O splicing do pré- RNAm é o processo pelo qual os introns são removidos e os exons são unidos para produzir um RNAm maduro. Esse processo é catalisado por um complexo denominado spliceossomo. RNF113A é uma proteína detectada em complexos pré- e pós-catalíticos. Neste trabalho analisamos a participação de RNF113A no spliceossomo de mamíferos e suas interações com outros componentes do spliceosomo. Nossos resultados mostraram que a super- expressão de RNF113A em células HEK293T aumentam o nível dos snRNAs U1, U2, U5 e U6 e de PRPF19. A imunoprecipitação de RNF113A revelou maior concentração de PRPF19, hBRR2 e SF3b2. Além disso, observamos maior quantidade dos snRNAs U5 e U6 associados à RNF113A. As frações de imunoprecipitação foram analisadas por espectrometria de massas e mostraram interação de RNF113A com proteínas que participam na transcrição, ubiquitinação, maturação do pré-RNAm e splicing. Estes resultados indicam que a associação de RNF113A ao spliceossomo ocorre a partir de suas interações com os snRNAs U5 e U6 e com proteínas relacionadas, como a hBRR2. / Splicing of pre-mRNA is the process by which introns are removed and exons are joined together to produce a mature mRNA competent for translation. It is catalyzed by the complex called spliceosome. RNF113A is a protein detected in pre- and post-catalytic complexes. In this work we analyzed RNF113A participation on spliceosome and its interactions with other spliceosome components. Our results showed that overexpression of RNF113A in HEK293T led to increased levels of U1, U2, U5, U6 snRNAs and PRPF19. RNF113A also associates to PRPF19, hBRR2 and SF3b2, as observed by immunoprecipitation followed by RT-qPCR and western blot. Consistently, U5 and U6 snRNAs were observed in association with RNF113A. Immunoprecipitation fractions were also analyzed by mass spectrometry and results showed interaction of RNF113A with proteins that participate in processes such as transcription, ubiquitination, pre-mRNA maturation and splicing. These results suggest RNF113A associates to spliceosome by interacting with U5 and U6 snRNAs and with related proteins, for example hBRR2.

With the increase of agricultural production, there is an improvement in the use of mineral fertilizers, which may cause different environmental problems, besides the soil salinization. A possible alternative for reducing the application of these products is the use of plant growth-promoting bacteria (PGPB), that can be used alone or in co-inoculation, resulting in an alternative environmentally and economically feasible. Better results can be obtained if the interaction among bacteria-bacteria and bacteria-plant be elucidated, and strategy developed to optimize these interactions. Thus, the plant growth-promoting Bacillus sp. RZ2MS9, previous described as a potential PGPB in maize and soybean, was GFP-tagged and monitored alone and co-inoculated with Azospirillum brasilense (Ab-v5::pWM1013) during maize colonization. The interaction of tagged strains in maize were monitored by fluorescent microscopy (FM) and quantitative PCR (qPCR), demonstrating an endophytic behavior of Bacillus sp. RZ2MS9. Although the non-detection of Ab-v5::pWM1013, the co-inoculation resulted in the best increase in root and shoot dried weight, root volume and in root diameter, showing that inoculation with more than one strain can be a good choice to development of bio-fertilizers. One important system to bacterial interaction is the quorum sensing (QS). The QS is an important cell-cell communication system that allows bacterial cells to recognize their own population and modulate their gene expression. This, system is also involved in the interspecific communication, including other bacterial species and plants. In the other hand, enzymes able to detect and degrade these molecules evolved, the called quorum quenching (QQ) system, that has been evolved in some bacteria as competitive advantage for niches colonization. The aiiA gene, was one of the first gene related with the QQ in Bacillus. The aiiA was found in Bacillus sp. RZ2MS9 genome. Through construction of a new QQ biosensor, Agrobacterium tumefaciens At11006, and validated by A. tumefaciens NTL4, the ability of RZ2MS9 to degrade QS molecules was confirmed. The knockout of aiiA gene was performed using the CRISPR-Cas9 system, confirming this gene function. By these results, the influence of QQ system of Bacillus sp. RZ2MS9 during maize colonization and RZ2MS9 - A. brasilense - maize can be better investigated, opens the possibility to better understand the role of QQ system in the interaction among PGPB and plants. / Concomitantemente ao aumento da produção agrícola, há o aumento do uso de fertilizantes minerais, que pode acarretar no desenvolvimento de diferentes problemas ambientais, além de causar a salinização dos solos. Uma possível alternativa para tentar reduzir a aplicação desses produtos é o uso de bactérias promotoras de crescimento de plantas (BPCPs), que podem ser usadas isoladamente ou em co-inoculação com outras bactérias, tornando-as uma alternativa ambientalmente e economicamente viável. Melhores resultados podem ser obtidos se a interação bactéria-bactéria e bactéria-planta for elucidada, permitindo que estratégias sejam desenvolvidas para otimizar essas interações. Em vista disso, a bactéria Bacillus sp. RZ2MS9, previamente descrita como uma potencial BPCP em milho e soja, foi marcada com GFP e monitorada durante a colonização de milho inoculada sozinha, bem como em co-inoculação com Azospirillum brasilense (Ab-v5::pWM1013). A interação dessas linhagens marcadas em milho, foi monitorada por microscopia de fluorescência (FM) e PCR quantitativo (qPCR), revelando um comportamento endofítico de Bacillus sp. RZ2MS9. Em plantas