Advancement in the study of host-microbe interactions has shown that microbes can induce and maintain long lasting changes in gene expression in host cells to facilitate beneficial symbiosis through changes in methylation of the host’s genomic DNA. The beneficial symbiosis between Hawaiian Bobtail squid, Euprymna scolopes and Gram negative bioluminescent bacteria Vibrio fischeri provides an excellent system for studying beneficial microbes’ effect on host DNA methylation. The symbiosis is highly specific, in that only V. fischeri colonizes the squid’s symbiotic organ from a background of 106 diverse bacteria per mL of sea water. DNA methylation (DNAm) refers to the covalent addition of methyl (CH3) groups to the nucleotides of organism’s genomic DNA. The most well researched DNA methylation type is 5- methyl cytosine methylation (5mC). Previous publications show DNAm provides an extra tier of regulation for organisms to control their gene expression, without altering their DNA sequences. Two types of DNAm have been discovered in invertebrate systems: gene promoter methylation and gene body methylation. The amount of methylated cytosine on gene bodies is positively correlated with the specific gene’s expression state. We hypothesize that V. fischeri plays an important role in regulating host DNA methylation during both colonization of the animals (juvenile) and maintenance of the symbiosis I (adult). To start to address this hypothesis, our specific aims are (1) validate DNA methylation in E. scolopes; (2) identify DNA methylation machinery genes in squid at the transcript level and quantify the level of their expression based on state of symbiosis; (3) analyze squid DNA methylation at the whole genome level as well as gene specific level.

Photorhabdus luminescens est une entérobactérie retrouvée en symbiose avec les nématodes du genre Heterorhabditis. Dans les sols, ce complexe némato-bactérien est pathogène d’insectes ravageurs et est utilisé en contrôle biologique. Le nématode pénètre dans l’insecte et libère la bactérie dans l’hémolymphe. Photorhabdus va ensuite se multiplier et secréter divers facteurs de virulence comme des toxines. L’insecte meurt de septicémie puis le nématode et la bactérie vont se nourrir du cadavre. Une fois les ressources épuisées, le complexe némato-bactérien va se reformer et sortir du cadavre à la recherche d’une nouvelle cible. Plusieurs exemples d’hétérogénéité phénotypique ont été décrits chez cette bactérie amenant chacun à la présence de sous-populations dans une culture bactérienne. Cette hétérogénéité phénotypique peut-être causée par des mécanismes épigénétiques et plus précisément par la méthylation de l’ADN. Chez les entérobactéries, la méthyltransférase Dam est très conservée. Elle méthyle les adénines des sites GATC et est impliquée dans la réparation des erreurs lors de la réplication de l’ADN, la régulation du cycle cellulaire mais aussi la régulation de divers gènes. Cette méthyltransférase est en compétition avec certain régulateurs transcriptionnel. Selon qui de la méthyltransférase ou du régulateur se fixera en premier, le gène sera ou non exprimé donnant naissance à deux sous-populations. Cette thèse a pour objectif de mettre en évidence les rôles de la méthyltransférase Dam chez Photorhabdus luminescens. Dans un premier temps, j’ai montré que la surexpression de Dam (Dam+) amène une diminution de la mobilité et du pouvoir pathogène de la bactérie mais à l’inverse augmente sa capacité à former des biofilms. Une analyse transcriptomique (RNAseq) a montré des différentiels d’expression de certains gènes impliqués dans les phénotypes observés. En recombinant la souche de Photorhabdus Dam+ avec les nématodes hôtes, l’effet sur la pathogénicité a été augmenté en comparaison des résultats après injection de la bactérie seule. L’établissement de la symbiose némato-bactérienne avec cette souche Dam+ n’est pas significativement impacté par rapport à la souche sauvage. Enfin l’analyse du méthylome (détection de tous les sites méthylés sur le génome grâce à la technique SMRT) de Photorhabdus dans diverses phases de croissance nous a permis de déterminer que la méthylation par Dam semble être stable aux différents temps de la croissance bactérienne testés chez Photorhabdus. Le méthylome de la souche Dam+ a confirmé l’hypothèse que cette surexpression augmentait le taux de méthylation des sites GATC sur le génome. La comparaison combinée entre le RNAseq et les sites GATC différentiellement méthylés entre la souche contrôle et Dam+ a mis en évidence certains gènes candidats ressortant de ces deux analyses. En effet, certains gènes sont différentiellement exprimés dans les deux souches et ont un différentiel de méthylation au niveau de sites GATC dans leur région promotrice, l’étude détaillée de leur régulation par la méthylation fait maintenant partie des perspectives et permettront peut-être d’expliquer une partie des phénotypes observés chez Photorhabdus luminescens. / Photorhabdus luminescens is an Enterobacteriaceae