O nucléolo é uma organela subnuclear formada pela atividade transcricional dos genes ribossomais 18S-5.8S-26S (rDNA 45S) e consequente biogênese dos ribossomos. A atividade destes genes resulta na região organizadora do nucléolo (NOR), na forma de uma constrição secundária em cromossomos metafásicos. As constrições secundárias se condensam progressivamente durante a mitose e se descondensam ao final da telófase quando a reestruturação do nucléolo se inicia. Genomas que apresentam mais de um locus de rDNA 45S deve apresentar, obrigatoriamente, pelo menos um par de NORs, enquanto os demais loci poderão ou não serem expressos. O controle da expressão dos genes ribossomais e a formação da cromatina nucleolar são modulados por eventos epigenéticos. Embora alguns pontos sobre o funcionamento dos genes ribossomais e a formação do nucléolo estejam bem estabelecidos, questões como o padrão de condensação da cromatina nucleolar durante a mitose, o padrão de funcionamento de sítios adicionais de genes ribossomais, o papel das modificações epigenéticas na dinâmica da cromatina nucleolar e na expressão do rDNA 45S e o mecanismo de herança dos genes ativos, permanecem abertas. A espécie Crotalaria juncea (Leguminosae-Papilionoideae), com 2n=2x=16 cromossomos, que possui um locus de rDNA 45S no braço curto do cromossomo 1, que sempre forma constrição secundária, e um sítio adicional com atividade facultativa no braço curto do cromossomo 4, é um excelente modelo para o estudo destas questões. No contexto apresentado, foram estudadas a dinâmica de condensação das NORs durante o ciclo celular e sua correlação com a atividade dos genes ribossomais, incluindo o locus adicional, e ainda o papel da metilação da citosina do DNA durante estes processos. Os resultados demonstram que a cromatina da região organizadora do nucléolo segrega em um estado descondensado durante a mitose, na forma de constrição secundária, ou seja, tal estrutura não se condensa durante a metáfase e não volta a se distender no início da telófase. Aparentemente, o que causa correlações equivocadas entre a atividade nucleolar e a observação morfológica da constrição secundária na metáfase é a contração forçada da cromatina da NOR causada por agentes antimitogênicos. Este modelo de segregação em um estado aberto pode ser explicado pela descrição de diversas proteínas que permanecem diretamente ligadas ou indiretamente associadas à região da NOR durante a mitose, funcionando como uma barreira física para a compactação. Ambos os sítios, principais e adicionais, do rDNA 45S presentes em Crotalaria juncea apresentam atividade transcricional, embora o locus do cromossomo 4 mostre atividade facultativa. Ao contrário do que foi anteriormente proposto, uma vez ativo, o locus adicional permanece descondensado durante todo o ciclo mitótico, seguindo o mesmo comportamento dos sítios principais. As constrições secundárias e a cromatina nucleolar são hipermetiladas em nível citológico, independentemente de sua atividade. A aparente hipometilação observada no rDNA 45S em cromossomos mitóticos e núcleos interfásicos se deve ao menor grau de compactação da região organizadora do nucléolo e, consequentemente, à baixa densidade de cromatina. / The nucleolus is a subnuclear organelle formed as a result of transcriptional activity of ribosomal RNA genes 18S-5.8S-26S (45S rDNA) and subsequent ribosome biogenesis. This activity forms the nucleolar organizing region (NOR) as a secondary constriction in metaphase chromosomes. The secondary constrictions progressively condense during mitosis and decondense at the end of telophase, when nucleoli start to reassemble. Genomes presenting more than one 45S rDNA locus must have at least one pair of NOR bearing chromosomes, while other loci may be expressed or not. Ribosomal gene expression and nucleolar chromatin assembly are modulated by specific epigenetic events. Although some topics related to rDNA gene activity and nucleolus formation are well understood, questions such as the behavior of nucleolar chromatin condensation during mitosis, standard functions associated with rDNA additional sites, role of epigenetic modifications in nucleolar chromatin and 45S rDNA expression processes, and inheritance mechanism of active genes, remain to be solved. Crotalaria juncea (Leguminosae - Papilionoideae) has 2n=2x=16 chromosomes and carries a 45S rDNA locus at the short arm of chromosome 1, always presenting a secondary constriction, and an additional site with facultative activity at the short arm of chromosome 4, being an excellent model to resolve these questions. Thus, this study aimed to study NOR condensation dynamics during the cell cycle and its correlation with ribosomal gene activity, including the additional locus, while analyzing the role of rDNA cytosine methylation during this process. The results show that NOR chromatin segregate in a decondensed way throughout mitosis, as a secondary constriction. In other words, this structure does not condense during metaphase and the NOR is not reassembled at the beginning of telophase. Misinterpretations relating nucleolar activity with morphological observations of secondary constrictions, appear to be induced by the artificial contraction of NOR chromatin caused by antimitotic drugs. This segregation model in an open state may be supported by strong diversity of proteins that are maintained attached to NORs during mitosis, serving as a physic barrier for condensation. Both principal and additional 45S rDNA sites of C. juncea are transcriptionally active, although the additional locus in chromosome 4 presented facultative activity depending upon ribosomal request. Unlike what was previously proposed, once the additional site is activated, it remains in an open configuration throughout the cell cycle, similarly to principal site behavior. Secondary constrictions and nucleolar chromatin are hypermethylated at cytological level, regardless of their activity. The seeming hipomethylated state of 45S rDNA in interphase nucleus and mitotic chromosomes is due to a lower compaction level of nucleolar organizing regions and subsequent low chromatin density.

