A percepção e aquisição de nutrientes essenciais do meio ambiente estão associadas com o desenvolvimento do fungo saprófita A. fumigatus em um ambiente hostil. O fosfato inorgânico é um dos nutrientes essenciais para o desenvolvimento deste fungo. Os sistemas para aquisição de fosfato em células eucarióticas têm sido caracterizados como sistema de alta afinidade, o qual é ativado em resposta a ausência externa de fosfato e sistema de baixa afinidade, o qual assegura um suprimento de fosfato em concentrações normais ou altas de fosfato extracelular. Como um passo inicial para o entendimento da via PHO em A. fumigatus, caracterizou-se o homólogo PHO80, PHO84 e PHO85 aqui denominados phoBPHO80, phoDPHO84 e phoAPHO85, respectivamente. Resultados mostraram que o mutante phoBPHO80 apresenta um defeito no crescimento polarizado e que existe uma interação entre o metabolismo de PhoBPHO80, da calcineurina e do cálcio. As hibridações de microarray realizadas com RNA obtido das cepas mutante phoBPHO80 e selvagem mostraram que os genes Afu4g03610 (phoDPHO84), Afu7g06350 (phoEPHO89), Afu4g06020 (phoCPHO81) e Afu2g09040 (transportador vacuolar Vtc4) estão mais expressos no background do mutante phoBPHO80 ou em concentração de 0.1 mmol/L de fosfato. Nossos resultados indicam que a mutação phoBPHO80 pode afetar o acúmulo de polifosfato em vacúolos em alta ou baixa concentração de fosfato extracelular. Não obteve-se êxito na deleção da quinase phoAPHO85 desta forma pode-se levar em consideração que o gene phoAPHO85 parece ser essencial em A. fumigatus. Surpreendentemente, a cepa com a deleção de phoDPHO84 não apresentou nenhum fenótipo diferente da sua cepa selvagem. Além do mais, as cepas mutantes phoBPHO80 e phoDPHO84 não apresentaram redução na virulência em um modelo murino de aspergilose invasiva. Nossos resultados sugerem também, que a deleção da proteína quinase A está contribuindo para um decréscimo na expressão de genes PHO em A. fumigatus. / Environmental sensing and retrieval of nutrients from the environment are associated with growth of A. fumigatus in inhospitable environments. Phosphate is an ion that is essential for fungal growth. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in Aspergillus fumigatus, we characterized the PHO80, PHO84 and PHO85 homologues, here denominaded phoBPHO80, phoDPHO84 and phoAPHO85, respectively. We show that the phoBPHO80 mutant has a polar growth defect (i.e., a delayed germ tube emergence) and, by phenotypic and phosphate uptake analyses, establish a link between PhoBPHO80, calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild-type and phoBPHO80 mutant cells identify Afu4g03610 (phoDPHO84), Afu7g06350 (phoEPHO89), Afu4g06020 (phoCPHO81), and Afu2g09040 (vacuolar transporter Vtc4) as more expressed both in the phoBPHO80 mutant background and under phosphate-limiting conditions of 0.1 mM Pi. Epi-fluorescence microscopy revealed accumulation of poly-phosphate in phoBPHO80 vacuoles, which was independent of extracellular phosphate concentration. We also tried to isolate the phoAPHO85 deletion strain without succes after several times what raises the interesting possibility that the phoAPHO85 null mutant might be essential in Aspergillus fumigatus. Surprisingly, phoDPHO84 deletion mutant is indistinguishable phenotypically from the corresponding wild-type strain. mRNA analyses suggest that protein kinase A absence supports the expression of PHO genes in A. fumigatus. Furthermore, phoBPHO80 and phoDPHO84 mutant are fully virulent in a murine low dose model for invasive aspergillosis.

