Diferenças no timing da melanização e esclerotização do exoesqueleto são evidentes quando se compara a morfologia externa de abelhas de hábitos sociais e as solitárias. A esta diferença convencionamos chamar de heterocronia da maturação cuticular, o termo heterocronia significando variações no tempo relativo, ou ritmo, de um evento ontogenético em relação ao ancestral ou entre taxons. Propusemos que as abelhas sociais, que após a ecdise permanecem na colônia por vários dias, alcançariam a maturidade de alguns sistemas orgânicos, entre eles o tegumento, muito mais tarde que as espécies de abelhas solitárias que ao emergir partem imediatamente para atividades extra-nidais. Neste contexto, o objetivo deste trabalho consistiu em testar esta hipótese utilizando o tegumento em maturação das espécies de abelhas sociais, Apis mellifera e Frieseomelitta varia, e da espécie solitária Centris analis, em estudos comparativos de expressão gênica, ultraestrutura e quantificação de hidrocarbonetos cuticulares (CHCs). Para isto utilizamos sequenciamento de mRNA (RNA-seq), microscopia eletrônica de transmissão (MET) e cromatografia de gás e espectrometria de massas (CG/MS). Os perfis de expressão de genes da via de melanização/esclerotização cuticular (ebony e tan) diferenciaram as espécies sociais da solitária, assim como a expressão de genes com função na via de metabolismo de quitina (Cda5, Idgf4 e chitooligosacchariodolytic-domain-like) e de genes codificadores de proteínas estruturais da cutícula (CPR14, CPR17, CPR18, CPR25, CPR23, CPR26, Apd-3 e Apd-like). Genes com função na regulação da maturação cuticular (FTZ-F1, E74, Hr46 e Hr4) se mostraram co-expressos nas espécies sociais e os perfis de expressão destes genes, exceto Hr46, e de outros reguladores (Ethr, Hr38, Rickets e Ptx-1) também diferenciaram as espécies sociais da solitária. Ressaltamos em nossas análises os genes do ciclo circadiano, cuja expressão tem relação com a deposição de quitina cuticular, além de genes de vias de pigmentação não melanínicas. As análises de MET, abrangendo outras três espécies de abelhas (Bombus brasilienses: primitivamente eussocial; Euglossa cordata: facultativamente social; Tetrapedia diversipes: solitária), mostraram diferenças consistentes entre a ultraestrutura e espessura das cutículas das espécies sociais e solitárias, o que reforçou nossos resultados de RNA-seq. A quantificação absoluta dos CHCs diferenciou as abelhas sociais da solitária, consistente com a hipótese de heterocronia da maturação cuticular e com os perfis de expressão de genes envolvidos na biossíntese de CHCs. Assim, além de desvendar transcriptomas de tegumento de três espécies de abelhas, a comparação da expressão gênica aliada à análise de ultraestrutura da cutícula e quantificação de CHCs levaram à caracterização de diferenças no processo de maturação cuticular entre as espécies sociais e solitárias / Differences in the timing of exoskeleton melanization and sclerotization processes are evident when comparing the external morphology of social and solitary bee species. Such differences may constitute a relevant example of cuticular maturation heterochrony, this term referring to a genetic change in timing of an ontogenetic process relative to an ancestor or between taxons. We proposed that social bees, which remain protected inside the colony for many days before initiating outside nest activities, would reach the maturity of some organic systems, such as the integument (epidermis and cuticle), later than solitary bees, which start such activities immediately after ecdysis. We tested this hypothesis in a comparative study of the developing integument of eusocial bees, Apis mellifera and Frieseomelitta varia, and the solitary bee Centris analis. Using RNA-seq, we verified that the expression profiles of genes involved in cuticular melanization and sclerotization (ebony and tan), chitin deposition and organization (Cda5, Idgf4, chitooligosacchariodolytic-domain-like), and cuticle formation (CPR14, CPR17, CPR18, CPR25, CPR23, CPE26, Apd-3, Apd-like) were positively, correlated between the two eusocial species, but not between the eusocial and the solitary species. Some of the genes with roles in regulating exoskeleton maturation (FTZ-F1, E74, Hr46, Hr4) were co-expressed only in the eusocial species. The expression profiles of these genes (except Hr46) and other regulatory genes (Ethr, Hr38, Rickets, Ptx-1) were also positively correlated exclusively in the eusocial bees. We also highlighted the expression of genes involved in non-melanin pigment production and the expression of circadian rhythm genes that could be related to chitin layers deposition. Transmission electron microscopy analysis of the integument of the two eusocial and the solitary bee species, in addition to other three bee species (the primitively eusocial Bombus brasilienses; the facultatively social Euglossa cordata; the solitary bee Tetrapedia diversipes), showed differences in cuticle ultrastructure and thickness, thus supporting the RNA-seq data. In agreement with our hypothesis, CHC quantifications were consistent with the expression levels of genes involved in CHC biosynthesis, thus differentiating the superficial cuticle layer of the eusocial and solitary species. Together, the integument transcriptomes, ultrastructure, and CHC quantification allowed us to characterize differences in the timing of cuticle maturation in social and solitary bees

