Deux parties principales composent cette thèse. La première d'entre elles est consacrée à la valvométrie, c'est-à-dire ici l'étude de la distance entre les deux parties de la coquille d'une huître au cours du temps. La valvométrie est utilisée afin de déterminer si de tels animaux sont en bonne santé, pour éventuellement tirer des conclusions sur la qualité de leur environnement. Nous considérons qu'un processus de renouvellement à quatre états sous-tend le comportement des huîtres étudiées. Afin de retrouver ce processus caché dans le signal valvométrique, nous supposons qu'une densité de probabilité reliée à ce signal est bimodale. Nous comparons donc plusieurs estimateurs qui prennent en compte ce type d'hypothèse, dont des estimateurs à noyau.Dans un second temps, nous comparons plusieurs méthodes de régression, dans le but d'analyser des données transcriptomiques. Pour comprendre quelles variables explicatives influent sur l'expression de gènes, nous avons réalisé des tests multiples grâce au modèle linéaire FAMT. La méthode SIR peut être envisagée pour trouver des relations non-linéaires. Toutefois, elle est principalement employée lorsque la variable à expliquer est univariée. Une version multivariée de cette approche a donc été développée. Le coût d'acquisition des données transcriptomiques pouvant être élevé, la taille n des échantillons correspondants est souvent faible. C'est pourquoi, nous avons également étudié la méthode SIR lorsque n est inférieur au nombre de variables explicatives p. / There are two main parts in this thesis. The first one concerns valvometry, which is here the study of the distance between both parts of the shell of an oyster, over time. The health status of oysters can be characterized using valvometry in order to obtain insights about the quality of their environment. We consider that a renewal process with four states underlies the behaviour of the studied oysters. Such a hidden process can be retrieved from a valvometric signal by assuming that some probability density function linked with this signal, is bimodal. We then compare several estimators which take this assumption into account, including kernel density estimators.In another chapter, we compare several regression approaches, aiming at analysing transcriptomic data. To understand which explanatory variables have an effect on gene expressions, we apply a multiple testing procedure on these data, through the linear model FAMT. The SIR method may find nonlinear relations in such a context. It is however more commonly used when the response variable is univariate. A multivariate version of SIR was then developed. Procedures to measure gene expressions can be expensive. The sample size n of the corresponding datasets is then often small. That is why we also studied SIR when n is less than the number of explanatory variables p.

La spondyloarthrite (SpA) est un rhumatisme inflammatoire chronique fréquent et invalidant. Plus d’une vingtaine de locus de susceptibilité à la maladie ont été identifiés à ce jour, dont HLA-B27 situé dans le complexe majeur d’histocompatibilité (CMH). L’objectif de ce travail était d’identifier de nouveaux facteurs génétiques de susceptibilité à la SpA grâce à une double approche d’études familiales et de génomique fonctionnelle. Dans la première partie, nous avons génotypé des familles multiplex de SpA. L’analyse de liaison non paramétrique a révélé la présence, en plus du CMH, d’un nouveau locus significativement lié à la SpA en 13q13. L’étude de ce locus nous a permis de restreindre la région d’intérêt à un intervalle de 1,3 Mb, dont le séquençage est en cours. Par ailleurs, l’étude d’association intra-familiale a identifié un SNP intronique de MAPK14 significativement associé à la SpA. Enfin, nous avons montré que l’un des SNPs du gène IL23R connu pour être associé à la spondylarthrite ankylosante était en fait associé à la présence d’une sacro-iliite radiologique dans la SpA. Parallèlement aux études familiales, nous avons comparé le transcriptome de cellules dendritiques de neuf patients atteints de SpA à celui de dix témoins sains. Nous avons ainsi identifié 81 gènes différentiellement exprimés. Nous avons aussi montré que l’expression génique d’ERAP1 (et à un moindre degré son expression protéique et son niveau d’activité enzymatique) étaient sous le contrôle de polymorphismes de ce gène associés à la SpA. / Spondyloarthritis (SpA) is a frequent and disabling chronic rheumatic disease. To date, more than 20 susceptibility loci have been identified, including HLA-B27 in the major histocompatibility complex (MHC). Most of the disease heritability remains to be elucidated. The aim of the study was to identify new genetic factors of susceptibility to SpA using an approach combining genetics and functional genomics. In the first part of this work, we genotyped SpA multiplex families with microarrays of 250,000 SNPs. Non parametric linkage analysis revealed a new locus significantly linked to SpA outside the MHC, in 13q13. Further studies on this locus allowed us to map the disease interval to a 1.3 Mb region, which will be soon sequenced. Moreover, family-based association study identified a significant association between one intronic SNP in MAPK14 and SpA. We also showed that one of the known ankylosing spondylitis-associated SNP in IL23R was indeed associated with sacroiliitis in SpA. We have also compared dendritic cells gene expression between nine SpA patients and ten controls and identified 81 genes differentially expressed. Moreover, we showed that ERAP1 gene expression (and at a less extent protein expression and enzymatic activity) is under the control of several polymorphisms in the gene which has previously been associated with SpA.