found in soils in symbiosis with a nematode from the genus Heterorhabditis. This nemato-bacterial complex is highly pathogenic against insect pest crops and so used in biocontrol. The nematode enters into the insect and releases Photorhabdus in the hemolymph of the insect. Photorhabdus multiplies and produces diverse virulence factors as toxins. Insect die from septicemia and both nematodes and bacteria feed on the nutrients in the cadaver. Once nutrients are lacking, the nematodes and the bacteria reassociate and exit from the cadaver to find new insects to infect. Photorhabdus is switching between pathogenic and symbiotic state. This bacterium displays phenotypic heterogeneity as we observe subpopulations coexisting in a same bacterial culture. Phenotypic heterogeneity can be explained by epigenetic mechanisms such as DNA methylation. In Enterobacteriaceae, Dam methyltransferase is broadly distributed. It methylates the adenine of GATC sites. Dam is involved in post-replicative mismatch repair, cell-cycle regulation and also gene transcription regulation. This methyltransferase can be in competition with some transcriptional regulators. Depending on which will bind first on the promoter region, gene will be expressed or not, leading to the rise of two subpopulations. This thesis aims to understand roles of Dam in Photorhabdus luminescens. Overexpression of the methyltransferase leads to a decrease in motility and pathogenicity of Photorhabdus Dam+ strain whereas it increases biofilms formation. A transcriptomic analysis (RNAseq) revealed differential expression of genes involved in the observed phenotypes. Symbiosis establishment does not seem to be strongly impacted in Dam+ strain as the only difference observed when compared to the nematode associated with the control strain is the same as with bacteria alone (a delayed virulence). A methylome analysis was also done (screening of all methylated sites in the genome using SMRT sequencing) in several growth conditions which revealed that DNA methylation is stable over growth kinetics. Dam+ strain methylome analysis confirmed the hypothesis that Dam overexpression increases GATC methylation over the genome. Comparative analysis of methylome and RNAseq experiments between control and Dam+ strains highlighted several common genes. In fact, some genes are differentially expressed between both strains and also have GATC sites differentially methylated in their promoter region. Their transcription regulation by methylation is a future aim and may give some explanation for a part of the phenotypes observed in Photorhabdus luminescens.

En attente d'autorisation pour diffusion du résumé / En attente d'autorisation pour diffusion du résumé

Amongst the many processes that shape the final set of RNA molecules present in eukaryote cells, splicing emerges as the most prominent mechanism for message diversification. In recent years, applications of high throughput sequencing to RNA, known as RNA sequencing, have opened new avenues for the study of transcriptome composition, and have enabled further characterisation of such mechanism. In this thesis, I focus on the application of this technology to the study of human transcript diversity and its potential impact on the protein repertoire. In the first results chapter, I explore the extent of transcriptome diversity by asking whether there is a preference for the production of specific alternative transcripts within each given gene. I show that while many alternative transcripts can be detected, the expression of most protein coding genes tends to be dominated by one single transcript (major transcript). Such findings are validated in the second chapter, and are further used to explore changes in splicing patterns in a disease context. By analysing healthy and tumor samples from kidney cancer patients, I show that most of the detected splicing alterations do not lead to big changes in the relative abundance of major transcripts, at least in a recurrent manner. In addition, I introduce a framework to visualise the most extreme changes in splicing and to evaluate their potential functional impact. In the third chapter, I investigate the role of spliceosome assembly dynamics on the regulation of splice site choice. I show that depletion of PRPF8, a core spliceosomal component, leads to the preferential retention of a subset of introns with weaker splice sites, and also introduces alterations in the rate of co-transcriptional splicing. Finally, in the last chapter, I explore the validation of changes in alternative transcript abundance at the protein level, through the integration of results derived from RNA sequencing datasets with those obtained from proteomics experiments. Altogether, the findings described in this thesis provide a global picture on the extent of alternative splicing in the diversification of the transcriptome, expand current knowledge on the splicing reaction, and open new possibilities for the integration of transcriptomics and proteomics data.