A cana-de-açúcar é uma gramínea C4 de alta biomassa que acumula grandes quantidades de sacarose e é utilizada para produção de etanol, um combustível de baixa emissão de carbono. Restrições bióticas e abióticas afetam significativamente a produtividade das culturas, pois elas podem prejudicar severamente o crescimento e desempenho da planta. Compreender as bases moleculares para essa perda de produtividade ajudará na investigação das estratégias de mitigação. Para estudar estes dois tipos de estresses, plantas jovens de cana-de-açúcar foram submetidas à herbivoria e à privação de água. Uma investigação foi realizada para estudar as mudanças transcricionais em cana-de-açúcar sujeita ao ataque da Diatraea saccharalis, usando macroarranjo para monitorar a seleção de transcritos, contendo sequências de ESTs de serina proteases e inibidores de serina proteases de cana-de-açúcar do banco de dados SUCEST. Análises do macroarranjo revelaram sequências diferencialmente expressas em resposta à herbivoria. PCR em tempo real confirmou que 10 ESTs homólogos à inibidores de protease (4 homólogos aos inibidores do tipo Bowman-Birk de arroz e milho (BBI), 5 homólogos à inibidores de proteinase de milho (MPI) e 1 homólogo ao inibidor de subtilisina) e 3 ESTs homólogos à serina proteases das famílias S1, S10 e S14 foram positivamente regulados pela herbivoria. Embora a função dos inibidores de protease na defesa está bem estabelecida, o envolvimento de proteases de planta na resposta à herbivoria ainda precisa ser elucidado. Neste trabalho nós mostramos que uma protease da família S14 foi induzida em resposta ao ataque da lagarta e ao ferimento mecânico em cana-de-açúcar. Curiosamente, sequências homólogas de arroz e Arabidopsis também responderam aos mesmos tratamentos, sugerindo um papel conservado desta protease S14 na defesa contra herbívoros. Uma importante aplicação destes resultados é a identificação de genes para utilização em estratégias biotecnológicas para melhorar a resistência da cana-de-açúcar a insetos. Outra investigação foi realizada para estudar os parâmetros fisiológicos e perfis transcricionais de genes responsivos ao estresse hídrico em plantas jovens de cana-de-açúcar. Resultados deste trabalho indicaram que a interrupção da irrigação resultou em efeitos fisiológicos mensuráveis e análises de expressão de genes selecionados de resposta ao estresse revelaram expressão diferencial significativa entre os grupos irrigado e não irrigado. Resultados do RNA-Seq revelaram atividade transcricional de 24.142 transcritos de folhas de cana-de-açúcar submetidas à seca. Análises de expressão gênica em resposta à seca revelaram 68 (resposta precoce) e 2.390 (resposta tardia) transcritos diferencialmente expressos no 3º e 7º dia de tratamento, respectivamente. O decréscimo em vários parâmetros fisiológicos foi observado depois de seis dias de privação de água. Reduções na taxa de fotossíntese, condutância estomática e transpiração foliar ocorreram antes que fossem observadas alterações físicas visíveis, mas estas foram precedidas por mudanças significativas na expressão de genes com papel na fotossíntese. RNA-Seq identificou novos transcritos com papéis na defesa precoce e tardia à seca e a validação por PCR em tempo real confirmou os resultados obtidos pelo RNA-Seq. Isto irá incentivar mais pesquisas sobre a eficiência do uso da água em cana-de-açúcar, levando a identificação de variedades com maior tolerância às condições ambientais adversas. / Sugarcane is a high biomass tropical C4 grass crop which accumulates large quantities of sucrose and is used for bioethanol production, a low-carbon emission fuel. Biotic and abiotic constraints significantly impact crop productivity, because they can severely impair plant growth and performance. Understanding the molecular basis for this loss in productivity will aid in identifying strategies for mitigation. To study these two types of stresses, young sugarcane plants were subject to herbivore and water privation. An investigation was undertaken to study the sugarcane transcriptional changes following Diatraea saccharalis damage, using macroarrays to monitor a selection of transcripts, containing sequences of sugarcane ESTs of serine proteases and serine proteinase inhibitors from the SUCEST (Sugarcane EST Project) database. Macroarray analyses revealed differently expressed sequences in response to herbivory. Real-Time PCR confirmed that 10 ESTs homologous to proteinase inhibitors (4 homologous to maize and rice Bowman-Birk inhibitors (BBI), 5 homologous to maize proteinase inhibitors (MPI) and 1 homologue to subtilisin inhibitor) and 3 ESTs homologous to serine proteases of the S1, S10 and S14 family were positively regulated by herbivory. While the protease