co-inoculadas, apesar da linhagem Ab-v5::pWM1013 não ter sido detectada por qPCR, a co-inoculação resultou no aumento do peso seco das raízes e da parte aérea, no volume e no diâmetro do sistema radicular, demonstrando que a inoculação com mais de uma linhagem bacteriana pode ser uma boa alternativa para o desenvolvimento de bio-fertilizantes. O quorum sensing (QS) é um importante sistema de comunicação célula-célula que permite que as bactérias reconheçam sua própria população e modulem sua expressão gênica. Este sistema também está envolvido na comunicação interespecífica, incluindo outras espécies bacterianas e plantas. Co-evolutivamente, enzimas capazes de detectar e degradar essas moléculas evoluíram, dando origem ao chamado quorum quenching (QQ), sistema que evoluiu em algumas bactérias como uma vantagem competitiva para a colonização de nichos. O gene aiiA, foi um dos primeiros genes relacionados ao sistema QQ descrito no gênero Bacillus, gene este que foi anotado no genoma de RZ2MS9. Através da construção de uma nova linhagem biossensora de QQ, Agrobacterium tumefaciens At11006, e validada através da linhagem A. tumefaciens NTL4, a capacidade de RZ2MS9 de degradar moléculas de QS foi confirmada. O knockout do gene aiiA foi realizado utilizando o sistema CRISPR-Cas9, confirmando a função desse gene. Através dos resultados obtidos neste trabalho, a influência do sistema QQ de Bacillus sp. RZ2MS9 durante a colonização do milho, bem como a interação RZ2MS9 - A. brasilense - milho pode ser melhor investigada, abrindo a possibilidade de uma melhor compreensão do papel do sistema QQ na interação entre bactérias promotoras de crescimento e plantas.

Hipopituitarismo congênito é caracterizado por deficiência hormonal múltipla devido a mutações de fatores de transcrição envolvidos na embriogênese hipofisária. As células-tronco estão presentes na hipófise e são caracterizadas por dar origem a uma célula progenitora e uma célula indiferenciada por divisão assimétrica. Estão envolvidas na hipófise em processos de alta demanda metabólica em diferentes fases da vida. Em estudos prévios, observou-se o acúmulo dos marcadores de células-tronco Sox2 e Nr2e1 no camundongo Ames, que apresenta mutação no gene Prop1. O Sox2 é o marcador consenso de células-tronco na hipófise enquanto que o Nr2e1, nunca antes caracterizado na hipófise, é essencial para a manutenção de células-tronco e neogenese no cérebro. A perda de função deste gene pode causar agressão e falta de instinto materno em camundongos. Com isso, o objetivo desse projeto foi utilizar o animal modelo zebrafish para avaliar o papel repressor do gene prop1 e caracterizar o gene nr2e1 bem como, confirmar se o mesmo está envolvido com a diferenciação terminal na hipófise, e sua interferência no comportamento do animal mutado. O zebrafish se encaixa adequadamente nesse projeto pois é de fácil manutenção, econômico e com rápido desenvolvimento. No presente estudo criou-se 2 modelos de zebrafish utilizando-se a técnica de edição genômica conhecida como CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) para nocautear os genes prop1 e nr2e1. Esta técnica permite uma interrupção específica e substituição de bases no genoma, resultando em uma alta especificidade, baixa toxicidade celular e é herdável. O zebrafish homozigoto com mutação no gene nr2e1 se desenvolve e reproduz como o animal controle, porém apresenta um comportamento mais exploratório quando comparado com o animal selvagem e o heterozigoto. A imunofluorescência para o anticorpo Sox2 no animal mutado mostrou se diferente do selvagem, pois apresenta um aumento da expressão temporal e o mesmo não se colocaliza com o Nr2e1. A imunofluorescência feita com os hormônios não se mostrou diferente entre o mutado e o selvagem. Conclui-se diante dos achados de normalidade do desenvolvimento, fertilidade, ausência de co-localização com o gene Sox2 e presença de hormônios como Tsh, Fsh e Gh, que o gene nr2e1 não é crucial na diferenciação terminal na hipófise porém o animal mutado apresenta um comportamento diferente do animal selvagem. Os resultados da caracterização do zebrafish com mutação no gene prop1 ainda estão em andamento devido a dificuldade de se estabelecer essa linhagem / Congenital hypopituitarism is characterized by multiple hormone deficiencies due to mutations in transcription factors involved in pituitary embryogenesis. Stem cells, which by definition can each give rise to a progenitor and an undifferentiated cell by asymmetric division, are present in the pituitary gland and are important during periods of high metabolic demand in different phases of life. In previous studies, the accumulation of the stem cell markers Sox2 and Nr2e1 was observed in the Ames mouse, which harbors a mutation in Prop1. Sox2 is the consensus stem cell marker in the pituitary gland, while the role of Nr2e1 in the pituitary development has not been characterized although it is essential for neural stem cell maintenance and neogenesis in the brain and its loss of function causes pathological aggression and lack of maternal instinct in mice. In this project, the zebrafish animal model was used to characterize the role of nr2e1, to confirm whether this gene can be involved in the pituitary terminal differentiation, and to determine the effects of this gene on animal behavior. The zebrafish is a particularly appropriate model for use in this project because it is easy to maintain, is economical, and has a rapid metabolism and growth rate. In the present study, we created 2 zebrafish models by knocking out prop1 and nr2e1 using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) genome-editing technique. This technique enables highly specific gene/reading frame interruption and/or base substitution in the genome, with low cellular toxicity and high heritability. Zebrafish with homozygous nr2e1 mutations develop and reproduce similarly to wild-type zebrafish, but present a more exploratory behavioral pattern compared to wild-type and heterozygous zebrafish. Based on immunofluorescence, Sox2 expression was higher in the mutant zebrafish than in the wild type and was not co-localized with Nr2e1 expression. Hormone expression did not differ between wild-type and mutant zebrafish. We conclude that nr2e1 is not crucial in the terminal differentiation of the hormone-forming pituitary gland; however, it induces a distinct behavioral phenotype at the larval stage. Analyses of zebrafish harboring a prop1 mutation are ongoing owing to issues with the establishment of the lineage