Introdução: Mecanismos epigenéticos, como a metilação de DNA, desempenham um papel importante na neurobiologia da depressão. Enquanto o estresse aumenta a metilação de DNA e reduz a expressão de genes envolvidos na plasticidade neuronial, inibidores de DNA metiltransferases (DNMTi), enzimas que catalisam a metilação de DNA, aumentam rapidamente a expressão gênica e induzem efeitos tipo-antidepressivos em modelos animais. Considerando, ainda, que antidepressivos convencionais podem interferir com mecanismos epigenéticos, este trabalho testou a hipótese de que drogas DNMTi induzem efeito tipo-antidepressivo agudo e sustentado em modelos animais. Além disso, avaliamos se o efeito de antidepressivos convencionais e de DNMTis sobre os níveis de mRNA e de metilação de DNA em diferentes genes associados a depressão e regulados por mecanismos epigenéticos (BDNF, TrkB, 5-HT1A, NMDA e AMPA) em estruturas encefálicas (hipocampo dorsal, ventral e córtex pré-frontal) de animais submetidos a modelo animal de depressão. Métodos: Para tanto, ratos Wistar foram submetidos ao modelo do desamparo aprenddo [learned helplessness, LH, pré-teste (PT), 40 choques inescapáveis nas patas]. Os animais receberam injeções sistêmicas de DNMTi (5-AzaD ou RG108), antidepressivos (imipramina ou fluoxetina), ou veículo, por 1 ou 7 dias, e foram submetidos a sessão teste do desamparo aprendido (T, 30 choques escapáveis) no último dia. Adicionalmente, um grupo independente foi submetido ao mesmo protocolo experimental e sacrificados 1 h após a última injeção. As estruturas encefálicas foram dissecadas para posterior análise molecular [imunoprecipitação de DNA metilado (meDIP) e quantificação de RNAm por qRT-PCR). Resultados: O estresse dos choques nas patas aumentou o número de falhas no teste. O tratamento com DNMTi agudamente, assim como com antidepressivos (tratamento repetido), foi capaz de atenuar essas alterações comportamentais, efeito considerado tipo-antidepressivo nesse modelo. Ainda, o estresse aumentou a metilação de DNA e reduziu os níveis de RNAm para BDNF e TrkB, enquanto que o tratamento com RG108 atenuou essas alterações moleculares no córtex pré-frontal de ratos. Conclusão: Os presentes resultados indicam que DNMTi, diferente de antidepressivos convencionais, são capazes de induzir rápido e sustentado efeito tipo-antidepressivo. Além disso, BDNF e TrkB parecem ser importantes para a resposta comportamental induzida pela inibição de DNMTs no córtex pré-frontal de ratos submetidos ao LH. / Introduction: Epigenetic mechanisms, such as DNA methylation, are thought to play an important role in the neurobiology of depression. While stress increases DNA methylation and decreases the expression of genes involved in neuronal plasticity, DNA methyltransferases inhibitors (DNMTi) increases gene expression and induces antidepressant-like effects in animal models. Considering that conventional antidepressants could interfere with epigenetic mechanisms, this work tested the hypothesis that acute treatment with DNMTi would induce acute and long-lasting antidepressant-like effects. Furthermore, we evaluated whether the stress could induce changes in the mRNA and DNA methylation levels in different genes involved with depression and regulated by epigenetic mechanisms (BDNF, TrkB, 5-HT1A, NMDA and AMPA) in different brain structures [dorsal hippocampus, ventral hippocampus and prefrontal cortex (PFC)] and whether such changes would be attenuated by systemic treatment with DNMTi (acutely) and antidepressants (chronically). Methods: Male Wistar rats were submitted to the learned helplessness model (LH; pretest session, 40 inescapable foot shocks). The animals received systemic injection the DNMTi (5-AzaD or RG108), antidepressants (imipramine or fluoxetine) or vehicle for one or seven days and were submitted to the LH test (30 escapable foot shocks) in the last day. Additionally, one independent group were submitted to the same experimental protocol and sacrificed one hour after last injection for collection of brain samples to further molecular analyses (methylated DNA immunopreciptation and mRNA levels by qRT-PCR). Results: Exposure to inescapable footshocks increased the number of escape failures in the test. Treatment with DNMTi (acute), as well as with antidepressants (repeated treatment), attenuated stress-induced behavioral responses, an antidepressant-like effect in this model. Moroever, stress increased DNA methylation and decreased RNAm levels of BDNF and TrkB, while treatment with RG108 attenuated molecular changes induced by stress in rat PFC. Conclusion: The present results indicate that DNMTi, different from conventional antidepressants, are able to induce rapid and sustained antidepressant-like effects. In addition, BDNF and TrkB appear to be important for behavioral response induced by inhibition of DNMTs in the rat PFC submitted to the LH.