inhibitor\'s function in defense is well established, the involvement of plant proteases in response to herbivory still remains to be elucidated. In this work we show that a sugarcane encoding S14 family protease member was upregulated in response to both D. saccharalis damage and wound treatment. Interestingly, homologous sequences from rice and Arabidopsis also responded to the same treatments, suggesting a conserved role of this S14 protease in defense against herbivores. One important application of these results is the identification of genes for use in biotechnological strategies to improve sugarcane insect resistance. Another investigation was undertaken to study the physiological parameters and transcriptional profiles of genes responsive to water stress in young sugarcane plants. Results of this work indicated that termination of irrigation resulted in measurable physiological effects in sugarcane plants and analysis of the expression of the chosen stress-response genes revealed significant differential expression between the control and treatment groups. RNA-Seq results revealed transcriptional activity of 24.142 transcripts from sugarcane leaf subjected to water stress. Gene expression analyses in response to water deprivation revealed 68 (early response) and 2,390 (later response) differentially expressed transcripts on day 3 and day 7, respectively. Sustained decreases in various physiological parameters were observed in water-stressed sugarcane plants after six days of water deprivation. Reductions in photosynthesis rate, stomatal conductance and leaf transpiration occurred before visible physical changes were observed, but this was preceded by significant changes in expression of genes with roles in photosynthesis. RNA-seq identified novel transcripts with roles in early and late response to drought stress and Real-Time qPCR validation confirmed the RNA-Seq results. This will inform further research on water use efficiency in sugarcane, leading to identification of varieties with improved tolerance to adverse environmental conditions.

Estudos recentes têm revelado que a maior parte dos transcritos gerados em células humanas é composta por RNAs não-codificadores de proteínas (ncRNAs). Uma parte desses ncRNAs compreende a classe de RNAs curtos, que possuem menos que 200 nucleotídeos. Os micro-RNAs (miRNAs) fazem parte dessa classe e têm sido alvo de grande interesse, pois são preditos como possíveis reguladores de mais de 60% dos RNAs mensageiros (mRNAs) humanos. Outra classe dos ncRNAs é composta por ncRNAs longos (lncRNAs, com mais de 200 nucleotídeos), que são transcritos a partir de regiões intergênicas e intrônicas do genoma humano e possuem várias funções, muitas delas relacionadas ao controle da expressão de mRNAs. Recentemente, os lncRNAs têm sido caracterizados quanto à sua estrutura e função. No entanto, muito pouco se sabe sobre os mecanismos pelos quais os lncRNAs são regulados. Este trabalho teve como objetivo avaliar se lncRNAs são regulados por miRNAs em células humanas. Para tanto, identificamos lncRNAs ligados ao complexo de silenciamento induzido por RNA (RISC) em células da linhagem HeLa, utilizando um método aqui desenvolvido de geração de bibliotecas de cDNA direcionadas para sequenciamento em larga escala na plataforma 454/Roche. Em paralelo, sequenciamos os miRNAs ligados ao RISC nestas mesmas células. Os resultados obtidos mostram que centenas de lncRNAs de diversas classes se ligam ao RISC em células HeLa, juntamente com milhares de mRNAs e várias centenas de miRNAs. Entre os miRNAs, encontramos 37 que são preditos como alvejando os lncRNAs detectados. Estes miRNAs constituem possíveis reguladores dos lncRNAs e, portanto, nosso trabalho estabelece um mapa experimental de interações diretas entre lncRNAs e miRNAs. Dentre os lncRNAs identificados ligados ao RISC neste trabalho, destaca-se o TUG1, lincRNA sabidamente envolvido na regulação de genes relacionados à apoptose e ao ciclo celular. Mostramos por ensaio de super-expressão de miRNAs e qPCR que TUG1 é regulado pelo miRNA-148b, um dos miRNAs por nós detectados que possui um sítio alvo altamente conservado em mamíferos localizado na extremidade 3\' de TUG1. Em conjunto, este trabalho contribui para o entendimento da regulação dos níveis de expressão de lncRNAs em células humanas e abre perspectivas para a modulação de miRNAs como estratégia de regulação dos níveis e das funções de lncRNAs. / Recent studies have revealed that the largest fraction of the transcripts generated in human cells is composed of non-protein coding RNAs (ncRNAs). A portion of these RNAs encompasses the class of short RNAs, which are less than 200 nucleotides in length. Micro-RNAs (miRNAs) are part of this class and are of great interest, as they are predicted to target over 60% of the human messenger RNAs (mRNAs). Another class of ncRNAs is composed of long ncRNAs (lncRNAs, longer than 200 nucleotides), which are transcribed from intergenic and intronic regions of the human genome and have several functions, many of them related to the control of the mRNA expression. Recently, the