In eukaryotes, distinct nutrient signals are integrated in order to produce robust cellular responses to fluctuations in the environment. This process of signal integration is attributed to the crosstalk between nutrient specific signaling pathways, as well as the large degree of overlap between their regulatory targets. In the budding yeast Saccharomyces cerevisiae, these distinct pathways have been well characterized. However, the significant overlap between these pathways confounds the interpretation of the overall regulatory logic in terms of nutrient-dependent cell state determination. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling pathway in budding yeast, focussing on carbon and nitrogen signaling. We build a computational model of this pathway to reconcile the available experimental data with our proposed molecular mechanism. We evaluate the robustness of the model fit to data with respect to the variations in the values of kinetic parameters used to calibrate the model. Finally, we use the model to make novel, experimentally testable predictions of transcription factor activities in mutant strains undergoing complex nutrient shifts. We also propose a novel framework, called BoolODE for utilizing published Boolean models to generate synthetic datasets used to benchmark the performance of algorithms performing gene regulatory network inference from single cell RNA sequencing data. / Doctor of Philosophy / An important problem in biology is how organisms sense and adapt to ever changing environments. A good example of an environmental cue that affects animal behavior is the availability of food; scarcity of food forces animals to search for food-rich habitats, or go into hibernation. At the level of single cells, a range of behaviors are observed depending on the amount of food, or nutrients present in the environment. Moreover, different types of nutrients are important for different biological functions in single cells, and each different nutrient type will have to be available in the right quantities to support cellular growth. At the subcellular level, intricate molecular machineries exist which sense the amounts of each nutrient type, and interpret this information in order to make a decision on how best to respond. This interpretation and integration of nutrient information is a complex, poorly understood process even in a simple unicellular organism like the budding yeast. In order to understand this process, termed nutrient signaling, we propose a mathematical model of how yeasts respond to nutrient availability in the environment. Our model advances the state of knowledge by presenting the first comprehensive mathematical model of the nutrient signaling machinery, accounting for a variety of experimental observations from the last three decades of yeast nutrient signaling. We use our model to make predictions on how yeasts might behave when supplied with different combinations of nutrients, which can be verified by experiments. Finally, the cellular machinery that helps yeasts respond to nutrient availability in the environment is very similar to the machinery in cancer cells that causes them to grow rapidly. Our proposed model can serve as a stepping stone towards the construction of a model of cancer's responses to its nutritional environment.