Le positionnement des nucléosomes le long des génomes eucaryotes est crucial étant donné qu’il affecte l’accessibilité de l’ADN à des protéines impliquées dans la transcription, la réplication, ou encore la réparation de l’ADN. Si il est aujourd’hui admis que les remodeleurs de chromatine ainsi que les préférences des nucléosomes pour certains motifs d’ADN constituent les deux principaux déterminants du positionnement des nucléosomes in vivo, leur importance relative fait encore l’objet de controverses. Dans le cadre de cette problématique nous avons développé une stratégie d’assemblage de répétitions de la séquence 601 positionnante de nucléosome directement dans le génome de Saccharomyces cerevisiae. Cette technique assistée par la technologie CRISPR/Cas9 et des oligonucléotides chevauchants s’est révélée très efficace et a permis d’assembler des répétitions sur une étendue d’environ 15 kilobases. Nous avons ainsi pu isoler trois souches se caractérisant par trois longueurs d’ADN de liaison de respectivement 20, 50 et 90 paires de bases séparant deux 601 consécutifs tout le long des répétitions. Ces longueurs d’ADN de liaison ont été choisies du fait de leur compatibilité avec les modèles de la fibre de 30 nm étudiés in vitro et parce qu’elles sont fréquemment observées chez les eucaryotes. Nous avons ensuite regardé si ces répétitions de la séquence 601 suffisent à dicter la succession des nucléosomes de S. cerevisiae selon le pas de chromatine attendu. Pour cela, nous avons eu recours à une approche de MNase-seq afin d’analyser les positions des dyades des nucléosomes dans les répétitions. Les résultats de ces analyses révèlent de façon intéressante l’incapacité de la séquence 601 à positionner le nucléosome dans ce contexte cellulaire et cela malgré l’étendue de la région de 601 répétés constituée. Nous avons également analysé le positionnement des nucléosomes chez ces trois mêmes souches suite à l’inactivation de Chd1, l’un des deux principaux architectes du paysage nucléosomal chez la levure, afin de s’affranchir de son potentiel effet sur le positionnement des nucléosomes dans la région 601. Nos résultats montrent que l’absence de Chd1 ne permet pas de rétablir un positionnement des nucléosomes sur les monomères de 601, suggérant que le 601 n’est pas positionnant in vivo ou que la région répétée est sous l’influence d’autres facteurs de remodelage. D’un point de vue méthodologique, notre technique de construction de répétitions in vivo permet d’envisager des approches simplifiées de biologie synthétique pour la construction de librairies de répétitions dans le génome de S. cerevisiae. / Nucleosome positioning along eukaryotic genomes is crucial as it influences DNA accessibility for DNA binding proteins involved in DNA replication, transcription and repair. It is now accepted that both nucleosome preferences for some DNA sequences and remodeling factors play an important role in nucleosome positioning in vivo. However their relative importance remains a matter of debate. To investigate the role played by DNA sequence in nucleosome positioning in a cellular context we developped a strategy to assemble tandem DNA repeats of a nucleosome positioning sequence directly into Saccharomyces cerevisiae’s genome. This method is assisted by CRISPR/Cas9 and overlapping oligonucleotides and it turned out to be very efficient as it allowed to synthetize about 15 kilobases of tandem DNA repeats inside a yeast chromosome. Using this apporoach we obtained three yeast strains differing by the DNA linker length separating two consecutive monomeres of the 601 nucleosome positioning sequence. We chose three lengths of linker (20, 50 and 90 pb) for two reasons. First, they are compatible with the formation of a 30 nm chromatin fiber in vitro, and second, nucleosome repeat length of 167, 197 and 237 pb are found in eukaryotic genomes. We then verified if nucleosomes are effectively positioned according to the theoretic DNA linker lengths we designed in the “601” repeated region. To that goal we performed MNase-seq analysis to deduce nucleosomes dyads positions in the repeats. Interestingly our results show that the 601 sequence is not able to dictate strong nucleosomes positioning differing from the natural nucleosome repeat length of about 165 pb along the repeats in an in vivo context. We further investigated positions of dyads in the same three strains after inactivating the gene coding for the chromatin remodeler Chd1, which could potentially be responsible of the nucleosomes organization in the repeated area. Our results show no effect of Chd1, indicating that the “601” sequence has no positionning effect in vivo or that other trans-acting factors are implicated in nucleosome positioning in the engineered repeats. Finally, this work provides a new fast and simple approach for synthetic DNA repeats construction inside the yeast genome and could easily be applied for other synthetic chromatin engineering approaches.