Le syndrome sec de Gougerot Sjögren (SGS) est une maladie auto-immune chronique qui présente des dommages progressifs et irréversibles des glandes exocrines lacrymales et salivaires. Cette pathologie affecte entre 0.1 et 3 % de la population et est plus commune chez les femmes avec un ratio de 9 femmes pour 1 homme. Dans la glande salivaire, une infiltration lymphocytaire est observée et est associée avec la destruction de l'épithélium sécrétoire, qui joue un rôle central dans l'initiation et le développement du SGS. Le processus physiopathologique est loin d’être compris et semble dépendant de phénomènes épigénétiques. En effet, des perturbations importantes de la méthylation de l'ADN sont observées dans les cellules épithéliales en lien avec le niveau d’infiltration lymphocytaire des glandes salivaires.L'objectif de ce travail est de mieux comprendre les changements épigénétiques au cours du SGS et en particulier les défauts de méthylation/déméthylation de l’ADN observés dans les Cellules Epithéliales de Glandes Salivaires (SGEC) et leurs rôles dans le développement de la pathologie.Dans ce but, Une étude globale de la méthylation de l'ADN a été réalisée après culture cellulaire destinée à isoler les SGEC de patients SGS. La puce « human methylation 450k » d’Illumina utilisée couvre plus de 485 000 sites CpG du génome. Des analysesbioinformatiques nous ont permis d'obtenir un panel de gènes différentiellement méthylés. Nous avons ainsi mis en évidence l’importance de la voie calcique (déméthylée, connue pour avoir un impact sur la salivation) et de la voie WNT (hyperméthylée). De plus nous avons pu identifier une régulation interféron et montrer l’importance d’un changement du type d'interféron (I à II) lors de l’évolution vers un lymphome de type MALT. En outre, nous montrons qu’il existe une inter-relation forte entre les processus épigénétiques et les facteurs génétiques associés au SGS. Enfin la dernière partie de ce travail met en lumière l’implication d’un environnement inflammatoire dans le contrôle du processus de méthylation/déméthylation de l’ADN dans les cellules épithéliales.Ainsi, les altérations du méthylome des SGECs pourraient contribuer à la pathophysiologie du SGS et à son évolution en un lymphome du MALT, ceci en lien avec son environnement inflammatoire. / Sjögren Syndrome (SjS) is a chronic autoimmune disease characterized by a progressive and irreversible damage of exocrine glands, particularly salivary and lacrymal glands. This pathology affects between 0.1 and 3% of the population and is more common in women with a ratio of 9 women for 1 man. In salivary glands, a lymphocytic infiltration is observed and associated with the destruction of the secretory epithelium, which plays a central role in initiation and development of the SjS. The process remains incompletely clarified and contains a strong epigenetic component. Indeed, important disturbances of the process of DNA methylation are observed in epithelial cells and they are linked with the level of lymphocyte infiltration in salivary glands.The objective of this work is to better understand epigenetic changes during the SjS and in particular the DNA methylation/demethylation defects observed in Salivary Gland Epithelial Cells Epithelial (SGEC) and their roles in the pathology development.For that purpose, a global study of DNA methylation was done on 12 patients SGECs with the Infinium HumanMethylation450 BeadChip (Illumina). The 450k HM allows to cover more than 485,000 CpG sites on the whole genome. Bioinformatic analysis allowed us to obtain genes panels which are differentially methylated during this pathological phenomenon. In an interesting way, we identified the potential involvement of the calcic (hypomethylated, known to impact salivation) and WNT pathways (hypermethylated). Besides we were able to identify interferon regulation and the shift from interferon type I to type II with mucosa associated lymphoid tissue (MALT) lymphoma evolution. Furthermore, the simultaneous genomic–epigenomic analysis revealed significant associations between SjS-associated genetic risk factors and epigenetic modifications. Finally, the last part of this work highlights inflammatory environment involvement to control DNA methylation/demethylation in salivary gland epithelial cells.Altogether, alterations of DNA methylation in SGEC may contribute to SjS pathophysiology and evolution to MALT and this in link with the inflammatory environment.

The mammalian epigenome is globally reprogrammed at two stages of development; this involves the erasure and re-establishment of DNA methylation by both passive and active mechanisms, including DNA repair pathways, and occurs concurrently with an increase in developmental potency. In addition to Uhrf1 and the Tet enzymes, the interplay between activation induced cytidine deaminase (AID) and the DNA repair machinery has been implicated in epigenetic reprogramming of various in vivo and in vitro systems including mouse primordial germ cells, zygotes and induced pluripotent stem cells. AID deaminates cytosine to uracil and can also deaminate methylcytosine, whereas the primary role of UNG is to maintain the integrity of the genome through erasure of uracil. In this thesis, I have aimed to investigate the role of DNA repair in demethylation. To do this I have focused on the specific role of AID and UNG in the demethylation of a static system – primed serum ESCs and a dynamic system – serum to 2i (naïve) to epiblast-like ES cells. As the role of both AID and UNG involves genomic uracil, the central theme of my thesis is the impact of accumulation of uracil on DNA methylation levels in the genome. Therefore, my first aim was to develop a quantitative method to detect low levels of genomic uracil in DNA firstly, by mass spectrometry and secondly, by whole genome sequencing. In Chapter Three, I show that the impact of deamination during DNA preparation can be minimised, such that the level of genomic ESC uracil can be accurately determined as around 12,000 uracil per genome and that, as anticipated, Ung null ESCs have almost twice the genomic uracil content of wildtype ESCs. Secondly, I address the main question which is the impact of uracil accumulation on methylation levels. In order to do this, I generate two cell lines: Ung knockout and Aid over expressing, both of which should result in an increase in genomic uracil. I demonstrate that while over expression of Aid stimulates demethylation in static system and in a dynamic demethylating system, the impact of Ung knockout is less clear. In (static) serum ESCs, loss of Ung results in hypomethylation however, in order to transition to 2i (naïve) ESCs, a process which involves demethylation of the genome, it appears the Ung is required as loss of this gene inhibits proper demethylation. As such, I conclude that UNG-mediated DNA repair functions alongside passive demethylation, by reduction of UHRF1 levels, to demethylate 2i ESCs. To probe the mechanism by which accumulation of uracil in the genome alters methylation levels, I investigate the impact of Ung KO and Aid OE on global levels of DNA damage. I show that both cell lines have a greater incidence of double strand breaks compared to a wild type cell line, and accordingly, upregulate their DNA damage response pathway and the expression of certain repair genes. I suggest that increasing genomic levels of uracil causes genomic instability and that DNA demethylation occurs as a consequence of the repair of extensive DNA damage. More broadly, I suggest that ESCs are uniquely poised, due to their heightened DNA damage response, to use uracil as an intermediate of DNA demethylation. Interestingly, I also note that the biological impact on serum ESCs of loss of Ung appears to be an increase in pluripotency.