Moorella thermoacetica est une bactérie d’altération anaérobie thermophile sporulée produisant les spores les plus thermorésistantes isolées à ce jour en industrie agroalimentaire. Les spores de M. thermoacetica peuvent survivre aux traitements d’appertisation appliqués dans l’industrie de la conserve et représente la principale cause d’altération de conserves peu acides après incubation à 55 °C. Les mécanismes mis en place pendant la sporulation, ainsi que l’impact des facteurs environnementaux sur la sporulation et les propriétés des spores de Moorella sont largement méconnus.L’objectif de ces travaux était donc de caractériser l’impact de la température sur les caractéristiques de sporulation et de résistance des spores ainsi que de déterminer les mécanismes moléculaires impliqués dans la sporulation. Nous avons montré que la capacité de sporulation est meilleure lorsque la sporulation est effectuée à la température optimale (55 °C) en comparaison avec les températures limites basse et haute (45 °C et 65 °C, respectivement). De plus, les spores de M. thermoacetica produites à 45 °C sont plus sensibles à la chaleur humide et aux biocides que les spores produites à 55 °C. La structure des spores ainsi que leur composition protéique varient en fonction de la température de sporulation. Une étude RNAseq menée au cours de la sporulation de M. thermoacetica en conditions optimales régulées a montré que la plupart des 167 gènes de sporulation, identifiés in silico dans le génome de M. thermoacetica ATCC39073, est sur-exprimée pendant la sporulation. Ces résultats suggèrent que les mécanismes décrits chez d’autres espèces endosporulées sont conservés chez Moorella.L’ensemble des données acquises montrent que la température joue un rôle essentiel dans les caractéristiques de sporulation et de résistance des spores de M. thermoacetica mais également que les mécanismes moléculaires impliqués dans la sporulation semblent conservés au regard des données disponibles pour d’autres espèces. / Moorella thermoactica is a spoilage anaerobic and thermophilic spore-former producing the most highly heat-resistant spores isolated so far in food industry, which enables the bacteria to survive the sterilization process applied in cannery. M. thermoacetica is the main cause of low acid canned food spoilage after incubation at 55 °C. Little is known about sporulation mechanisms and spore properties according to environmental conditions.In this work, we aimed at characterizing the impact of environmental conditions on sporulation and spore resistance properties, as well as describing the molecular mechanisms underlying sporulation. We showed that sporulation capacities are higher when sporulation is performed at the optimal temperature (55 °C) that at limit temperatures (45 °C and 65 °C). Besides, spores are less resistant to wet heat and biocides when formed at 45 °C than at 55 °C. We showed that the ultrastructure and spore protein composition varied according to sporulation temperature. Moreover, the study of gene expression by RNAseq during sporulation in optimal regulated conditions showed that most of the 167 genes involved in the sporulation process and identified in silico in M. thermoacetica ATCC 39073 genome, were up-regulated during sporulation, suggeting that the mechanisms described in other endospore-formers are conserved in Moorella.Altogether, our results showed that sporulation temperature strongly impacts sporulation and spore properties of M. thermoacetica and that sporulation mechanisms tend to be conserved in Moorella considering data available on other endospore-formers.

O Transtorno do Espectro Autista (TEA) é um transtorno neuropsiquiátrico grave caracterizado por comprometimento da capacidade de interação social e comunicação e pela presença de interesses, atividades e comportamentos repetitivos e restritos. O TEA apresenta alta heterogeneidade genética e pode ser enquadrado em diferentes modelos de herança, o que torna difícil apontar os fatores genéticos associados ao transtorno e compreender de que forma eles interagem e ocasionam, em última instância, sua manifestação clínica. Ainda, fenômenos como penetrância incompleta e discordância entre gêmeos monozigóticos são frequentemente observados em famílias com indivíduos afetados, tornando ainda mais complexo o entendimento do envolvimento de cada um dos fatores genéticos na etiologia do TEA. Uma forma de contornar esses problemas é a utilização de abordagens transcriptômicas no estudo desse transtorno. Nesse contexto, a busca por variantes patogênicas deixa de ser o principal foco do estudo e a atenção volta-se para a investigação de vias de sinalização e processos biológicos que estejam desregulados durante o processo de diferenciação neuronal e que