A percepção e aquisição de nutrientes essenciais do meio ambiente estão associadas com o desenvolvimento do fungo saprófita A. fumigatus em um ambiente hostil. O fosfato inorgânico é um dos nutrientes essenciais para o desenvolvimento deste fungo. Os sistemas para aquisição de fosfato em células eucarióticas têm sido caracterizados como sistema de alta afinidade, o qual é ativado em resposta a ausência externa de fosfato e sistema de baixa afinidade, o qual assegura um suprimento de fosfato em concentrações normais ou altas de fosfato extracelular. Como um passo inicial para o entendimento da via PHO em A. fumigatus, caracterizou-se o homólogo PHO80, PHO84 e PHO85 aqui denominados phoBPHO80, phoDPHO84 e phoAPHO85, respectivamente. Resultados mostraram que o mutante phoBPHO80 apresenta um defeito no crescimento polarizado e que existe uma interação entre o metabolismo de PhoBPHO80, da calcineurina e do cálcio. As hibridações de microarray realizadas com RNA obtido das cepas mutante phoBPHO80 e selvagem mostraram que os genes Afu4g03610 (phoDPHO84), Afu7g06350 (phoEPHO89), Afu4g06020 (phoCPHO81) e Afu2g09040 (transportador vacuolar Vtc4) estão mais expressos no background do mutante phoBPHO80 ou em concentração de 0.1 mmol/L de fosfato. Nossos resultados indicam que a mutação phoBPHO80 pode afetar o acúmulo de polifosfato em vacúolos em alta ou baixa concentração de fosfato extracelular. Não obteve-se êxito na deleção da quinase phoAPHO85 desta forma pode-se levar em consideração que o gene phoAPHO85 parece ser essencial em A. fumigatus. Surpreendentemente, a cepa com a deleção de phoDPHO84 não apresentou nenhum fenótipo diferente da sua cepa selvagem. Além do mais, as cepas mutantes phoBPHO80 e phoDPHO84 não apresentaram redução na virulência em um modelo murino de aspergilose invasiva. Nossos resultados sugerem também, que a deleção da proteína quinase A está contribuindo para um decréscimo na expressão de genes PHO em A. fumigatus. / Environmental sensing and retrieval of nutrients from the environment are associated with growth of A. fumigatus in inhospitable environments. Phosphate is an ion that is essential for fungal growth. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in Aspergillus fumigatus, we characterized the PHO80, PHO84 and PHO85 homologues, here denominaded phoBPHO80, phoDPHO84 and phoAPHO85, respectively. We show that the phoBPHO80 mutant has a polar growth defect (i.e., a delayed germ tube emergence) and, by phenotypic and phosphate uptake analyses, establish a link between PhoBPHO80, calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild-type and phoBPHO80 mutant cells identify Afu4g03610 (phoDPHO84), Afu7g06350 (phoEPHO89), Afu4g06020 (phoCPHO81), and Afu2g09040 (vacuolar transporter Vtc4) as more expressed both in the phoBPHO80 mutant background and under phosphate-limiting conditions of 0.1 mM Pi. Epi-fluorescence microscopy revealed accumulation of poly-phosphate in phoBPHO80 vacuoles, which was independent of extracellular phosphate concentration. We also tried to isolate the phoAPHO85 deletion strain without succes after several times what raises the interesting possibility that the phoAPHO85 null mutant might be essential in Aspergillus fumigatus. Surprisingly, phoDPHO84 deletion mutant is indistinguishable phenotypically from the corresponding wild-type strain. mRNA analyses suggest that protein kinase A absence supports the expression of PHO genes in A. fumigatus. Furthermore, phoBPHO80 and phoDPHO84 mutant are fully virulent in a murine low dose model for invasive aspergillosis.