Disease and bleaching are two conditions which commonly lead to coral death. Among coral species, susceptibility to disease and bleaching is variable, and Pseudodiploria strigosa tends to be diseased more than Diploria labyrinthiformis, while D. labyrinthiformis bleaches more readily. The focus of this dissertation was to investigate and compare multiple components of these two coral species, and identify how they may relate to disease and bleaching resistance. Compenetnts examined included the surface mucopolysacharide layer (SML) thickness, gene expression, microbial associates, and a white plague aquarium study. The SML thickness decresased with increasing temperature regardless of coral species, indicating that SML thickness does not likely play a role in differences between susceptablities of these two coral species. However, Diploria labyrinthiformis had a lower mortality rate at 31°C, had fewer differentially expressed genes assossiated with stress, and upregulated genes associated with innate immunity in the summer, all of which may contribute to its relative disease resistance. The bacterial associates of each coral species were also monitored. Differences between the two coral species were primarily caused by Clostridia, Gammaproteobacteria, and rare species which may contribute to the relatively higher disease susceptibility of P. strigosa. Lastly, an aquarium study suggested that a potential pathogen of the Roseobacter clade infects both D. labyrinthiformis and P. strigosa, and might be transmitted by the Cryptochiridae gall crab, indicating that potential disease vectors associated with these two coral species may also play a role in disease resistance and resilience.

The demise of reef-building corals potentially lies on the horizon, given ongoing climate change amid other anthropogenic environmental stressors. If corals cannot acclimatize or adapt to changing conditions, dramatic declines in the extent and health of the living reefs are expected within the next half century. The primary and proximal global threat to corals is climate change. Reef-building corals are dependent upon a nutritional symbiosis with photosynthetic dinoflagellates belonging to the group Symbiodinium. The symbiosis between the cnidarian host and algal partner is a stress-sensitive relationship; temperatures just 1°C above normal thermal maxima can result in the breakdown of the symbiosis, resulting in coral bleaching (the loss of Symbiodinium and/or associated photopigments) and ultimately, colony death. As ocean temperatures continue to rise, corals will either acclimatize or adapt to changing conditions, or will perish. By experimentally preconditioning the coral Acropora millepora via sublethal heat treatment, the coral acquired thermal tolerance, resisting bleaching during subsequent hyperthermal stress. The complex nature of the coral holobiont translates to multiple possible explanations for acclimatization: acquired thermal tolerance could potentially originate from the host itself, the Symbiodinium, or from the bacterial community associated with the coral. By examining the type of in hospite Symbiodinium and the bacterial community prior acclimation and after thermal challenge, it is shown that short-term acclimatization is not due to a distinct change in the dinoflagellate or prokaryote community. Though the microbial partnerships remain without considerable flux in preconditioned corals, the host transcriptome is dynamic. One dominant pattern was the apparent tuning of gene expression observed between preconditioned and non-preconditioned treatments, showing a modulated transcriptomic response to stress. Additionally several genes were upregulated in association with thermal tolerance, including antiapoptotic genes, lectins, and oxidative stress response genes. Upstream of two of these thermal tolerance genes, inhibitor of NFκB and mannose-binding lectin, DNA polymorphisms were identified which vary significantly between the northern and southern Great Barrier Reef. The impact of these mutations in putative promoter regions remains to be seen, but variation across thermally-disparate geography serves to generate hypotheses regarding the role of regulatory element evolution in a coral adaptation context.