sejam compartilhados pelos indivíduos afetados. Usando como principal ferramenta o sequenciamento do transcriptoma de células progenitoras neurais (NPC) e neurônios derivados de células-tronco pluripotentes induzidas (iPSC), identificamos uma série de alterações transcricionais importantes entre pacientes e controles, sugerindo que, a despeito da grande heterogeneidade genética associada ao transtorno, essas alterações se refletem em processos biológicos comuns. Nossos resultados são consistentes com os obtidos em trabalhos anteriores realizados com outros modelos de estudo e as linhagens celulares geradas a partir de nosso protocolo parecem refletir de forma fidedigna o perfil de expressão do cérebro fetal. Ainda, em um caso particular incluído neste estudo, investigamos as consequências transcricionais e funcionais de uma duplicação na região 17p13.3 - alteração previamente implicada em outros casos de autismo - nas células neuronais deste paciente, contribuindo para a compreensão do papel desta duplicação na patofisiologia do TEA. Dessa forma, nosso trabalho reforça a validade do uso de células neurais derivadas de iPSC e de abordagens transcricionais para o estudo de transtornos do neurodesenvolvimento / Autism Spectrum Disorder (ASD) is a severe neuropsychiatry disorder characterized by impaired social interaction and communication, restricted interests and repetitive behaviors. ASD is highly genetically heterogeneous and can be caused by different inheritance models, which hampers the identification of the genetic factors associated to the disorder. Incomplete penetrance and discordance between monozygotic twins are often observed in families of affected individuals, making it even more complex to understand the involvement of genetic factors in ASD. Applying transcriptomic approaches to study this disorder is an interesting way to overcome these problems. In this context, searching for pathogenic variants is no longer the study\'s main focus. Instead, one aims to investigate signaling pathways and biological process that are deregulated during neuronal differentiation and shared by affected individuals. Based on the transcriptome sequencing of neural progenitor cells (NPC) and neurons derived from induced pluripotent stem cells (iPSC), we were able to identify a series of important transcriptional alterations between patients and controls, which suggest that despite the great genetic heterogeneity associated to ASD, those alterations are reflected in common biological processes. Our results are consistent with those obtained in previous studies performed with other models and the lineages generated by our protocol seem to reliably reflect fetal brain expression profile. Moreover, in a particular case included in this study, we investigated transcriptional and functional consequences of a duplication located at 17p13.3 - an alteration previously found in other autism cases - in the neuronal cells of this patient, contributing towards a better comprehension of the role of this duplication in ASD pathophysiology. Hence, our work reinforces the validity of the use of neural cell derived from iPSC and transcriptional approaches in the studies of neurodevelopmental disorders

O corpo lúteo (CL) canino é responsável pela síntese de E2 durante o diestro. O E2 atua de forma autócrina e/ou parácrina sobre essa glândula. O mecanismo de atuação do E2 depende da razão entre receptor alfa (ERα) e receptor beta (ERβ). A ligação ao ERα tem efeito proliferativo e ao ERβ antiproliferativo. O objetivo deste trabalho foi entender a sinalização mediada pelo ERα e ERβ no processo de formação e regressão do CL. CLs foram obtidos de cadelas não prenhes (n=30) nos dias 10, 20, 30, 40, 50 e 60 (n=5/grupo) após a ovulação (po). No dia da ovariossalpingohisterectomia foi colhido sangue para mensuração das concentrações de P4 e E2. Dezoito CLs (n=3/grupo) foram submetidos ao sequenciamento de RNA (RNAseq). Os genes diferencialmente expressos (DE) identificados pelo RNAseq foram submetidos ao software oPOSSUM3 para identificação das regiões de ligação mais representadas nos fatores de transcrição relacionados aos genes do ERα (ESR1) e ERβ (ESR2). A análise de expressão temporal revelou a presença de 5.116 diferencialmente expressos (DE) em pelo menos uma comparação e 1.106 não foram anotados ainda no genoma canino, destes genes DE 295 apresentavam regiões de ligação de fatores de transcrição em comum com ESR1 e ESR2. Dez genes DE foram selecionados para validação dos resultados de RNAseq através do qPCR; usando o GAPDH como gene de referência. Desses genes, quatro apresentaram regioes em comum com ESR2 (LEF-1; PAPPA; NDGR2 ATP1A1) e um com ESR1 (CAV1) e os demais controlam proliferação celular (CTNNB1; CCND1; IGFBP 3, 4 e 5). A