L’infertilité est considérée actuellement par l’organisation mondiale de la santé (OMS) comme une préoccupation majeure de santé affectant plus de 50 millions de couples dans le monde. Dans les pays occidentaux, la majorité des couples infertiles ont recours aux techniques d’assistance médicale à la procréation (AMP) pour obtenir une grossesse. Malgré le succès de ces techniques, près de la moitié des couples qui ont recours à l’AMP sortent du parcours de soin sans enfant. Une partie de ces échecs est expliquée par l’altération de la gamétogenèse. Chez l’homme, la spermatogenèse fait interagir des centaines de gènes spécifiquement exprimés dans le testicule. L’abondance de ces gènes suggère que les troubles de la spermatogenèse présentent une forte composante génétique. Récemment, les avancées techniques ont favorisé l’identification de gènes responsables de ces anomalies mais la grande majorité des cas d’infertilité masculine reste classée comme idiopathique. L’objectif de la thèse est d’identifier de nouvelles causes génétiques responsables d’infertilité masculine et d’élucider les mécanismes physiopathologiques associés à ces anomalies.Au cours de ma thèse j’ai participé avec l’équipe GETI (génétique, épigénétique et thérapies de l’infertilité) à l’exploration génétique et moléculaire de deux phénotypes distincts d’anomalies spermatiques liés à des défauts post-méiotiques de la spermatogenèse : une forme rare d’azoospermie non obstructive (ANO) et le phénotype d’anomalies morphologiques multiples du flagelle spermatique (AMMF). Enfin j’ai joué un rôle important dans la création et l’analyse de modèles murins pour caractériser la pathogénie de ces anomalies.L’analyse génétique de deux frères infertiles nés de parents consanguins et présentant une ANO idiopathique associée à un arrêt post-méiotique de la spermatogenèse nous a permis d’identifier un variant homozygote délétère dans le gène SPINK2 qui code pour un inhibiteur de sérine-protéases. L’étude des souris KO pour ce gène nous a permis d’observer que les souris mâles adultes sont infertiles et miment parfaitement les phénotypes spermatique et testiculaire observés chez nos patients. Nous avons montré que la protéine codée par ce gène est exprimée dans l’acrosome à partir du stade de spermatide ronde. En l’absence de Spink2, l’activité protéolytique non-neutralisée des protéases cibles qui transitent par le Golgi cause sa fragmentation et bloque la spermiogénèse au stade de spermatide ronde. Nous avons également pu observer que les spermatozoïdes provenant de patients et de souris hétérozygotes présentent un taux élevé d’anomalies morphologiques et une baisse de la mobilité progressive conduisant à une hypofertilité à expressivité variable. Ces résultats montrent pour la première fois que l’oligo-tératozoospermie et l’azoospermie peuvent constituer un continuum pathologique dû à une même pathogénie.Nous avons également réalisé le séquençage exomique complet d’une cohorte de 78 individus AMMF non apparentés et avons identifié chez 49 sujets des mutations bi-alléliques délétères dans 11 gènes candidats dont DNAH1, CFAP43, CFAP44, WDR66 et FSIP2, soit un rendement diagnostique de 63%. Ces résultats confirment l’hétérogénéité génétique du phénotype MMAF et l’efficacité diagnostique du séquençage haut débit dans son exploration. Nous avons également validé l’implication de certains gènes candidats (n=4) dans ce phénotype chez le modèle murin knock-out créé par la nouvelle technologie d’édition du génome, CRISPR/Cas9.Dans son ensemble, ce travail montre l’intérêt et l’efficacité de la combinaison du séquençage exomique et de la technique de CRISPR/Cas9 pour étudier les troubles de la spermatogenèse et l’infertilité masculine. / Infertility is currently considered by the World Health Organization (WHO) as a major health concern affecting more than 50 million couples worldwide. In western countries, the majority of infertile couples seek assisted reproductive technologies (ART) to achieve a pregnancy. Despite the success of these techniques, almost half of these couples fail to obtain a child. Part of these failures are explained by the alteration of gametogenesis. In humans, spermatogenesis involves hundreds of genes specifically expressed in the testis. The abundance of these genes suggests that spermatogenic defects are associated with a strong genetic component. Recently, technical advances have led to the identification of numerous causative genes, but the vast majority of male infertility cases remain idiopathic. The aim of the present thesis is to identify new genetic causes responsible for male infertility and to elucidate the physiopathological mechanisms associated with these anomalies.During my thesis, I participated with the team GETI (genetics, epigenetics and therapies of infertility) in the genetic exploration of two phenotypes of male infertility related to post-meiotic defects of spermatogenesis: a rare form of non-obstructive azoospermia and the phenotype of multiple morphological abnormalities of