La spermatogenèse chez les mammifères est une fonction biologique complexe incluant des processus de prolifération cellulaire, de méiose et de différenciation uniques visant à la production des gamètes mâles au sein du testicule. Si l’épithélium séminifère est bien décrit sur le plan de son organisation et de la morphologie des cellules qui le composent, les processus par lesquels les cellules germinales diploïdes indifférenciées entrent en méiose pour donner ensuite des cellules haploïdes subissant par la suite de nombreuses transformations morphologiques, ne sont pas totalement décryptés. Ils reposent sur l’expression coordonnée et séquentielle de gènes dont les produits spécifiques de chaque stade de développement des cellules germinales sont essentiels aux étapes clés de la spermatogenèse. La transcriptomique depuis les années 1990 et la protéomique depuis les années 2000 ont contribué à l’amélioration de la connaissance de ces mécanismes. Une étude protéomique visant à caractériser par des approches systématiques et différentielles les protéomes des cellules de Sertoli et de la lignée germinale, et d’autre part une étude récente, réalisée dans notre unité, qui a permis de caractériser et de quantifier le transcriptome des cellules testiculaires isolées de rat en utilisant le séquençage de novo des transcrits (RNA-Seq), ont été à la base de mes travaux de thèse. Cette dernière étude a mis en évidence l’accumulation de longs ARNs non codants (lncRNAs) et de transcrits testiculaires non annotés (TUTs) aux stades méiotique et post- méiotique de la spermatogenèse chez le rat. Dans ce contexte, mon travail a consisté à valider le potentiel codant de nombreux gènes exprimés dans les cellules germinales par une approche dite PIT (Proteomics Informed by Transcriptomics) couplant protéomique Shotgun et RNA-Seq. Dans ce type d’approche, les séquences protéiques déduites des transcrits des différents types cellulaires, assemblés par RNA-Seq, sont intégrées dans une base personnalisée de séquences protéiques utilisée pour interroger les données de spectrométrie de masse obtenues à partir de protéines de cellules méiotiques et post-Méiotiques. L’approche PIT a permis de montrer que 69 TUTs ou lncRNA (correspondant à 44 loci) codent pour des protéines dans les cellules méiotiques et post méiotiques. L’expression post-Méiotique de deux nouveaux transcrits, l’un codant pour la protéine VAMP9, une protéine de la famille SNARE, et l’autre pour une nouvelle énolase T-ENOL a pu être confirmée. L’expression post-Méiotique de T-ENOL a été confirmée par immunohistochimie à l’aide d’un anticorps polyclonal produit contre la protéine recombinante. Cette approche nous a également permis d’identifier de nouvelles isoformes de protéines connues spécifiques de chaque stade de la spermatogenèse. Les cellules germinales et les cellules de Sertoli entretiennent le dialogue nécessaire au bon déroulement de la spermatogenèse. Une autre partie de mon travail a consisté à identifier des protéines membranaires des cellules germinales et des corps résiduels, susceptibles d’intervenir dans le dialogue entre les cellules de Sertoli et les cellules germinales, par une approche protéomique de quantification relative ICPL. Cette approche a permis d’établir une liste de 166 protéines différentiellement exprimées entre les spermatocytes pachytène, les spermatides rondes et les corps résiduels, qui sont susceptibles de jouer un rôle dans la spermiogénèse. Grâce aux annotations de le Gene Ontology, j’ai pu établir une liste de 8 protéines ayant un rôle supposé dans la transduction du signal, la reconnaissance cellulaire ou bien la différenciation. Par ailleurs, j’ai pu établir par protéomique Shotgun un premier protéome des cellules de Sertoli, des cellules germinales et des corps résiduels chez le rat. / Spermatogenesis in mammals is a complex biological function including cellular processes such as proliferation, meiosis and differentiation, aiming to the production of male gametes in the testis. If the seminiferous epithelium is well described in terms of organization and cellular morphology of cells that compose it, the processes by which undifferentiated diploid germ cells enter meiosis and give haploid cells that undergo many morphological transformations, are not fully decrypted. These processes rely on the coordinated and sequential expression of genes, including specific products for each stage of germ cell development These gene products are essential at each key stage of spermatogenesis. Transcriptomics