expressão proteíca de PAPPA e IGFBP 3, 4 e 5 (componentes do sistema IGF) foi avaliada também por imunohistoquímica. Durante a primeira metade do diestro, nossos resultados indicam que a sinalização mediada pelo E2 ocorre via interação do ERα com CAV-1 (sinalização não genômica), ativando as vias de sinalização IGF e WNT/βcatenina, regulando o processo de proliferação celular. Enquanto na segunda metade, o ERβ regularia a expressão gênica de NDGR2 e ATP1A1, contribuindo para a regressão do CL. Assim nos resultados sugerem que o E2 atue tanto como um fator luteotrófico e quanto regulador da regressão do CL canino. / The canine corpus luteum (CL) is responsible for E2 synthesis during diestrus, which acts in an autocrine and / or paracrine manner in this gland. The E2 mechanism of action depends on the ratio between alpha (ERα) and beta (ERβ) receptor The binding to ERα has a proliferative effect whereas to ERβ an antiproliferative. The objective of this study was to understand the signaling mediated by ERα and ERβ in the formation and regression of the CL. CLs were obtained from non-pregnant bitches (n = 30) on days 10, 20, 30, 40, 50 and 60 (n = 5 / group) post-ovulation (po). On the day of ovariohysterectomy blood was collected for measurement of P4 and E2 concentrations. Eighteen CLs (n = 3 / group) were subjected to RNA sequencing (RNA-Seq). Genes differentially expressed (DE) identified by RNA-Seq were submitted to oPOSSUM3 software for detection of over-represented transcription factors binding sites (TFBS) related to the ERα (ESR1) and ERβ (ESR2) genes. The temporal expression analysis revealed the presence of 5116 differentially expressed (DE) genes in at least one comparison, and 1106 genes, which have not been recorded to the canine genome yet From these, 295 genes showed TFBS in common with ESR1 and ESR2. Ten DE genes were selected to validate the results of RNA-Seq by qPCR; using GAPDH as reference gene. Of these genes, four had TFBS in common with ESR2 (LEF-1; PAPPA; NDGR2; ATP1A1) and one with ESR1 (CAV1) and others genes were chosen because they control cell proliferation (CTNNB1; CCND1, IGFBP 3, 4 and 5). Protein expression of the IGF related genes (PAPPA and IGFBP 3, 4 and 5) was also evaluated by immunohistochemistry. During the first half of diestrus, it appears that E2 mediated signaling occurs via interaction of ERα with CAV-1 (non-genomic signaling), activating signaling pathways of IGF and WNT / βcatenin, then regulating the cell proliferation process. Whereas in the second half, ERβ appears to regulate NDGR2 and ATP1A1 gene expression, contributing to the regression of the CL. Thus our results suggest that E2 may act as a luteotrophic and also a luteolytic factor in the canine CL.

Ácaros Brevipalpus yothersi Baker (1949) são vetores do citrus leprosis virus C (CiLV-C), o mais comum causador da leprose dos citros. Esta é considerada, atualmente, a doença viral de maior importância na cultura dos citros no Brasil e ocorre também em países da América do Sul e Central, além do México, na América do Norte. A doença prejudica a vida útil da planta, devido à queda de folhas e frutos, e seca de ramos, podendo levá-la à morte quando o ataque é demasiadamente severo. O controle e manejo da leprose são basicamente atribuídos ao uso de acaricidas, demandando dos produtores um acréscimo significativo no orçamento por defensivos agrícolas e potencial risco ao ambiente. Nos últimos anos, análises de expressão gênica (transcriptoma), envolvendo ácaros praga da agricultura, resultaram em informações importantes como o envolvimento de genes específicos no processo de resistência a acaricidas e desenvolvimento biológico. No entanto, ainda pouco se sabe sobre a interação do ácaro B. yothersi com o CiLV-C, tornando o estudo de transcriptoma muito significativo para a obtenção de informações aprofundadas sobre o atípico padrão vírus-vetor do patossistema leprose. Assim, através do sequenciamento de RNA (RNAseq), foi investigado o perfil de expressão diferencial entre ácaros B. yothersi virulíferos e avirulíferos. O RNAseq foi realizado em sistema Illumina HiSeq 2500, e os dados analisados com base em linguagem R e ferramentas do software Bioconductor. Os reads sequenciados foram mapeados no genoma de B. yothersi e foi feita análise de expressão utilizando DESeq2. Foram observados 5.690 genes diferencialmente expressos (GDE), sendo 2.736 transcritos induzidos em ácaros virulíferos. Os GDE foram analisados em banco de dados do NCBI, buscando por proteínas similares em artrópodes. Dentre os transcritos induzidos em B. yothersi, potencialmente em resposta ao CiLV-C, foram encontrados genes relacionados ao processo de detoxificação de xenobióticos, metabolismo primário e imunidade, com possível envolvimento na