the sperm flagella (MMAF). I have also played a key role in creation and analysis of transgenic mice to better characterize the pathogeny of the identified genetic causes in Human.Genetic analyses performed on two infertile brothers born form consanguineous parents and presenting an-idiopathic non-obstructive azoospermia associated with a post-meiotic arrest of spermatogenesis allowed us to identify a homozygous variant in the SPINK2 gene that encodes a serine-protease inhibitor. Phenotypic analysis of Spink2-/- adult male mice showed that they are infertile and perfectly mimic the sperm and testicular phenotypes observed in our patients. We showed that Spink2 protein is expressed from the round spermatid stage and localized in the acrosome, a lysosomal-like vesicle rich in proteases that play a key role during fertilization. When Spink2 is absent, the deregulated proteolytic activity of the targeted proteases such as acrosin leads to the fragmentation of the Golgi apparatus and arrest of spermiogenesis at the round spermatid stage. We also showed that sperm from heterozygous human and mice present a high level of morphological abnormalities and a decrease of progressive motility leading to a variable subfertility. These results showed for the first time that oligo-teratozoospermia and azoospermia could present a pathological continuum due to the same pathogeny.We also performed exome sequencing in a cohort of 78 non related MMAF subjects and identified in 49 cases deleterious bi-allelic mutations in a total of 11 candidate genes including DNAH1, CFAP43, CFAP44, WDR66 and FSIP2 giving a genetic diagnosis yield of 63%. These results confirm the genetic heterogeneity of MMAF and the efficiency of high throughput sequencing in genetic exploration of this phenotype. We also demonstrated the pathogenic implication of certain candidate genes (n=4) using knock-out mice created by the new technology of genome editing, CRISPR/Cas9.Overall, this work demonstrates the interest and effectiveness of combining exome sequencing and CRISPR/Cas9 system to study spermatogenesis disorders and male infertility.

Malgré les diagnostics précoces et les avancées thérapeutiques, le taux de mortalité chez les patients diagnostiqués d’un CCR au stade métastatique reste très élevé. L’objectif de ce travail a été d’étudier le rôle de la chimiokine CXCL12 et ses deux récepteurs CXCR4 et CXCR7 dans processus métastatique. J’ai comparé l’expression de la chimiokine CXCL12 dans des tumeurs coliques humaines avec les tissus sains associés puis je me suis intéressée aux mécanismes de régulation de cette expression et plus particulièrement la régulation épigénétique. J’ai montré que le promoteur de CXCL12 est méthylé dans 35% des CCR et qu’un défaut d’acétylation des histones du promoteur entraîne la perte d’expression de CXCL12. Des enzymes impliquées dans la régulation des mécanismes épigénétiques, potentiellement liées à ce défaut d’acétylation ont été identifiées par l’analyse des tumeurs par PCR Array et parmi ces facteurs, j’ai identifié l’histone acétyl-transférase PCAF dont l’expression est diminuée dans les tumeurs. Enfin, pour comprendre le rôle respectif de CXCR4 et de CXCR7 dans la dissémination métastatique, j’ai invalidé l’expression du gène des récepteurs dans la lignée colique humaine SW480 par Crispr-Cas9, puis j’ai comparé la capacité migratoire des cellules in vitro et leur potentiel métastatique in vivo. L’induction d’une perte d’expression du récepteur CXCR7 n’a pas eu d’impact sur le développement des métastases pulmonaire et hépatique in vivo, mais a entraîné une baisse de la migration in vitro. / Despite early cancer detection and therapeutic advances, the mortality rate in patients diagnosed with CRC at the metastatic stage remains very high. The aim of this work was to study the role of the chemokine CXCL12 and its two receptors CXCR4 and CXCR7 in the metastatic process. I compared the expression of the chemokine CXCL12 in human colon tumors with the associated healthy tissues, then I focused on the mechanisms regulating this expression and more particularly the epigenetic regulation. I have shown that the CXCL12 promoter is methylated in 35% of the CCR and that a lack of histone acetylation of the CXCL12 promoter causes the loss of its expression. Enzymes involved in the regulation of epigenetic mechanisms, potentially related to this acetylation defect, were identified by Array PCR on tumors and among these factors, the histone acetyl transferase PCAF, whose expression is decreased in tumors, was identified. Finally, to understand the respective role of CXCR4 and CXCR7 in metastatic spread, I invalidated the expression of both receptor genes in the human colonic line SW480 by Crispr-Cas9, and then compared the migratory capacity of the cells in vitro and their metastatic potential in vivo. Inducing a loss of expression of CXCR7 receptor did not have an impact on the development of pulmonary and hepatic metastases in vivo, but resulted in a decrease in in vitro migration.