since the 1990s, and proteomics since the 2000s have contributed to the improved. understanding of these mechanisms. A long term proteomic study aiming at characterizing the proteomes of Sertoli cells and germ cells, and a recent study that characterized and quantified the transcriptome of isolated rat testicular cells at high resolution using de novo sequencing of transcripts (RNA-Seq), have been the basis of my thesis work. The latter study showed the accumulation of long non-Coding RNAs (lncRNAs) and testicular unannotated transcripts (TUTs) at meiotic and post-Meiotic stages of spermatogenesis in the rat. In this context, my thesis work aimed at validating the coding potential of many genes expressed in germ cells using RNA-Seq combined with shotgun proteomics, a so-Called PIT (Proteomics Informed by transcriptomics) approach. In this approach, the protein sequences translated from the transcripts assembled by RNA-Seq in the different testicular cell types are integrated into a custom database of protein sequences used to query mass spectrometry data obtained from proteins of meiotic and post-Meiotic cells. The PIT approach showed that 69 TUTs or lncRNA (corresponding to 44 loci) code for proteins in meiotic cells and post meiotic cells, and we confirmed experimentally the meiotic and post-Meiotic expression for two new transcripts encoding for VAMP9, a protein of the SNARE family, and a new testicular enolase T-ENOL. The post-Meiotic expression of T-ENOL protein was confirmed by immunohistochemistry using a polyclonal antibody raised against the recombinant protein. This approach also allowed us to identify new isoforms of known proteins, specific to each stage of spermatogenesis. Germ cells and Sertoli cells maintain a dialogue which is necessary to the success of spermatogenesis and spermiogenesis. Another part of my work aimed at identifying membrane proteins, in germ cells and residual bodies, that may be involved in the dialogue between Sertoli cells and germ cells, using a ICPL relative quantification proteomic approach. The ICPL analysis enabled us to establish a list of 166 proteins whose expression is differential between pachytene spermatocytes, round spermatids and residual bodies. Their differential expression suggests that these proteins may play a role in spermiogenesis. Thanks to the Gene Ontology annotations, a list of 8 proteins with a putative role in signal transduction, cell recognition or differentiation, thus potentially involved in the dialogue between Sertoli and germ cells was drawn. In addition, I provided a first proteome of rat Sertoli cells, germ cells and residual bodies obtained by shotgun proteomics.

L'identification de biomarqueurs et de nouvelles cibles thérapeutiques constitue un enjeu majeur de la recherche biomédicale visant au développement de la médecine personnalisée. L'objectif de cette thèse est d'étudier, à l'aide de puces à ADN, les modulations transcriptionnelles associées à la pathogénèse et à la réponse thérapeutique dans le cas de deux pathologies: l'infection par le Virus de l'Hépatite C (VHC) et la Polyarthrite Rhumatoïde (PR).Des biomarqueurs prédictifs de la réponse au traitement standard interféron ont été identifiés grâce à un modèle cellulaire ex vivo. Par ailleurs, l'analyse de données d'expression de deux modèles d'infection par le VHC (réplicon et infectieux) a permis de mettre en évidence les modulations transcriptionnelles résultant de l'activité antivirale de la chloroquine, une alternative potentielle anti-VHC. Dans le cas de la PR, nous avons identifié des biomarqueurs dont l'expression est corrélée au succès thérapeutique de l'anti-TNF Enbrel. / The identification of biomarkers and new therapeutic targets is a major challenge of biomedical research for the development of personalized medicine. The objective of this thesis is to study, using DNA microarrays, transcriptional modulations associated with the pathogenesis and therapeutic response in the case of two diseases: infection with Hepatitis C Virus (HCV) and Rheumatoid Arthritis (RA).Predictive biomarkers of response to standard interferon treatment were identified using an ex vivo cell model. Furthermore, analysis of expression data of two models of infection with HCV (replicon and infectious) has highlighted the transcriptional modulations resulting from the antiviral activity of chloroquine, a potential anti-HCV alternative. In the case of RA, we have identified biomarkers whose expression correlates with the therapeutic success of Enbrel anti-TNF drug.