interação vírus-vetor. A expressão de 23 genes foi verificada por RT-PCR quantitativo em tempo real (RT-qPCR). As análises indicaram que os genes envolvidos em detoxificação são induzidos durante a interação entre o ácaro da leprose e o CiLV-C. / The false spider mite Brevipalpus yothersi Baker (1949) is recognized as vector of citrus leprosis virus C (CiLV-C), the most common causal agent of citrus leprosis disease. Currently, it is considered the viral disease of major importance in citrus in Brazil and occurs in countries of South and Central America, as well as in Mexico, North America. It reduces the lifespam of the plants due to leaf and fruit drop, dried branches, and can lead to death when the attack is severe. The management of leprosis is based primarily on the chemical control of the mite vector, increasing significantly the cost of production and harming the environment. On the last years, gene expression (transcriptome) analyzes involving phytophagous mites resulted in important data, such as the involvement of specific genes in the process of resistance to acaricides and biological development. However, there is little information about B. yothersi-CiLV-C interaction, making the transcriptome a very interesting tool to obtaining data regarding the atypical virus-vector relationship of the leprosis pathosystem. RNA sequencing (RNAseq) was used to investigate the differential expression profiles between viruliferous and aviruliferous B. yothersi mites. The RNAseq was performed using the Illumina HiSeq 2500 system, the data were analyzed using the R language and Bioconductor software packages. The sequenced reads were mapped on the genome of B. yothersi and expression analysis was performed in DESeq2. We identified 5.690 differentially expressed genes (DEGs), of which 2.736 transcripts were induced in viruliferous mites. The DEGs were analyzed in NCBI database, searching for similar proteins in arthropods. Among the transcripts induced in response to CiLV-C, there are genes related to the detoxification of xenobiotics, primary metabolism, immunity and possible involvement in the virus-vector interaction. Expression of 23 genes was verified by quantitative real-time RT-PCR (RT-qPCR). The analyzes indicate that detoxification genes are induced during the interaction between the false spider mite and CiLV-C.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The research on molecular interactions which cause genetic diseases has been the focus of many studies in recent years. With the inclusion of informatics in biological research, there was a great advance in the discovery of new solutions and diagnostic techniques for the treatment of diseases. Cancer is one of the diseases that have caused more interest among scientists around the world, and between their variations, are those caused by genetic defects that affect the genome maintenance mechanisms (GMM), which promote the proper functioning of the organism of an individual. Halazonetis and colaborators (2008) published a study involving of the metabolic pathways GMM, which identifies the appearance of a barrier that prevents the spread of cancer, but it is broken by initiating uncontrolled reproduction of defective cells that cause the cancerous tumors. The motivation of this work is to investigate the process of activation of anticancer barrier, using quantitative methods to analysis of the expression of genes and pathways. For this reason, it was used the Ontocancro ontology as analysis tool, being made several changes in its architecture for the realization of this study. / A investigação sobre as interações moleculares, que causam doenças genéticas têm sido foco de muitos estudos nos últimos anos. Com a inclusão da informática em pesquisas biológicas, houve um grande avanço na descoberta de novas soluções e técnicas de diagnósticos para o tratamentos de doenças. O câncer é uma das doenças que mais tem causado interesse entre cientistas do mundo inteiro, e entre suas variações, estão aquelas causadas por defeitos genéticos que afetam os mecanismos de manutenção do genoma (GMM), que promovem o bom funcionamento do organismo de um indivíduo. Halazonetis e colaboradores, em 2008, publicou um estudo envolvendo as vias metabólicas GMM, que identifica o surgimento de uma barreira que evita a propagação do câncer, mas é rompida dando início a reprodução descontrolada de células defeituosas que causam os tumores cancerígenos. A motivação desta dissertação consiste em investigar o processo de ativação da barreira anticâncer, usando métodos quantitativos para análise da expressão de genes e vias. Para isso, utilizou-se a ontologia Ontocancro como ferramenta de análise, sendo efetuadas diversas alterações em sua arquitetura para a realização deste estudo.