structure and function of lncRNAs have been characterized. However, little is known about the mechanisms involved in lncRNA regulation. This work aimed to evaluate whether lncRNAs are regulated by miRNAs in human cells. For this purpose, we identified lncRNAs bound to the RNA-induced silencing complex (RISC) in HeLa cells using a method developed here for the generation of strand-specific cDNA libraries for large scale RNA-sequencing in the 454/Roche plataform. In parallel, we sequenced the miRNAs bound to RISC in these cells. Our results show that hundreds of lncRNAs from diverse classes are bound to RISC in HeLa cells, along with thousands of mRNAs and several hundred miRNAs. Among the miRNAs we identified 37 that are predicted to target the detected lncRNAs. These miRNAs are possible regulators of the lncRNAs, and therefore our work establishes an experimental map of direct interactions between lncRNAs and miRNAs. The lncRNA TUG1, a lincRNA involved in the regulation of genes related to apoptosis and cell cycle, was identified among the lncRNAs bound to RISC. We showed by miRNA over-expression and qPCR that TUG-1 is regulated by the miRNA-148b, which is one of the miRNAs detected in our sequencings and has a binding site highly conserved in mammals located at the TUG1 3` end. Taken together, our results contribute to the understanding of the regulation of the lncRNA expression levels in human cells and open perspectives for the modulation of miRNAs as a strategy to regulate the levels and functions of lncRNAs.

Os mecanismos da infertilidade relacionada à endometriose ainda não foram esclarecidos, embora diversos estudos proponham um efeito deletério desta doença sobre a qualidade oocitária (QO). No entanto, a análise de oócitos em pacientes com endometriose não é rotineiramente exequível, uma vez que os oócitos humanos raramente são doados para pesquisa e sua aplicação em técnicas invasivas impede sua utilização em procedimentos de reprodução assistida. Neste contexto, as evidências sugerem que as células cumulus (CC) podem ser utilizadas como biomarcadores indiretos capazes de prever a QO. Desta forma, através de um estudo inédito, objetivamos determinar o perfil diferencial de transcritos em CC de mulheres inférteis, com e sem endometriose avançada, submetidas à estimulação ovariana controlada para injeção intracitoplasmática de espermatozoides. Para tanto, realizamos um estudo caso-controle, que analisou via sequenciamento de nova geração de RNA (RNA-Seq), 3 grupos (controle, endometriose III/IV sem endometrioma e endometriose III/IV com endometrioma), com 3 pools de 3 pacientes cada. Dentre os principais genes desregulados identificados nas comparações entre os grupos com endometriose avançada e mulheres sem a doença foram evidenciados transcritos com expressão alterada envolvidos na via de fosforilação oxidativa, genes relacionados aos processos da acetilação e conjugação de ubiquitina, além de genes associados a via de biossíntese do colesterol e do estradiol. Esses resultados demonstram que as CC de mulheres inférteis com endometriose avançada apresentam alterações moleculares possivelmente relacionadas ao desenvolvimento folicular e oocitário. Através do enriquecimento dos principais genes desregulados, nossos dados indicam as potenciais vias alteradas nesse processo que podem interferir na aquisição da competência gamética e por sua vez, mediar o comprometimento da fertilidade dessas pacientes. / The endometriosis related infertility mechanisms still remain to be elucidated, although several studies propose a deleterious effect of this disease on oocyte quality. However, the oocyte analysis in patients with endometriosis is not routinely feasible, since human oocytes are rarely donated to researches and their application in invasive techniques precludes their use in reproduction procedures. In this context, evidences suggest that cumulus cells (CC) could be used as indirect biomarkers capable of predicting oocyte quality. Thus, through an unprecedented study, we aimed to determine the differential transcripts profile in CC of infertile women with and without advanced endometriosis and its different stages, undergoing controlled ovarian stimulation for intracytoplasmic sperm injection. Therefore, we performed a case-control study, which analyzed by RNA next generation sequencing (RNA-Seq), 3 groups (control, endometriosis III/IV without endometrioma and endometriosis III/IV with endometrioma), with 3 pools of 3 patients each. The comparison of top deregulated genes among groups of advanced endometriosis and control patients show us altered genes associated with oxidative pathways, acetylation and ubiquitination process, aside from genes related to cholesterol and estradiol regulation. These data elucidated that CC of infertile woman with advanced endometriosis carried essential molecular alteration linked with follicular and gametic development. Through enrichment of the top deregulated genes, we can point out the potential pathways altered in this process toward oocyte commitment and infertility in these patients.