Le glioblastome (GB) est une tumeur hétérogène, agressive devant laquelle les possibilités thérapeutiques disponibles restent limitées. L’étude de la zone péritumorale macroscopiquement normale (ZMN) des GB est essentielle à la compréhension de ses mécanismes de progression et de récidive. Le premier objectif de ce travail de Thèse a été de comparer les données de transcriptomique et de protéomique issues de l’analyse de la zone tumorale des GB dans le cadre du Projet Gliome Grand Ouest. Le taux de concordance entre les 2 modalités est faible, retrouvant toutefois comme point commun une dysrégulation de la protéine légère des neurofilaments qui pourrait servir de biomarqueur potentiel des GB. Le deuxième objectif de ce travail de Thèse a été la caractérisation de la ZMN des GB. Nous avons mis en évidence que cette zone, dont l’aspect est similaire à première vue à celui du tissu cérébral sain, n’est pas une simple zone de transition entre le GB et le tissu cérébral sain. En effet, la ZMN est une entité spécifique possédant des caractéristiques qui lui sont propres, comme la présence d’un phénotype particulier de cellules tumorales infiltrantes et de cellules stromales et une sur’expression des protéines CRYAB et H3F3A. Ce travail de Thèse a aussi été l’occasion de développer de nouvelles techniques d’imagerie per-opératoire de la ZMN, afin d’évaluer la présence d’un contingent tumoral et ainsi optimiser la qualité de la résection chirurgicale. La caractérisation de cette ZMN nous permet de mieux appréhender son implication dans la tumorogenèse et la présence de caractéristiques spécifiques de cette zone ouvre la porte à la détection de biomarqueurs spécifiques, ainsi qu’au développement de thérapies ciblées. Ce travail de Thèse a été valorisé par 2 publications, 2 articles soumis et un brevet est en cours de dépôt et d’évaluation par un cabinet de brevet. / Glioblastoma (GB) is a heterogeneous andaggressive tumor, before which therapeutic options arelimited. The study of the macroscopically normalperitumoral brain zone (PBZ) of GB is essential tounderstand its mechanisms of progression andrecurrence.The first objective of this thesis work was tocompare the transcriptomic and proteomic data from theGB tumor area obtained through the “Grand Ouest”glioma Project. The concordance rate between the 2modalities is low. However, one of the common featureis the dysregulation of neurofilament light polypeptide,which could serve as a biomarker potential of GB.The second objective of this thesis was thecharacterization of the PBZ. We have shown that thisarea, similar at first glance to that of healthy braintissue, is not a simple transition area between the GBand healthy brain tissue but a specific entity withcharacteristics of its own. For example, the ZMNpresents a particular phenotype of infiltrating GB cellsand stromal cells and a surexpression of CRYAB andH3F3A proteins.This thesis work was also an opportunity todevelop new intraoperative imaging techniques of thePBZ, with the aim to assess the presence of a tumoralinfiltration and optimize the quality of the surgicalresection.The characterization of this PBZ allows us tobetter understand its involvement in tumorigenesis andthe presence of specific characteristics of this areaopens the door for the detection of specific biomarkersand the development of targeted therapies.This thesis work was led to 2 publications, 2articles submitted and a patent being evaluated andredacted by a patent office.

Les systèmes à deux composants jouent un rôle prépondérant dans l'adaptation des bactéries à leur environnement. L'objectif de ce travail de thèse était d'identifier et de caractériser des systèmes à deux composants chez la bactérie phytostimulatrice Azospirillum nécessaires à l'adaptation à la rhizosphère de sa plante-hôte. L'analyse de la distribution génomique des gènes appartenant à la famille des systèmes à deux composants dans les génomes d'Azospirillum disponibles a révélé l'existence d'un grand nombre de gènes codant des hisitidine kinases hybrides, et une analyse plus approfondie a montré une organisation multidomaines complexe de cette famille de protéines. Afin de comprendre leur rôle chez Azospirillum, nous avons, dans un premier temps, sélectionné et inactivé quatre gènes codant des histidine kinases hybrides présentant une architecture multidomaines complexe. A l'aide d'une approche multidisciplinaire combinant génétique, biochimie et phylogénie, nous avons mis en évidence pour la première fois chez Azospirillum, un système atypique à trois-composants nommé PreSKR contrôlant un grand nombre de processus impliqués dans la survie et la colonisation de la rhizosphère, qui agirait en modulant le taux intracellulaire de c-di-GMP. Dans un second temps, nous nous sommes focalisés sur une histidine kinase hybride exprimée au contact de la plante hôte ; cette protéine, appelée RsiK, s'avère être impliquée dans