elucidation of the mechanism of action.