Dans cette thèse, nous abordons le problème de l'identification et de la quantification de variants (épissage alternatif et polymorphisme génomique) dans des données de RNA-seq sans génome de référence, et sans faire un assemblage complet des transcripts. Basé sur l'idée que chaque variant correspond à un motif reconnaissable, qu'on appelle une bulle, dans un graphe de Bruijn construit à partir des lectures de RNA-seq, nous proposons un modèle pour les variants dans de tels graphes. Nous introduisons ensuite une méthode, appelé KisSplice, pour extraire les événements d'épissage alternatif, et nous montrons qu'il trouve plus d'événements corrects que les assembleurs de transcriptome traditionnels. Afin d'améliorer son temps d'exécution, nous proposons un nouvel algorithme polynomial pour énumérer les bulles. On montre qu'il est plusieurs ordres de grandeur plus rapide que les approches précédentes. Afin de réduire sa consommation en mémoire, nous proposons une nouvelle façon de représenter un graphe de Bruijn. Nous montrons que notre approche utilise 30% à 40% moins de mémoire que l'état de l'art. Nous appliquons les techniques développées pour énumérer les bulles à deux problémes classiques. Nous donnons le premier algorithme optimal pour énumérer les cycles dans des graphes non orientés. Il s'agit de la première amélioration à ce probléme en près de 40 ans. Nous considérons ensuite une variante du problème des K chemins plus courts: au lieu de limiter le nombre des chemins, nous limitons leurs poids. Nous présentons de nouveaux algorithmes qui utilisent exponentiellement moins mémoire que les approches précédentes / In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the idea that each variant corresponds to a recognizable pattern, a bubble, in a de Bruijn graph constructed from the RNA-seq reads, we propose a general model for all variants in such graphs. We then introduce an exact method, called KisSplice, to extract alternative splicing events and show that it outperforms general purpose transcriptome assemblers. We put an extra effort to make KisSplice as scalable as possible. In order to improve the running time, we propose a new polynomial delay algorithm to enumerate bubbles. We show that it is several orders of magnitude faster than previous approaches. In order to reduce its memory consumption, we propose a new compact way to build and represent a de Bruijn graph. We show that our approach uses 30% to 40% less memory than the state of the art, with an insignificant impact on the construction time. Additionally, we apply the techniques developed to list bubbles in two classical problems: cycle enumeration and the K-shortest paths problem. We give the first optimal algorithm to list cycles in undirected graphs, improving over Johnson’s algorithm. This is the first improvement to this problem in almost 40 years. We then consider a different parameterization of the K-shortest (simple) paths problem: instead of bounding the number of st-paths, we bound the weight of the st-paths. We present new algorithms using exponentially less memory than previous approaches

La formation du duramen est un processus physiologique clé impliqué dans la qualité du bois puisqu'il contribue notamment à sa durabilité naturelle. L'objectif de cette thèse est de comprendre les mécanismes mis en jeu lors de la formation du duramen chez le douglas. L'étude a été menée aux niveaux phénotypiques, biochimiques et moléculaires sur plusieurs génotypes de douglas. Des études phénotypiques, il ressort que la proportion de duramen serait sous influence génétique et très peu environnementale, et que l'expansion du bois de coeur se déroule principalement en automne-hiver. Afin de caractériser la composition biochimique du bois, une nouvelle méthode a été développée. Elle repose sur la dissolution du bois dans des liquides ioniques, les solutions obtenues sont ensuite immuno-marquées à l'aide d'anticorps dirigés contre des épitopes de polymères pariétaux. Cette méthode a permis d'observer l'évolution, cerne par cerne, de la composition pariétale du bois de l'aubier externe au coeur du duramen. Certains polymères sont plus abondants dans l'aubier (arabinanes), tandis que d'autres dans le duramen (pectines, xylanes et galactanes). En parallèle, les gènes impliqués dans la formation du duramen ont été étudiés par RNA-Seq à partir de douglas appartenant à un seul génotype et abattus en hiver. Les résultats montrent que des gènes codant des facteurs de transcription, des protéines de défense, des enzymes de la voie de biosynthèse des phénylpropanoides et des enzymes