la perception de surfaces et la régulation de la formation de biofilms. L'analyse du régulon par RNA-seq a révèlé que 78 gènes étaient contrôlés par ce système. La prévalence de la famille des histidine kinases hybrides chez Azospirillum couplée à l'approche fonctionnelle réalisée sur deux d'entre elle souligne l'importance des phosphorelais encore largement méconnus chez les bactéries rhizosphériques / Bacterial two-component systems play an important role in the ability of bacteria to adapt to various environments. The aim of this thesis was to identify and characterize two-component systems involved in the adaptation of the phytostimulatory bacteria Azospirillum to its host plant. Analysis of the genomic distribution of genes encoding two-component systems across Azospirillum available genomes revealed the existence of a high number of genes encoding hybrid histidine kinases, and further analyses highlighted a complex multi-domain organization of this family of proteins. In order to understand their role in Azospirillum, as a first step we selected and inactivated four genes encoding complex hybrid histidines kinases. Using a multidisciplinary approach which combines genetics, biochemistry and phylogeny, we brought to light for the first time in Azospirillum, an atypical three-component system named PreSKR which controls a wide variety of processes involved in survival and rhizosphere colonization likely by modulating c-di-GMP levels. As a second step, we focused on a gene encoding a hybrid histidine kinase named RsiK which is induced in contact with its host plant. RsiK is involved in surface sensing and biofilm formation regulation. Transcriptomic analysis of rsiK regulon by RNA-seq showed that 78 genes were under the control of this system. The prevalence of genes encoding hybrid histidine kinase family in Azospirillum, coupled with the functional characterization of two of them, highlight the importance of phosphorelays, still largely unrecognized in rhizospheric bacteria

Craniofacial development is a tightly regulated event that requires expression of many genes at a precise space-temporal specificity. Interference in the regulation of such genes and their pathways is known to lead to abnormal phenotypes affecting the face and cranium. In this manner, regulation of these pathways is further complicated by interaction between genetic and environmental factors such that disturbance to either may result in craniofacial malformation, as orofacial clefts. Despite several at-risk loci have been identified, they do not completely explain the high heritability observed for the orofacial clefts and many questions remain open. For example, concerning the orofacial clefts transcriptome, the gene pathways which may be dysregulated and the affected cellular processes are still poorly understood. Further, if there is gene expression dysregulation in orofacial clefts, the causes leading to that need to be elucidated, such as the investigation of epigenetic factors. Also, since the multifactorial contribution makes environment relevant to this malformation, epigenetic and epigenomic differences in orofacial clefts should clarified. At last, rare syndromic forms of orofacial clefts with still unknown molecular cause and mechanisms should be elucidated in order to better understand craniofacial development and their impact in non-syndromic forms. Therefore, the main objective of this study was to investigate the molecular mechanisms involved in the aetiology of orofacial clefts, which was focused in gene expression and epigenetic analysis in non-syndromic cleft lip and/or palate (NSCL/P) as well as genetic, gene expression, animal modelling and epigenetics in Richieri-Costa-Pereira Syndrome (RCPS), a rare autosomal recessive syndromic form of orofacial cleft. We found significant transcriptome differences in NSCL/P in comparison to controls, revealing the BRCA1-dependent DNA damage repair pathway as compromised in NSCL/P cells leading to DNA damage accumulation. Next, we studied the potential of DNA methylation in those cells and found a slight but significant increase of BRCA1 promoter DNA methylation in NSCL/P cells and a distinct DNA methylation distribution, point to a possible epigenetic contribution in this phenomenon. We also evaluated the contribution of DNA methylation in 8q24.21 region, one of the most replicated regions in NSCL/P Genome-wide association studies and found no significant differences in our sample. Attempting to investigate DNA methylation in NSCL/P in an epigenomic level, we analysed methylomes and found 578 methylation variable positions in NSCL/P, highly enriched in regulatory regions and in relevant gene pathways for craniofacial development as Epithelial-Mesenchymal Transition pathway. We also studied effect of DNA methylation in familial NSCL/P displaying incomplete penentrance and found a significant increase of CDH1 promoter