Hipopituitarismo congênito é caracterizado por deficiência hormonal múltipla devido a mutações de fatores de transcrição envolvidos na embriogênese hipofisária. As células-tronco estão presentes na hipófise e são caracterizadas por dar origem a uma célula progenitora e uma célula indiferenciada por divisão assimétrica. Estão envolvidas na hipófise em processos de alta demanda metabólica em diferentes fases da vida. Em estudos prévios, observou-se o acúmulo dos marcadores de células-tronco Sox2 e Nr2e1 no camundongo Ames, que apresenta mutação no gene Prop1. O Sox2 é o marcador consenso de células-tronco na hipófise enquanto que o Nr2e1, nunca antes caracterizado na hipófise, é essencial para a manutenção de células-tronco e neogenese no cérebro. A perda de função deste gene pode causar agressão e falta de instinto materno em camundongos. Com isso, o objetivo desse projeto foi utilizar o animal modelo zebrafish para avaliar o papel repressor do gene prop1 e caracterizar o gene nr2e1 bem como, confirmar se o mesmo está envolvido com a diferenciação terminal na hipófise, e sua interferência no comportamento do animal mutado. O zebrafish se encaixa adequadamente nesse projeto pois é de fácil manutenção, econômico e com rápido desenvolvimento. No presente estudo criou-se 2 modelos de zebrafish utilizando-se a técnica de edição genômica conhecida como CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) para nocautear os genes prop1 e nr2e1. Esta técnica permite uma interrupção específica e substituição de bases no genoma, resultando em uma alta especificidade, baixa toxicidade celular e é herdável. O zebrafish homozigoto com mutação no gene nr2e1 se desenvolve e reproduz como o animal controle, porém apresenta um comportamento mais exploratório quando comparado com o animal selvagem e o heterozigoto. A imunofluorescência para o anticorpo Sox2 no animal mutado mostrou se diferente do selvagem, pois apresenta um aumento da expressão temporal e o mesmo não se colocaliza com o Nr2e1. A imunofluorescência feita com os hormônios não se mostrou diferente entre o mutado e o selvagem. Conclui-se diante dos achados de normalidade do desenvolvimento, fertilidade, ausência de co-localização com o gene Sox2 e presença de hormônios como Tsh, Fsh e Gh, que o gene nr2e1 não é crucial na diferenciação terminal na hipófise porém o animal mutado apresenta um comportamento diferente do animal selvagem. Os resultados da caracterização do zebrafish com mutação no gene prop1 ainda estão em andamento devido a dificuldade de se estabelecer essa linhagem / Congenital hypopituitarism is characterized by multiple hormone deficiencies due to mutations in transcription factors involved in pituitary embryogenesis. Stem cells, which by definition can each give rise to a progenitor and an undifferentiated cell by asymmetric division, are present in the pituitary gland and are important during periods of high metabolic demand in different phases of life. In previous studies, the accumulation of the stem cell markers Sox2 and Nr2e1 was observed in the Ames mouse, which harbors a mutation in Prop1. Sox2 is the consensus stem cell marker in the pituitary gland, while the role of Nr2e1 in the pituitary development has not been characterized although it is essential for neural stem cell maintenance and neogenesis in the brain and its loss of function causes pathological aggression and lack of maternal instinct in mice. In this project, the zebrafish animal model was used to characterize the role of nr2e1, to confirm whether this gene can be involved in the pituitary terminal differentiation, and to determine the effects of this gene on animal behavior. The zebrafish is a particularly appropriate model for use in this project because it is easy to maintain, is economical, and has a rapid metabolism and growth rate. In the present study, we created 2 zebrafish models by knocking out prop1 and nr2e1 using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) genome-editing technique. This technique enables highly specific gene/reading frame interruption and/or base substitution in the genome, with low cellular toxicity and high heritability. Zebrafish with homozygous nr2e1 mutations develop and reproduce similarly to wild-type zebrafish, but present a more exploratory behavioral pattern compared to wild-type and heterozygous zebrafish. Based on immunofluorescence, Sox2 expression was higher in the mutant zebrafish than in the wild type and was not co-localized with Nr2e1 expression. Hormone expression did not differ between wild-type and mutant zebrafish. We conclude that nr2e1 is not crucial in the terminal differentiation of the hormone-forming pituitary gland; however, it induces a distinct behavioral phenotype at the larval stage. Analyses of zebrafish harboring a prop1 mutation are ongoing owing to issues with the establishment of the lineage