impliquées dans le remodelage de la paroi sont surexprimés dans la zone de transition par rapport à l'aubier. Des hormones, l'éthylène et le jasmonate notamment, semblent jouer un rôle important dans la maturation de l'aubier. / The heartwood formation is a key physiological process involved in wood quality because it contributes to its natural durability. The goal of this thesis is to understand mechanisms involved in the heartwood formation in douglas fir. This study has been carried out at phenotypic, biochemical and molecular levels from several douglas-fir genotypes. Thanks to phenotypic analysis, we showed that heartwood proportion is probably under genetic control, and little influenced by the environment. In douglas fir, heartwood expansion mainly occurs during autumn and winter. To characterize the biochemical composition of wood, a new method has been developed. The method implies the wood dissolution in ionic liquid, the solution obtained are then analyzed by immunodetection with monoclonal antibodies against plant cell wall glycan epitopes. Thanks to this method, the wood cell wall composition has been studied, ring-by-ring, from the outer sapwood to the inner heartwood. Some polymers are more abundant in the sapwood (arabinans) while others in the heartwood (pectins, xylans and galactans). Then, genes involved in the heartwood formation have been studied by RNA-Seq from trees belonging to one genotype sampled during winter. Results show that genes encoding transcription factors, defence related proteins, enzymes involved in phenylpropanoid biosynthesis and plant cell wall modification are upregulated in transition zone compared to sapwood. Hormones, ethylene and jasmonate especially, seem to play an important role during sapwood maturation.

La régulation de l’homéostasie du glucose dans l’organisme est la fonction principale des cellules beta sécrétrices d’insuline dans le pancréas endocrine. Le facteur de transcription à domaine « winged helix », RFX6, a récemment, été identifié comme un nouveau régulateur de la différenciation endocrine pancréatique en aval de Ngn3 chez le poisson zèbre, la souris et l’homme. De plus, diverses mutations de Rfx6 chez l’homme ont été identifiées et reliées au syndrome de Mitchell Riley notamment caractérisé par un diabète néonatal, une atrésie de l’intestin grêle et une malabsorption intestinale. Lors de mes travaux de thèse, une approche combinée de transcriptomique chez la souris et la recherche des sites de fixation de RFX6 dans une lignée cellulaire beta et dans les ilots pancréatiques a permis de démontrer son importance dans le maintien de l’identité et de la fonction de la cellule beta. Pour la première fois, l’identification des cibles directes de RFX6 in vivo a été réalisée et a permis l’identification de l’ensemble du répertoire des gènes régulés directement par RFX6 dans les cellules beta qui n’ont pas été révélés dans le système cellulaire. Cette étude aura également permis d’identifier Mlxipl comme principale cible directement régulée par Rfx6 à la fois chez la souris et l’homme. Les expériences réalisées ont ainsi permis de déterminer les gènes cibles directs de RFX6 et contribué à élucider le rôle de ce facteur de transcription dans la différenciation et la fonction des cellules beta sécrétrices d’insuline. / Glucose homeostasis regulation in the body is the main function of insulin secreting beta cells in the endocrine pancreas. The winged-helix transcription factor RFX6 has recently been identified as a new pancreatic endocrine differentiation regulator, downstream of Ngn3,in zebra fish, mouse and human. Moreover, several Rfx6 mutations in humans were discovered and linked to the Mitchell Riley syndrome, which is characterized by neonatal diabetes, intestinal atresia and malabsorption. My thesis consisted of using an approach combining transcriptomic analysis in mouse and the identification of RFX6 target genes in a beta cell line as well as in pancreatic islets. This work has demonstrated the crucial role of RFX6 in maintaining beta cell identity and function. For the first time, RFX6 target genes were identified in vivo as well as the whole repertoire of directly regulated RFX6 target genesin beta cells, which were previously unidentified in the beta cell line. These studies have also shown that Mlxipl is a main RFX6 regulated target gene in mice and human. Overall, this work has allowed the clear identification of RFX6 target genes, thus contributing inunderstanding the role of this crucial transcription factor in the differentiation and function of insulin secreting beta cells.