hypermethylation in penetrant cases in comparison to non-penetrants. Finally, by the use of different sequencing strategies and identity-by-descent analysis we mapped the mutation region of RCPS to EIF4A3 5\'UTR/promoter and found a complex structure of expanded repeats in RCPS patients leading to EIF4A3 downregulation. We were also able to validate the phenotypes using an animal modelling strategy in zebrafish. Because those repeats are CG rich, we investigated whether they were submitted to DNA hypermethylation in RCPS patients as a cause for EIF4A3 hypomorphism, however we found no evidence of methylation increase in RCPS. In conclusion, we were able to associate dysregulated pathways to NSCL/P susceptibility and DNA methylation differences to both non-familial and familial NSCLP. Besides, we were able to identify the genetic cause of RCPS, which now can be molecularly diagnosed. Altogether, our results add to the understanding of craniofacial development and the aetiology of orofacial clefts / O desenvolvimento craniofacial é um evento finamente regulado que requer a expressão de muitos genes em uma precisão espaço-temporal específica. A interferência na regulação de tais genes e suas respectivas vias é sabidamente causadora de fenótipos que afetam a face e o crânio. Neste sentido, a regulação destas vias é decorrente da interação entre fatores genéticos e ambientais, de tal forma que a perturbação de quaisquer destes fatores pode resultar em malformações craniofaciais, como as fissuras orofaciais. Apesar dos muitos loci de risco já identificados, estes não explicam completamente a alta herdabilidade observadas nas fissuras orofaciais e muitas questões permanecem em aberto. Por exemplo, em relação ao transcriptoma em fissuras orofaciais, as vias genéticas que podem estar desreguladas, assim como processos celulares afetados em decorrência, são ainda pouco compreendidos. Além disso, se há desregulação na expressão de genes em fissuras orofaciais, as causas que levam a essas diferenças necessitam ser elucidadas, como, por exemplo, por meio da investigação de fatores epigenéticos. Também, uma vez que o componente multifatorial torna a influência do ambiente relevante para esta malformação, diferenças epigenéticas e epigenômicas nas fissuras orofaciais devem ser melhor compreendidas. Por fim, formas raras e sindrômicas de fissuras orofaciais sem elucidação de causa moleculares devem ser estudadas para que melhor se compreenda o desenvolvimento craniofacial e o impacto destes mecanismos moleculares em formas não-sindrômicas. Portanto, nosso objetivo principal neste estudo foi investigar os mecanismos moleculares envolvidos na etiologia das fissuras orofaciais, com o foco na análise de expressão gênica e epigenètica em fissuras de lábio-palatinas não-sindrômicas (FL/P NS) e também o estudo genético, de expressão gênica, modelagem animal e epigenética na Síndrome de Richieri-Costa-Pereira (RCPS), uma forma sindrômica e autossômica recessiva de fissura orofacial. Nós encontramos diferenças significantes no transcriptoma de FL/P NS em comparação com controles, que revelaram o comprometimento da via do BRCA1 no reparo ao dano de DNA e o acúmulo de dano de DNA em células FL/P NS. Em seguida, nós estudamos o potencial da metilação de DNA nestas células e encontramos um pequeno, porém significante, aumento de metilação de DNA no promotor do BRCA1 e uma distribuição diferente de metilação, apontando para uma possível contribuição epigenética na desregulação do gene. Nós também avaliamos a contribuição da metilação de DNA na região 8q24.21, uma das mais associadas às FL/P NS por meio de Genome-wide association studies, porém não encontramos diferenças significantes na nossa amostra. Com o intuito de investigar a metilação de DNA em FL/P NS em uma escala epigenômica, nós analisamos o perfil de metilomas e encontramos 578 sítios diferencialmente metilados nas FL/P NS, altamente enriquecidos em regiões regulatórias e em vias relevantes para o desenvolvimento craniofacial como a via de Transição Epitélio-Mesenquimal. Nós também estudamos o efeito da metilação de DNA em casos famílias de FL/P NS com penetrância incompleta e encontramos um aumento significativo de metilação do promotor do CDH1 nos casos penetrantes em comparação aos não-penetrantes. Por último, por meio de diferentes estratégias de sequenciamento e análise de segregação de haplótipos nós mapeamos a mutação de RCPS na região 5\'UTR/promotor do EIF4A3 e encontramos uma estrutura complexa de expansão de repetições nos pacientes RCPS, ocasionando a diminuição da expressão do EIF4A3. Nós também reproduzimos fenótipos comparáveis aos da RCPS por meio de modelo animal em zebrafish. Uma vez que tais repetições são ricas em CG, nós investigamos se estas poderiam ser submetidas à metilação de DNA em pacientes RCPS como uma causa para a redução dos transcritos do EIF4A3, porém não encontramos evidências de aumento de metilação em RCPS. Em conclusão, nós conseguimos associar vias gênicas desreguladas à susceptibilidade para as FL/P NS e diferenças de metilação de DNA tanto em casos familiais como não-familiais de FL/P NS. Além disso, identificamos a causa genética de RCPS, sendo que a síndrome pode ser agora diagnosticada molecularmente. Em conjunto, nossos resultados adicionam ao conhecimento do desenvolvimento craniofacial e na etiologia das fissuras orofaciais