Le potentiel de génération thrombine (TGP en anglais) est une nouvelle mesure qui permet de quantifier in vitro l'activité globale de la thrombine reflétant bien les mécanismes in vivo de la coagulation. Ce méthode de dosage est sensible aux déficits de facteurs de coagulation, à la prise d'anti-coagulants et à de nombreux troubles de la coagulation. Au moment où j'ai débuté ma thèse, seuls deux polymorphismes génétiques, tous les deux situés dans le gène F2 codant pour la prothrombine, étaient connus pour influencer la variabilité plasmatique du TGP. Mon projet de thèse avait pour objectifs d'identifier de nouveaux facteurs génétiques, mais également épigénétiques, pouvant influencer les taux plasmatiques de TGP. Dans une première partie, j'ai mené la toute première étude d'association génome-entier (GWAS pour Genome Wide Association Study en anglais) sur 3 biomarqueurs (temps de latence, quantité totale de thrombine produite et niveau maximal de thrombine produite) du TGP dans deux études françaises rassemblant 1267 sujets et j'ai répliqué les résultats les plus significatifs dans deux autres études françaises indépendantes de 1344 sujets. Cette stratégie a permis de mettre en évidence qu'un polymorphisme génétique du gène ORM1 était associé de manière robuste au temps de latence, biomarqueur caractérisant le temps nécessaire pour initier la coagulation après induction. Dans la seconde partie de ma thèse, en suivant une stratégie similaire mais cette fois-ci en étudiant non plus des polymorphismes génétiques mais des marques de méthylation d'ADN, j'ai recherché si des niveaux de méthylation de site CpG, mesurés à partir d'ADN sanguin et couvrant l'ensemble du génome, pouvaient être associés à la variabilité des 3 mêmes biomarqueurs de TGP. Malheureusement, à partir de deux échantillons mis à ma disposition et rassemblant 425 sujets, je n'ai pas pu mettre en évidence d'association robuste entre des marques de méthylation sanguine et la génération trombine. / Thrombin Generation Potential (TGP) is a promising in vitro measurement that allows quantifying thrombin activity, in a close way to what happens in vivo. It is sensitive to coagulation factors deficiencies, anticoagulant proteins and is associated to thrombotic disorders. There exists two polymorphisms located in the F2 (prothrombin) gene known to influence TGP levels, and altogether they explain 11.3% of the TGP inter-individual variability. With the aims of identifying novel genetic and epigenetic factors that influence TGP variability, I have performed two different studies in the present work. First, I conducted the first genome-wide association study for the three TGP biomarkers (ETP, Peak and Lagtime) using imputation data from two French studies. The most significant single nucleotide polymorphisms (SNPs) were then replicated in two independent French studies. This analysis lead to the discovery of ORM1 as a new gene participating to the control of TGP. Second, I followed a similar strategy using this time whole blood DNA methylation levels at CpG sites to identify DNA methylation marks involved in TGP variability. I analyzed the association between methylation-wide patterns from a French study and a French-Canadian families measured for TGP. Unfortunately, I did not identify robust associations between whole DNA methylation levels and thrombin generation.

De nombreux mécanismes contrôlent et limitent la prolifération des éléments transposables (ET) dans les génomes dont ils menacent l'intégrité structurale et fonctionnelle. Chez les plantes l'interférence ARN (ARNi) joue un rôle important dans ces contrôles via des petits ARN d'environ 20nt qui guident la régulation de l'expression de séquences endogènes ou exogènes par deux types de mécanismes. Un premier mécanisme, partagé par de nombreux organismes eucaryotes, inhibe l'activité d'ARNm par un contrôle post-transcriptionnel. Un deuxième type de régulation, permet un contrôle transcriptionnel de l'activité des ET via un mécanisme appelé RNA directed DNA Methylation (RdDM) qui implique des siARN («  short-interfering RNA ») de 24nt qui guident la méthylation de l'ADN spécifiquement au niveau des séquences d'ET. Les siARN sont impliqués également dans la restauration progressive de la méthylation de l'ADN après une perte induite par la mutation du gène DDM1 (Decrease in DNA Methylation 1). L'objectif de cette thèse est de tirer avantage des technologies de séquençage à haut débit pour caractériser le contrôle des ET par les siARN chez la plante modèle Arabidopsis thaliana.Dans un premier temps, j'ai développé des méthodes et outils bioinformatiques afin de gérer efficacement les données de séquençage à haut débit de banques de petit ARN. Ces outils, regroupés en pipeline, visent à permettre l'étude de l'accumulation des siARN correspondant aux séquences d'ET ou de familles d'ET ainsi que leur visualisation de manière globale ou détaillée.Ces outils ont ensuite été appliqués pour caractériser, dans un contexte sauvage, l'association entre les siARN et les ET afin de déterminer des facteurs pouvant expliquer les différences d'abondance en siARN observées. Ces analyses, réalisées en tenant compte de l'état de méthylation de l'ADN et du contexte génomique des ET apportent une vue statique du contrôle des ET par les siARN et de leur impact sur les gènes situés à proximité.L'analyse de banques de petits ARN de mutants de la voie de l'ARNi a ensuite été réalisée afin mieux caractériser l'impact de la perte de méthylation de l'ADN sur les populations de siARN et notamment définir les mécanismes impliqués dans la production des siARN de 21nt induite dans le mutant ddm1. Ces analyses comparatives du contrôle des ET lors d'une perte de la méthylation de l'ADN ont permis de mettre en évidence une production de siARN de 24nt indépendante de la voie classique du RdDM et de proposer un modèle permettant d'expliquer la production de siARN de 21nt dans le mutant ddm1.Dans un dernier temps, j'ai cherché à mieux définir l'implication des siARN dans la restauration des états de méthylation de l'ADN. Les variations de méthylation de l'ADN induites par la mutation ddm1 ont été caractérisées ainsi que leur stabilité transgénérationnelle au sein d'une population d'epiRIL. La stabilité de l'hypométhylation de l'ADN a été étudiée, au regard de données de séquençage à haut débit de banques de petits ARN de lignées WT, ddm1 ainsi que pour 