L'hétérochromatine, de nature compacte et répétitive, limite l’accès à l'ADN et fait de la réparation des DSBs un processus difficile que les cellules doivent surmonter afin de maintenir leur intégrité génomique. Pour y étudier la réparation des DSBs, nous avons conçu un système CRISPR / Cas9 dans lequel les DSB peuvent être efficacement et spécifiquement induites dans l'hétérochromatine de fibroblastes de souris NIH3T3. En développant un système CRISPR / Cas9 hautement spécifique et robuste pour cibler l'hétérochromatine péricentrique, nous avons montré que les DSB en G1 sont positionnellement stables et réparés par NHEJ. En S / G2, ils se déplacent vers la périphérie de ce domaine pour être réparés par HR. Ce processus de relocalisation dépend de la résection et de l'exclusion de RAD51 du domaine central de l'hétérochromatine. Si ces cassures ne se relocalisent pas, elles sont réparées dans le cœur du domaine de l'hétérochromatine par NHEJ ou SSA. D'autre part, les DSBs dans l'hétérochromatine centromérique activent NHEJ et HR tout au long du cycle cellulaire. Nos résultats révèlent le choix de la voie de réparation différentielle entre l'hétérochromatine centromérique et péricentrique, ce qui régule également la position des DSBs. / Heterochromatin is the tightly packed form of repetitive DNA, essential for cell viability. Its highly compacted and repetitive nature renders DSB repair a challenging process that cells need to overcome in order to maintain their genome integrity. Developing a highly specific and robust CRISPR/Cas9 system to target pericentric heterochromatin, we showed that DSBs in G1 are positionally stable and repaired by NHEJ. In S/G2, they relocate to the periphery of this domain to be repaired by HR. This relocation process is dependent of resection and RAD51 exclusion from the core domain of heterochromatin. If these breaks fail to relocate, they are repaired within heterochromatin by NHEJ or SSA. On the other hand, DSBs in centromeric heterochromatin activate both NHEJ and HR throughout the cell cycle. Our results reveal the differential repair pathway choice between centromeric and pericentric heterochromatin that also regulates the DSB position.

Leishmania est un parasite eucaryote divergent responsable d’un large spectre de maladies à travers le monde. Ce parasite est caractérisé par une aneuploïdie mosaïque, constitutive, c’est-à-dire qu’au sein d’une population chaque cellule comporte une combinaison unique de mono-, di- et trisomies de chacun de ses 36 chromosomes. L’aneuploïdie mosaïque est générée et maintenue chez les générations suivantes grâce à un taux élevé de répartition asymétrique des chromosomes lors de la mitose, entrainant le gain ou la perte de chromosomes entiers. Ceci implique une régulation non-conventionnelle de la réplication, suivie d’une ségrégation permissive des chromosomes.L’objectif général de cette étude était de comprendre la dynamique de la réplication de l’ADN ainsi que de cartographier les sites d’initiation de la réplication chez Leishmania, en utilisant la technique du peignage moléculaire d’une part et celle du ChIP-seq d’une autre part. Nous avons ainsi pu caractériser les différents paramètres de progression de la fourche de réplication. Un des résultats majeurs qui ressort de cette étude est que Leishmania possède les plus grandes distances inter-origines et la plus grande vitesse de réplication parmi les autres eucaryotes déjà étudiés. Nous avons également pu estimer que le génome de Leishmania possède environ 168 origines de réplication. Afin d’étudier les acteurs impliqués dans la réplication de l’ADN chez Leishmania, nous avons développé l’outil génétique CRISPR/Cas9. Pour développer cet outil, nous avons basé notre approche sur une stratégie à deux vecteurs : l’un permet l’expression du single guide (sg)RNA et l’autre celle de l’endonucléase Cas9. La validation de cet outil génétique a été réalisée par le knock-out du locus PFR2 codant une protéine flagellaire. Dans un second temps, nous avons fait évoluer le CRISPR/Cas9 vers un système inductible pour réaliser les knock-out et des étiquetages au locus endogène de protéines d’intérêt. Nous avons utilisé ce nouveau système pour étudier la fonction de deux protéines potentiellement impliquées dans le complexe de reconnaissance des origines de réplication. Malgré une fuite du système, nous avons pu réaliser le KO des gènes Orc1b et Orc1/Cdc6 et suivre la progression du cycle cellulaire. Nous avons pu constater que la perte de ces gènes conduisait à un défaut de croissance ainsi qu’à l’apparition de cellules sans noyau. L’insertion d’une étiquette au locus endogène d’Orc1b nous a parmi de confirmer la localisation que nous avions obtenue avec une construction épisomale et va permettre d’étudier plus précisément le rôle de cette protéine.En conclusion, nous avons mis en évidence des paramètres de réplication originaux et démontré, en utilisant le CRISPR/Cas9, que les protéines Orc1b et Ocr1/Cdc6 étaient impliquées dans la duplication du noyau de Leishmania, ce qui est en accord avec leur rôle putatif dans la réplication de l’ADN. / Leishmania, a protozoan parasite which causes a large range of diseases worldwide, is characterized by a constitutive 'mosaic aneuploidy', i.e. each cell in a population possesses a unique combination of mono-, di- and trisomies for each of its 36 heterologous chromosomes. Mosaic aneuploidy is generated and maintained via high rates of asymmetric chromosomal allotments during mitosis, leading to the gain or loss of whole chromosomes. This implies an unconventional regulation of the replication, followed by a permissive segregation.The main objective of this study was to unravel DNA replication dynamics and to map the replication initiation sites in Leishmania using DNA combing and ChIP-seq analyses. First, we have characterized DNA replication fork parameters. One of the major findings of this study was that Leishmania exhibits the fastest replication speed and the largest interorigin distances among the eukaryotes tested so far. We have also estimated that the Leishmania major genome possesses 168 origins of replication.To study the actors involved in DNA replication, we first had to develop novel genetic tools. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR associated endonuclease 9) system is a recently discovered powerful technique for genome editing. In order to adapt this system to Leishmania, we have chosen a two-plasmid strategy: one for the expression of the single guide (sg) RNA and a second for the expression of the endonuclease CAS9. The proof of concept has been based on the disruption of the paraflagellar rod-2 (PFR2) loci by the CRISPR-Cas9 system. In a second attempt, we have developed an inducible CRISPR-Cas9 system, both to obtain knock outs and to perform marker-free endogenous gene tagging. We used the system to investigate the function of Origin Recognition Complex proteins. Although the system was leaky, the genome was edited as expected. We thus deleted Orc1b and Orc1/Cdc6 and monitored the cell cycle progression of the parasite. We found that the depletion of these nuclear proteins lead to a growth defect and to the appearance of zoids (anucleated cells). The endogenous tagging of Orc1b confirmed the localization previously obtained using an episomal expression vector, and will allow further investigation on the role of this protein.In total, we have shown the presence of original replication dynamics parameters in Leishmania, and using CRISPR Cas9, we have demonstrated that Orc1b and Orc1/Cdc6 are involved in the nuclear duplication of Leishmania, in agreement with their putative in DNA replication.

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are a major cause of Parkinson’s disease (PD), which is why modelling PD by replicating effects in animal models attracts great interest. However, the exact mechanisms of pathogenesis are still unclear. While a gain-of-function hypothesis generally receives consensus, there is evidence supporting an alternative loss-of-function explanation. Yet, neither overexpression of the human wild-type LRRK2 protein or its pathogenic variants, nor Lrrk2 knockout recapitulates key aspects of human PD in rodent models. Furthermore, there is conflicting evidence from morpholino knockdown studies in zebrafish regarding the extent of zygotic developmental abnormalities. Because reliable null mutants may be useful to infer gene function, and because the zebrafish is a more tractable laboratory vertebrate system than rodents to study disease mechanisms in vivo, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9) genomic editing was used to delete the ~60-kbp-long zebrafish lrrk2 locus containing the entire open reading frame. Constitutive removal of both the maternal and the zygotic lrrk2 function (mzLrrk2 individuals) causes a pleomorphic phenotype in the larval brain at 5 days post-fertilisation (dpf), including increased cell death, delayed myelination, and reduced and morphologically abnormal microglia/leukocytes. However, the phenotype is transient, spontaneously attenuating or resolving by 10 dpf, and the mutants are viable and fertile as adults. These observations are mirrored by whole-larva transcriptome data, revealing a more than eighteen-fold drop in the number of differentially expressed genes in mzLrrk2 larvae from 5 to 10 dpf. Additionally, analysis of spontaneous swimming activity shows hypokinesia as a predictor of Lrrk2 protein deficiency in larvae, but not in adult fish. Because the catecholaminergic (CA) neurons are the main clinically relevant target of PD in humans, the CA system of larvae and adult fish was analysed on both cellular and metabolic level. Despite an initial developmental delay at 5 dpf, the CA system is structurally intact at 10 dpf and later on in adult fish aged 6 and 11 months. However, monoamine oxidase (Mao)-dependent degradation of biogenic amines, including dopamine, is increased in older fish, possibly suggesting impaired synaptic transmission or a leading cause of cell damage in the long term. Furthermore, decreased mitosis rate in the larval brain was found, in the anterior portion only at 5 dpf, strongly and throughout the whole organ at 10 dpf. Conceivably, lrrk2 may have a more general role in the control of cell proliferation during early development and a more specialised one in the adult stage, possibly conditional, for example upon brain damage. Because the zebrafish can regenerate lost neurons, it represents a unique opportunity to elucidate the endogenous processes that may counteract neurodegeneration in a predisposing genetic background. To this aim, the regenerative potential of the adult telencephalon upon stab injury was tested in mzLrrk2 fish. Indeed, neuronal proliferation was reduced, suggesting that a complete understanding of Lrrk2 biology may not be fully appreciated without recreating challenging scenarios. To summarise, the present results demonstrate that loss of lrrk2 has an early effect on zebrafish brain development that is later often compensated. Nonetheless, perturbed aminergic catabolism, and specifically increased Mao-dependent aminergic degradation, is reported for the first time in a LRRK2 knockout model. Furthermore, a link between Lrrk2 and the control of basal cell proliferation in the brain, which may become critical under challenging circumstances such as brain injury, is proposed. Future directions should aim at exploring which brain cell types are specifically affected by the mzLrrk2 hypoproliferative phenotype and the resulting consequences on a circuitry level, particularly in very old fish (i.e., over 2 years of age).