Le processus transcriptionnel par l'ARN polymérase II (Pol II) chez les eucaryotes se déroule en trois étapes : L'initiation, l'élongation et la terminaison. De nombreux facteurs de transcription, des modifications de la chromatine (épigénétique) et des éléments régulateurs distants interviennent dans ce processus. La sous-unité RPB1 de l'ARN Pol II contient un domaine carboxyle terminale (CTD) composée d'une répétition de sept acides-aminés. Au travers de différentes modifications biochimiques, ce domaine coordonne le processus transcriptionnel par le recrutement de différents facteurs. Le CTD est également impliqué dans la coordination de la transcription au niveau de l'initiation, de l'élongation et de la terminaison par le biais de modifications épigénétiques et nucléosomales, mais aussi par l'action de régulateurs distants (enhancers) et probablement de changements de conformation tridimensionnelle du génome. Mon travail de thèse a consisté en l'étude de deux modifications biochimiques du CTD de l'ARN Pol II par traitement bioinformatique de données issues du séquençage haut-débit. J'ai pu montrer que la phosphorylation de la thréonine 4 influence l'élongation de la transcription chez l'humain. J'ai également montré que la phosphorylation de la tyrosine 1 est présente durant l'initiation, est préférentiellement localisée dans la direction anti-sens, est hyper-phosphorylée aux enhancers transcrits et tissus spécifiques et est une marque caractéristique de ces modules génomiques. Ce travail de doctorat a constitué une contribution à la compréhension du processus transcriptionnel chez l'humain par l'utilisation de méthodes bioinformatiques innovantes. / The biggest subunit of eukaryotic RNA polymerase II contains a carboxy-terminal domain (CTD) that consists in a repetition of seven amino-acids ranging from 26 in yeast to 52 in mammals. Specific biochemical modifications of CTD residues have been linked to specific stages of the transcriptional process. The CTD acts as a recruitment platform for processing factors that are involved in initiation, promoter proximal pausing, early and productive elongation (alternative splicing), 3' processing, termination and epigenetics.During my PhD, I used bioinformatics and high-throughput sequencing data to study two novel biochemical modifications of the CTD in human. I showed, in collaboration with biologists and bioinformaticians, that threonine 4 phosphorylation is important for proper elongation and probably termination of transcription. I showed also that tyrosine 1 phosphorylation is present during early transcription, antisense transcription (at divergent promoters) and is hyperphosphorylated at transcribed and tissue specific enhancers.Overall my doctorate has contributed to the understanding of the transcriptional process in human through the use of innovative bioinformatic methods.

Transgenic plants containing genes from Bacillus thuringiensis have been used as an alternative to chemical insecticides for insect pest control. The vegetative insecticidal proteins (Vip) secreted during the vegetative growth phase of bacteria are considered a second generation of insecticidal proteins since they do not share any structural or sequence homology with previously used crystal proteins (Cry) as well as having a wide insecticidal spectrum. One of the target pests for this protein is the fall armyworm (FAW) (Spodoptera frugiperda), the most important corn pest in South America. Previously it has been controlled by insecticides and maize expressing Cry proteins, but has rapidly evolved resistance to many control practices and remains a top concern for sustainable biotechnology control efforts. Thus, resistance characterization involving mode of action and genetics of resistance can help with Insect Resistance Management strategies, and improve the durability of control. In this dissertation, using two selected FAW population resistant to Vip3Aa20 Bt protein (Vip-R1and Vip-R2) we generated comparative proteomic and transcriptomic data among resistant and susceptible colonies. In the chapter 2, we bring FAW biology/ecology and Brazilian agriculture landscape data to support the high adaptive potential of this pest to genetically modified maize expressing Bt Cry proteins in Brazil. Proteomics studies in the chapter 3 revealed that neither Vip-R1 nor Vip-R2 showed difference between resistant and susceptible colonies either for Vip3Aa20 activation through proteolysis assay nor protein binding to the receptor. Transcriptomic sequencing and RNA-seq analysis in the chapter 4 showed strong evidence of ABC transporter genes associated with resistance as well as genes related to G-protein signaling pathway as downregulated. These results will be discussed in context of providing best management practices for managing FAW resistance to Vip, and extending the durability of Vip technology. / Plantas Transgênicas expressando genes de Bacillus thuringiensis (Bt) tem sido usadas como alternativa ao controle químico para controle de insetos praga. A proteina Vip (Vegetative Insecticide Protein) cuja secreção