4 lignées epiRIL, afin d'apporter une notion temporelle à l'étude du contrôle des ET par les siARN.Les résultats soulignent le rôle majeur des petits ARN pour le contrôle des éléments transposables afin de préserver l'intégrité structurale et fonctionnelle du génome et ce, via des mécanismes variés en fonction des ET. Ce travail ouvre la voie vers une analyse du contrôle des ET par les siARN basée sur une approche regroupant les ET en réseaux en fonction des séquences de siARN qu'ils partagent. Cela permettrait d'étudier les « connections-siARN » entre ET afin de, par exemple, explorer l'action en trans des siARN pour la restauration de la méthylation de l'ADN. / Many mechanisms control and limit the proliferation of transposable elements (TEs) which could otherwise threaten the structural and functional integrity of the genome. In plants RNA interference (RNAi) plays an important role in this control through small RNAs that guide the expression regulation of endogenous or exogenous sequences by two types of mechanisms. The first such mechanism, shared by many eukaryotic organisms, acts at the post-transcriptionnal level to inhibit the activity of mRNA. A second type of regulation allows the transcriptional control of TEs activity through a mechanism called RNA directed DNA methylation (RdDM) which involves 24nt long siRNA ("short-interfering RNA") that guide DNA methylation specifically on TEs sequences. Furthermore, siRNAs are also involved in the progressive restoration of DNA methylation after a loss induced by mutation of the DDM1 gene (Decrease in DNA Methylation 1). The aim of this thesis is to take advantage of high-throughput sequencing technologies to characterize these TEs controls mechanisms by siRNA in the model plant Arabidopsis thaliana .At first, I developed methods and bioinformatics tools to effectively manage data produced by high-throughput sequencing of small RNA libraries. These tools, combined in a pipeline, are designed to allow the study the accumulation of siRNA corresponding to TE sequences or TE families as well as their global or detailed visualization.These tools were applied to characterize, in a wild type background, the association between siRNA and TEs in order to define factors that may explain the observed differences in siRNA abundance . These analyses were performed by taking into account both DNA methylation states and genomic context. It provides a static view of siRNA control of TEs and their impact on nearby genes. Then, analysis of small RNA libraries from mutants of the RNAi pathway was performed to better characterize the impact of DNA methylation loss on siRNA populations and to define the mechanisms involved in the production of 21nt siRNA induced in the ddm1 mutant. These comparative analyses of the TE control after loss of DNA methylation allow us to highlight the production of 24nt siRNA independently of the classical RdDM pathway and to propose a model explaining the production of 21nt siRNA in the ddm1 mutant. At last, I tried to clarify the involvement of siRNA in the restoration of DNA methylation. Changes in DNA methylation induced by ddm1 mutation were characterized as well as their transgenerational stability in an epiRIL population. The stability of DNA hypomethylation has been studied in relation to high-throughput sequencing of small RNAs data from WT, ddm1 and 4 epiRIL lines. It provides a temporal view of the TE control by siRNA. The results highlight the important role of small RNAs in the control of transposable elements in order to preserve structural and functional integrity of the genome through a variety of mechanisms depending on TE sequences. This work opens the way to the analysis of the siRNA control on TEs based on approaches that combine TEs in networks based on their shared siRNA sequences. It would allow to study "siRNA-connections" between TEs in order to explore, for example, the action in trans of siRNA in the restoration of DNA methylation defect.

O sucesso da gestação, e nascimento da prole saudável, depende da adequada formação, desenvolvimento e funcionamento da placenta. Entretanto, são observadas altas perdas durante o primeiro terço da gestação de embriões bovinos produzidos por transferência de núcleo de célula somática (TNCS), principalmente causadas por alterações placentárias, decorrentes da incompleta reprogramação epigenética no desenvolvimento embrionário. Normalmente, após a fecundação, o DNA paterno é desmetilado durante as primeiras horas do desenvolvimento, enquanto o DNA materno é desmetilado de forma passiva. Entretanto nos embriões TNCS a desmetilação do DNA é tardia e incompleta, resultando numa alteração do padrão epigenético, principalmente nos níveis de metilação (5mC) e hidroximetilação (5hmC) do DNA e nas histonas. Além disso, na gestação TNCS há expressão precoce das moléculas do complexo de histocompatibilidade principal de classe I (MHC-I), associada ao aumento de infiltrados inflamatórios na placenta e à rejeição imunológica ao feto. O objetivo desse trabalho foi de verificar, na placenta bovina TNCS e controle, os níveis globais de 5mC e 5hmC, e de algumas modificações de histonas importantes na formação do trofectoderma ou por serem modificações clássicas, além de imunolocalizar moléculas de MHC-I. Para tanto foram utilizadas amostras de placentônio TNCS no primeiro (n = 5) e terceiro (n = 6) terço gestacional; e como controle, placentônios com controle no primeiro (n = 6) e terceiro (n = 6). Foram realizadas reações de imunohistoquímica para modificações no DNA (5mC, 5hmC) e nas histonas (H3K4me3, H3K27me3, H3K9ac, H3K9me2/3) e para MHC-I (Qa-2 e IL-A88); além de reações de PCR quantitativo para enzimas responsáveis pelas modificações no DNA (DNMT1, TET1, TET3), para alguns genes relacionados com o desenvolvimento da placenta (PAG9, PHDLA2, SNRPN e TSSC4) e para isoformas de MHC-I (NC1-4 e JSP-1). Houve aumento dos níveis globais de metilação, e diminuição de hidroximetilação, na placenta TNCS durante o primeiro trimestre gestacional. Os níveis de H3K4me3 foram estáveis na placenta controle e crescentes na placenta TNCS, enquanto que a H3K27me3 decresceu na placenta controle e foi estável na placenta TNCS. Na placenta TNCS, aos 60 dias, foram observados os menores níveis globais H3K9ac, porém H3K9me2/3 não diferiram entre as idades e tipos gestacionais estudados. Foi identificado MHC-I no trofoblasto do placentônio