Leishmania é um gênero de protozoários tripanossomatídeos, dimórficos, causadores das leishmanioses. As espécies do subgênero Viannia, como Leishmania (Viannia) braziliensis, são causadoras da leishmaniose cutânea e cutâneo-mucosa nas Américas Central e do Sul. A regulação da expressão gênica em Leishmania ocorre preferencialmente no nível póstranscricional com a participação de elementos regulatórios de ação cis e trans e proteínas ligantes de RNA. Neste contexto, RNAs não codificadores (ncRNAs) conhecidos por seus papéis regulatórios em diversos organismos, ainda são pouco explorados em Leishmania. Sendo assim, o presente estudo analisou o transcriptoma de L. braziliensis explorando o conteúdo codificador e não codificador do parasita. A investigação de expressão diferencial (DE), incluindo análises de enriquecimento de ontologias gênicas, confirmou padrões de expressão, por categoria funcional, como os já reportados para outras espécies de Leishmania durante o desenvolvimento. No entanto, a avaliação do conjunto desses genes DE, empregando a ortologia como parâmetro, sugeriu uma possível contribuição de genes parálogos para a diversidade entre espécies de Leishmania. Para a análise de ncRNAs, um pipeline desenvolvido por Patrícia C. Ruy possibilitou a identificação e caracterização de 11372 ncRNAs putativos em L. braziliensis. Análises acerca dos padrões de expressão diferencial foi conduzido e trinta e cinco ncRNAs putativos foram categorizados, selecionados e submetidos a Northern blotting para avaliação do tamanho e confirmação do padrão de expressão; seis genes foram selecionados para análises funcionais subsequentes. Para avaliação de uma possível função para os ncRNAs a serem investigados, foram gerados parasitos nocaute de cinco desses ncRNAs. O crescimento dos parasitos nocaute em cultura axênica não foi afetado pela ausência dos genes mas o perfil de infecção de macrófagos in vitro foi afetado em 4 dos 6 transfectantes; sugerindo que os ncRNAs sejam funcionais. Cinco ncRNAs foram submetidos a ensaios de pull-down e o conjunto de proteínas ligantes desses transcritos foi identificada. Esse estudo do transcriptoma de L. braziliensis contribui para o entendimento da modulação da expressão dos genes codificadores de proteínas, revela o conteúdo de ncRNA putativos, sua expressão diferencial durante o seu desenvolvimento e ensaia os primeiros estudos funcionais sobre os últimos / Leishmania is a genus of trypanosomatid protozoan parasites, causative agents of leishmaniases. Viannia sub-genera species as Leishmania (Viannia) braziliensis are the causative agents of cutaneous and muco-cutaneous leishmaniasis in Central and South America. The gene expression in this parasites is regulated via post-transcriptional mecanisms comprising the action of cis and trans regulatory elements and RNA binding proteins. In this context, non coding RNAs poorly explored as putative factors involved in regulation of gene expression in Leishmania must be investigated. In this study the transcriptome of coding and ncRNAs of L. braziliensis were analysed. Differential expression analysis, including gene ontology enrichment analysis, during the parasite development revealed the expected paterns for gene expression in Leishamnia spp. A comparative analysis, considering up-regulated genes suggested a contribution of paralogues genes to diversity between Leishmania. spp. To uncover putative ncRNAs, a computational pipeline was previous designed identifying and characterizing 11,372 putative ncRNAs in L. braziliensis, allowing a classification into different ncRNAs classes. The differential expression analysis revealed similar patterns to those observed for protein coding genes. Thirty-five putative ncRNAs were categorized, selected and subjected to Northern blotting being 6 of them selected to functional analysis. These selected group was investigated conducting and stablishing knockout lines, that revealed phenotypic differences concerning diminishing in promastigote growth and in vitro macrophage infection, suggesting possible functional roles of ncRNAs in L. braziliensis. Finnaly, the protein interactions of these ncRNAs were revealed and must be explored in the future to uncover possible regulatory roles of this ncRNAs until now, putative in L. braziliensis. This work represents an outline of L. braziliensis transcriptome contributing to improve the understanding of coding and noncoding RNA content in the parasite