é realizada durante fase de crescimento da bacteria é considerada como segunda geração de proteinas inseticidas em função desta não apresentar similaridade de sequencias com todas as outras proteinas cristal (Cry), apresentando ainda maior espectro de controle de pragas. Uma das pragas alvo desta proteina é a lagarta-do-cartucho do milho (Spodoptera frugiperda), considerada a mais importante na cultura do milho na América do Sul. Larvas desta espécie foram sempre controladas com inseticidas e mais recentemente, milho expressando proteínas Cry. No entanto, esta praga tem desenvolvido resistência para várias ferramentas de controle, trazendo preocupação para a sustentabilidade das taticas de controle geradas através da biotecnologia. Dessa forma, estudos de caracterização da resistencia envolvendo modo de ação e characteristicas genéticas envolvidas com resistência pode contribuir para melhorar estratégias de Manejo de Resistencia de Insetos (IRM) e aumentar a durabilidade destas tecnologias para o controle. Nesta dissertação, foi gerado dados proteômicos e de transcriptoma comparando uma população de S. frugiperda resistente a Vip3Aa20 com a susceptivel. No capítulo 2, abordamos as características de bio-ecologia da praga associado ao sistema de cultivo suportando o alto potencial adaptativo desta espécie para hibridos de milho expressando proteinas Bt no Brazil. No capitulo 3, estudos de proteômica mostrou que Vip-R1 e Vip-R2 quando comparado com SUS, não demostraram diferenças para ativação da proteina nem ausencia de ligação da proteína com receptor de membrana no intestino do inseto. Dados de transcriptoma descritos no capitulo 5 mostrou forte evidências de que a baixa expressão de genes relacionados ao sistema transportador ABC pode estar associado com resistência bem como genes da via de sinalização das proteínas G. Estes resultados serão discutidos em um contexto para suportar boas praticas de manejo de resistência para lagarta-do-cartucho e assim estender a durabilidade da tecnologia Viptera® no campo.

L’identification des mutations constitutionnelles à l’origine d’une prédisposition génétique au cancer est essentielle à la prise en charge médicale des patients et de leurs familles. Depuis l’implémentation des technologies de séquençage à haut-débit dans les laboratoires diagnostiques, le principal défi n’est plus la détection des variations génétiques mais leur interprétation et leur classification. La question de l’interprétation de la variation est particulièrement cruciale lorsqu’elle conditionne la stratégie thérapeutique. Ainsi, il est essentiel de disposer de tests simples adaptables en routine diagnostique pour faciliter l’interprétation des variations génétiques. Dans ce contexte, nous avons utilisé un test fonctionnel développé par notre équipe pour classer des variations dans le gène TP53 à l’origine du syndrome de Li-Fraumeni et pour appréhender la corrélation génotype - phénotype chez les patients LFS. Dans un deuxième temps, nous avons évalué la pertinence d’une approche multi-omique (RNA-Seq et métabolomique) pour discriminer les cellules sauvages des cellules avec mutation hétérozygote du gène TP53 ou des gènes BRCA impliqués dans la prédisposition génétique aux cancers du sein et de l’ovaire. Sur la base des données de transcriptome, un modèle mathématique a été développé pour détecter les variants correspondant à des mutations délétères. Nous avons ensuite sélectionné les biomarqueurs les plus discriminants pour les intégrer dans un test fonctionnel de RT-MLPA dédié à la voie p53. Nous avons enfin adapté cet essai pour qu’il soit réalisable sur une simple prise de sang, sans immortalisation des lymphocytes du patient. / The identification of the constitutional mutation responsible for a genetic predisposition to cancer is essential to the clinical management of the patient and its relatives. With the implementation of high-throughput sequencing to the diagnostic routine of these pathologies, the challenge no longer lies within the detection of alterations but in their biological and clinical interpretation. While specific treatments are emerging, simple functional assays to help with the interpretation of the detected variants are needed. In this context, we used a functional test developed by our team to classify variations in the TP53 gene responsible for Li-Fraumeni syndrome and to understand the genotype-phenotype correlation in LFS patients. On the other hand, we assessed the relevance of a multi-omic approach (RNA-Seq and metabolomics) to discriminate wild-type cells from cells with a deleterious heterozygous mutation in TP53 or in the BRCA genes implicated in genetic predisposition to breast and ovarian cancers. Based on the transcriptomic data, a mathematical model has been developed to detect variants corresponding to deleterious mutations. Then we selected the most discriminating biomarkers and integrated them into a RT-MLPA functional assay dedicated to the p53 pathway. We finally adapted this test to be feasible on a simple blood test, without immortalization of the patient's lymphocytes.