bovino nas idades analisadas, com variações de intensidade dependendo da isoforma detectada, além de que a placenta controle e a TNCS apresentam padrões diferentes na expressão de MHC-I. De modo geral, o menores níveis de metilação do DNA encontrados na placenta TNCS aos 60 dias de gestação, indica ser um mecanismo compensatório para ativar a expressão gênica. Visto que a as modificações de histona levam a um estado repressivo da expressão gênica, já que a bivalência entre H3K4me3 e H3K27me3 e os níveis de H3K9ac estão diminuídos. Ainda na placenta TNCS aos 60 dias, há uma alta expressão de MHC-I, levando a resposta imune do sistema materno contra os tecidos fetais. Portanto vários eventos são presentes e parecem contribuir para instabilidade da gestação inicial em clones, coincidindo com a alta taxa de perdas gestacionais nessa fase / Pregnancy success depends of adequate placental formation, development and function. Therefore, the highest loses rates are found during first trimester pregnancies of bovine embryos produced by somatic cell nuclear transfer (NT), majorly by placental alterations, due to incomplete epigenetic reprogramming during embrionary development. Normally, after fecundation, paternal DNA is actively demethylated at first hours of development; where as maternal DNA is passively demethylated. However in NT embryos the DNA demethylation is late and incomplete, resulting in changes of epigenetic patterns, majorly in methylation (5mC), hydroxymethylation (5hmC) and histone levels. Furthermore, in NT pregnancy there is premature expression of class I major histocompatibility complex (MHC-I), associated with inflammatory infiltrates increases and immunological rejection against fetus. The aim of this work was to evaluate global levels of 5mC, 5hmC and some posttranslational histone modifications and MHC-I molecules expression of bovine placenta in NT and control models. For this, NT and control bovine placentome were collected at first (n = 6) and third (n = 6) trimester of pregnancy. Immunohistochemistry reactions were performed to assay DNA methylation (5mC) and (5hmC) and posttranslational histone modifications (H3K4me3, H3K27me3, H3K9ac, H3K9me2/3) and MHC-I molecules (Qa-2 e IL-A88). Quantitative PCR reactions were performed to evaluate the expression of DNA modifications related enzymes (DNMT1, TET1 and TET2), MHC-I classical (JSP-1) and non-classical (NC1-4) isoforms, and imprinted genes expression (SNRPN, TSSC4 and PHDLA2). In the NT placenta there was an increase in the global methylation and decreased hydromethylation level at first trimester. Levels of H3K4me3 were constant at control placenta while increased in NT placenta. For H3K27me3, the levels decreased in control placenta and were stable at NT counterparts. At 60 days of pregnancy in NT placenta, were observed low levels of global H3K9ac, but no differences of H3K9me2/3 levels were found between pregnancy ages or type. We identified MHC-I at bovine placentomal trophoblast in all ages analyzed, with intensity variation of different isoforms. In general, low levels of DNA methylation at day 60 of pregnancy of TNCS placenta, indicates a compensatory mechanism to active genic expression. Since histone modifications, in this period, leads to repressive status, because bivalence of H3K4me3 and H3K27me3 and levels of H3K9ac were diminished. Also at day 60 of pregnancy of TNCS placenta, MHC-I is highly expressed and leads to maternal immune response against fetus tissue. In conclusion, several events are present and apparently contribute to early clone pregnancy instability, coinciding with high pregnancy losses in that phase

Mouse embryonic stem cells (mESCs) are an excellent model to study epigenetics and chromatin structure, owing to their self-renewal capabilities and tolerance of dynamic changes to DNA and histone modifications. Culturing conditions impact on the ability of mESCs to effectively recapitulate in vivo developmental states, and this is exemplified by refined culture conditions (termed 2i) that promote a pluripotent ground state. 2i-cultured mESC populations are homogeneous, naïve, and distinct from conventional (serum/LIF-cultured) cells, which exist as a metastable population. Remarkably, 2i-cultured mESCs also display global DNA hypomethylation, with methylation patterns more comparable to the cells of the E3.5 pre-implantation blastocyst. This is distinct from conventional serum-cultured cells, which display DNA methylation profiles that resemble later-stage E6.5 post-implantation epiblasts. The ability to transition between 2i- and serum-culture states is an attractive model for studying the dynamic role of DNA methylation in a variety of processes. DNA hypomethylation has been linked with depletion of the Polycomb-mediated repressive histone mark H3K27me3 from its normal target loci. Polycomb repressive complexes (PRC1 and PRC2) are important developmental regulators that maintain the repression of lineage-specific genes through generating compact higher-order chromatin structures. Polycomb target sites are primarily unmethylated CpG islands (CGIs). However, under conditions of DNA hypomethylation, new (previously methylated) binding sites are unveiled, and Polycomb is redistributed from its normal CGI target regions to intragenic regions. Thus, shifting mESCs to ground state conditions results in both DNA methylation and Polycomb patterns that are quite distinct from their serum-cultured counterparts. In my PhD, I sought to investigate the effect of DNA hypomethylation and Polycomb redistribution on higher-order chromatin structure in the ground state. I used a targeted, single-locus approach (FISH) as well as a genome-wide approach (Hi-C) to analyse differences in chromatin structure between conventionally cultured and ground state mESCs. My work suggests that chromatin structure is globally altered in hypomethylated 2icultured mESCs, with a similar state present in E3.5 mouse blastocysts. Using mESC lines in which DNA methylation levels can be directly manipulated, I was able to dissect the molecular mechanism driving higher-order structure changes in 2i medium, and showed the importance of DNA methylation in directing Polycomb-mediated chromatin compaction. My results may be important in considering the impact of DNA-methylation mediated reprogramming in multiple developmental, disease and regenerative medicine contexts.

The Atlantic salmon (Salmo salar) is an iconic species that dominates the global finfish production sector with increasing market demand. The Scottish industry and government alone aspires for expansion of the sector to 210,000 t by 2020 with 154, 000 t produced in 2013. As such, there are pressures to improve sustainable development in particular to minimise the genetic impact of escapees on wild populations and reduce sea lice infection which are required for the granting of “green licenses” in Norway. The use of triploidy has been tested in the 1980’s with little success owing to suboptimal rearing conditions leading to elevated mortalities, poorer growth and a higher prevalence of deformities, in particular of the skeleton. Collectively: recent success of triploid trout farming, expansion to the salmon production sector and potential resulting pressure on wild stocks through escapee increases have reinstated interest to implement artificially induced triploid Atlantic salmon in commercial production. As diploid Atlantic salmon have undertaken extensive domestication to achieve the high quality production and welfare standards observed to date, triploid conspecifics too require husbandry optimisation to realise potential. In particular, industrialisation requires that higher observations of deformities and inconsistent growth trajectories during seawater ongrowing be resolved through optimisation of rearing regimes and subsequent standardization of husbandry protocols. Triploids possess additional genomic material and increased cell size yet reduced frequency that reflects known differences in physiology and supports that, in effect, triploids should be considered as a new species relative to diploid conspecifics. Therefore, this doctoral thesis aimed to study nutrition and temperature effects on triploid Atlantic salmon traits throughout the production cycle from ‘egg to plate’. Nutrition trials aimed to improve growth potential and mitigate skeletal deformities both in freshwater (FW) and saltwater (SW) whilst attempts were made to define a window of smoltification to ensure optimal ongrowing performance. Finally, impacts of embryonic temperature regimes that are known to impact long term performance and deformity development in triploids, were examined in relation to DNA regulation and yolk composition in an attempt to underpin potential mechanisms for the environmental impact of temperature on developmental phenotype. One of the main restrictions to triploid Atlantic salmon implementation is the increased prevalence and severity of skeletal deformities, particularly after the maring phase. The work performed in this thesis first demonstrated that protein and/or phosphorous (P) supplementation throughout SW ongrowing not only reduced the level of severely deformed (≥ 10 deformed vertebrae observable by x-radiography) individuals by 30 % but also sustained 6.8 % faster growth and improved harvest grade compared to triploids fed a standard grower diet (chapter 2). Comparison of x-radiography and severely deformed individuals between harvest and sea transfer highlighted that protein and P supplementation arrested deformity development whereas prevalence increased in triploids fed a standard grower diet. This implied that severe deformities were of FW origin and strongly suggest requirement for improved nutrition in FW to optimise SW performance. Therefore investigation of higher dietary P inclusion in FW was investigated and results showed significantly reduced number of deformed vertebrae and no severely deformed individuals in those fed 19.7 g total P Kg-1 compared with those fed 13.0 & 16.7 g total P Kg-1 (chapter 3). Most deformities were localised in the central (vertebrae 27 – 31) and caudal (vertebrae 52 – 57) regions for all treatments. However, triploids fed lower dietary P displayed a particular increase in prevalence within the tail region (vertebrae 32- 47) which is consistent with SW ongrowing reports and results from chapter 2, further highlighting FW origin of higher vertebral deformities reported in SW ongrowing in triploids. Higher P supplementation in FW also significantly improved growth in triploid parr compared to diploids and lower supplementation. However, this effect did not transpire in later FW smolt stages where weights were significantly higher in triploids fed lower compared to higher P supplementation. Expression of target genes involved in osteogenesis and bone P homeostasis in vertebrates were then analysed and a ploidy effect of osteogenic genes alp, igf1r and opn as well as a dietary effect on P homeostasis gene fgf23 was apparent in the parr stages but not smolt. In addition, stronger ploidy-diet effects were also observed in parr stages for whole body mineral concentrations. Collectively, growth, gene expression and whole body mineral content results indicate these earlier parr life stages may be more sensitive to P supplementation. This pronounced effect may be a consequence of seasonal accelerated growth associated with this period, where higher temperatures were also observed. The potential for shorter P supplementation windows in commercial production was addressed in chapter 4 with hope to cut economic cost to raw mineral inclusion in feed and also mitigate potential anthropogenic eutrophication on the environment that may be induced by P leached through uneaten feed and faeces. Triploids were fed higher dietary P (17.4 g total P Kg-1) until either early (5 g) or later (20 g) parr stages, or smolt (83 g) and monitored for performance throughout freshwater (FW) development. During later parr development (30 g), x-radiography assessment demonstrated that increased dietary P reduced the number of deformities and severely deformed individuals with no indication that feeding P for shorter windows improved skeletal integrity. Hence, P supplementation may be required throughout FW development for optimal skeletal performance. In addition, no differences in deformities were observed between triploid treatments at smolt. An effect of dietary P supplementation on whole body mineral concentration was observed in the early and later parr stages that was not as pronounced as smolt, which is consistent with results in chapter 3. Together, these results indicate that skeletal assessment during early developmental stages may not reflect smolt performance most likely as a consequence of seasonal effects of improved linear growth in the cooler winter temperatures prior to smolt where reversible deformities observed at parr may also be alleviated. In the same study (chapter 4), the inclusion of the probiotic Pediococcus acidilactici (Bactocell™) was also tested as a means to enhance gut assimilation as suggested in previous studies and therefore reduce the levels of P supplementation. Results clearly indicate superior skeletal performance in parr (30 g) as well as significantly less deformed vertebrae and no severely deformed individuals. However, at smolt (~83g), no effects of the dietary probiotic treatment were observed which may also be attributed to seasonal effects. Overall, nutritional research clearly indicate triploids require higher dietary P for optimal growth and skeletal development, which although is not consistent between life stages, is ultimately required throughout FW for optimal skeletal development at smolt. The use of probiotics offer a promising avenue for reduced P requirement in FW feed and further research should verify results and assess long-term performance. Timing of SW transfer according to correct parr-smolt transformation (PST) is essential for survival and growth performance in ongrowing where feeding and growth rate accelerate post-transfer. So far, SW transfer regimes and in particular the smoltification ‘window’ remains loosely defined in triploid Atlantic salmon and it is crucial that this be addressed to ensure optimal ongrowing survival and performance.

INTRODUÇÃO: A expansão e disseminação do consumo de crack e cocaína no Brasil vem se tornando um grave problema de saúde pública nos últimos vinte anos. Diferentes abordagens biológicas têm sido investigadas utilizando o fenótipo de abuso/dependência de crack/cocaína, cujos resultados têm demonstrado a participação importante do substrato genético, assim como a sua interação com os fatores ambientais no desenvolvimento desse transtorno. OBJETIVOS: Investigar o padrão de metilação do DNA do genoma de indivíduos que apresentam abuso/dependência de cocaína e de crack, comparando ao padrão de metilação de indivíduos controles. MÉTODOS: Foram selecionados 24 dependentes de cocaína e crack e 24 controles saudáveis, pareados por sexo e idade. Utilizando amostras de DNA extraídas de sangue periférico de cada um dos participantes, foi realizada a técnica de metilação global com o ensaio Illumina Infinium Human Methylation450 (450K) BeadChip. Os resultados iniciais foram normalizados considerando a heterogeneidade celular e analisados utilizando o pacote ChAMP (Chip Analysis Methylation Pipeline) para identificar genes e/ou regiões gênicas diferencialmente metiladas que possam representar fatores de vulnerabilidade para o comportamento de abuso/dependência do crack e da cocaína. Os processos biológicos e vias celulares com os quais os sítios diferencialmente metilados estão envolvidos foram explorados usando as ferramentas disponibilizadas pelo \"WebGestalt\" e pelo \"UCSC Genome Browser\". RESULTADOS: Foram observados 250 sítios diferencialmente metilados, associados a 246 genes na comparação dos perfis de metilação entre os casos e controles, sendo que 49% destes estavam localizados nas regiões promotoras dos genes, sugerindo que esses sítios podem estar relacionados com a expressão gênica. Alterações estatisticamente significantes no padrão de metilação entre casos x controles foram observadas em 23 sítios CpG (p-valor ajustado < 10-5 e |?beta| = 0,1). Observou-se também que três regiões diferencialmente metiladas foram associadas a genes hipometilados (BMP8A, GPR88 e RNF166) (p-valor ajustado < 0.05), cada uma com pelo menos três sítios. Alterações estatisticamente significantes também foram observadas em seis genes hiper-representados: CALCA, NCOA2, DRD2, EHMT1, EHMT2, MAP2K1, MAPK3 e MAPK1, envolvidos em processos biológicos e moleculares. CONCLUSÕES: Observou-se diferenças estatisticamente significativas no padrão de metilação genômico de usuários/dependentes de crack e cocaína quando comparados aos controles saudáveis em amostra de DNA extraídas de sangue periférico. Comparação de estudos de expressão em tecido cerebral correlacionaram-se parcialmente com os achados apresentados. Outros estudos utilizando amostras independentes são necessários para confirmar esses achados. A confirmação desses resultados poderá contribuir na identificação e compreensão dos mecanismos biológicos envolvidos na dependência do crack/cocaína / BACKGROUND: The expansion and dissemination of crack and cocaine in Brazil has become a progressive and serious public health problem during the last twenty years. Different biological approaches have been investigated using the crack/cocaine abuser/dependent phenotype, with results confirming the important role of the genetic component, as well as its interaction with environmental factors. OBJECTIVES: To investigate the DNA methylation pattern levels in the genome of individuals with crack and cocaine abuse/dependence and comparing it with the DNA methylation pattern of the genome of control subjects. METHODS: 24 crack and cocaine abusers/dependents and 24 healthy controls were selected and matched by sex and age. Using DNA samples from peripheral blood of each participant, a global methylation technique was performed using the Illumina Infinium Human Methylation450 (450K) Bead Chip assay. The initial results were normalized for cellular heterogeneity and re-analyzed using ChAMP package (Chip Methylation Analysis Pipeline) to identify differentially methylated genes or/and DNA regions that may represent biological/genetic risk factors for crack and cocaine abuse/dependence behavior. The biological processes and cellular pathways were explored using tools provided by \"WebGestalt\" and \"UCSC Genome Browser\". RESULTS: 250 differentially methylated sites associated with 246 genes in methylation comparison profiles between cases and controls were identified, of which almost half were located in the promoter regions of genes (49%), suggesting that these sites may be related to gene expression. Statistically significant changes in the methylation patterns between cases and controls were observed in 23 CpG sites (adjust p-value < 10-5 and |deltabeta| = 0.1). In addition, three differentially methylated regions were associated with hipomethylated genes (BMP8A, GPR88 e RNF166) (adjust p-value < 0.05), each one with at least three sites. Statistically significant changes were also observe with six hiper-represented genes: CALCA, NCOA2, DRD2, EHMT1, EHMT2, MAP2K1, MAPK3 e MAPK1, which are involved in biological and molecular processes. CONCLUSIONS: Crack and cocaine users/dependents presented significant statistical differences in the methylation pattern when compared to healthy controls in DNA samples extracted from peripheral blood. Results from gene expression studies using brain tissue can be correlated with our results. In order to confirm the present findings, future studies should be replicated using independent samples. The confirmation of these results will contribute to the understanding of the biological mechanisms involved in crack/cocaine dependence