Récemment, des analyses dans divers organismes eucaryotes ont révélé que l'ensemble du génome est transcrit et produit en plus des ARNs messagers, une grande variété d’ARNs non codants de différentes longueurs. Les ARNs non codants de plus de 200 nucleotides, classés comme longs ARNs non codants (LARNnc), représentent la classe la plus abondante de transcripts non codants. Les études des fonctions des LARNnc suggèrent que beaucoup d'entre eux seraient impliqués dans la régulation de la transcription. L'objectif de ma thèse de doctorat était d'élucider les mécanismes de la régulation transcriptionnelle médiée par des LARNnc dans différents systèmes eucaryotes. Dans mon premier projet, j'ai étudié le rôle d'un long ARN non codant antisens dans la régulation transcriptionnelle du gène PHO84, codant un transporteur de phosphate à haute affinité, chez S. cerevisiae. Des études antérieures ont montré que la suppression d’une proteine de l’exosome Rrp6 entraîne une augmentation de l'expression antisens et la répression de PHO84. Il a été suggéré que la perte de Rrp6 entraîne une stabilisation antisens au locus PHO84, entraînant le recrutement de l'histone de-acétylase Hda1 et la répression de PHO84. Cependant, le mécanisme par lequel Rrp6p régule la transcription de PHO84 n’était pas connu. En combinant des méthodes à l’échelle de cellule unique, des approches biochimiques et génétiques, nous avons montré que les niveaux d'ARN antisens sont régulés principalement lors de l'élongation par le complexe Nrd1-Nab3-Sen1, qui nécessite Rrp6 pour un recrutement efficace à l`extrémité 3`de PHO84. De plus, nous révélons l'expression anticorrelé du sens et de l'antisens, En résumé, nos données suggèrent que la transcription antisens régule le seuil d'activation du promoteur PHO84. Dans mon second projet, j'ai étudié les rôles des ARNs dérivés des amplificateurs (ARNa) dans la regulation de la transcription. En utilisant les cellules de cancer du sein MCF7 comme système modèle, nous avons cherché à déterminer comment les ARNa induits par l'oestrogène (E2) participent à la régulation de la transcription médiée par le recepteur d’oestrogène (ERα) au niveau de l'allèle unique. À l'aide de l’hybridation fluorescente à l’échelle de molécule unique (smFISH), nous avons révélé qu`après induction d'E2, les ARNa sont induits avec une cinétique similaire à celle des ARNm cibles, sont localisés exclusivement dans le noyau, principalement associés à la chromatine, et sont moins abondants que les ARNm. De manière surprenante, nous avons constaté que les ARNa sont rarement co-transcrits avec leurs loci cibles, indiquant que la transcription active des gènes ne nécessite pas la synthèse continue ou l'accumulation d'ARNa sur l'amplificateur. En outre, en utilisant des mesures de la distance à sous-diffraction, nous avons démontré que la cotranscription des ARNa et des ARNm se produit rarement dans une boucle amplificateurpromoteur. De plus, nous avons révélé que la transcription basale d'ARNa n'exige pas ERα ou l'histone méthyltransférase MLL1 qui active l'amplificateur par la mono-méthylation H3K4. Dans l'ensemble, nos résultats ont montré que les ARNa peuvent jouer un rôle lors de l'activation du promoteur, mais ne sont pas nécessaires pour maintenir la transcription de l'ARNm ou pour stabiliser les interactions amplificateur-promoteur. / Transcription is the initial step in gene expression and is subject to extensive regulation. Recently, analyses in diverse eukaryotes have revealed that in addition to protein coding genes, transcription occurs throughout the noncoding genome, producing non-coding RNAs of various lengths. Non-coding RNAs longer than 200 nucleotides, classified as long non-coding RNAs (lncRNAs), represent the most abundant class of non-coding transcripts, whose functions however are poorly understood. Recent studies suggest that many lncRNAs might have roles in transcription regulation. The goal of my PhD thesis was to elucidate the mechanisms of lncRNA mediated transcription regulation in different eukaryotic systems. For my first project, I investigated the role of an antisense long noncoding RNA in transcription regulation of the high-affinity phosphate transporter gene PHO84 in the unicellular eukaryote S. cerevisiae. Previous studies showed that deletion of the nuclear exosome component Rrp6 results in increased antisense expression and repression of PHO84. It was suggested that the loss of Rrp6 results in antisense stabilization at the PHO84 locus, leading to recruitment of the histone de-acetylase Hda1 and repression of PHO84. However, most of the mechanistic details of how Rrp6p functions in regulating PHO84 transcription were not understood. Combining single cell methods with biochemical and genetic approaches, we showed that antisense RNA levels are regulated primarily during transcriptional elongation by the Nrd1-Nab3-Sen1 complex, which requires Rrp6 for efficient recruitment to the 3’end of PHO84. Furthermore, we reveal anti-correlated expression of sense and antisense, which have distinct modes of transcription. In summary, our data suggest a model whereby antisense transcriptional read-through into the PHO84 promoter regulates the activation threshold of the gene. For my second project, I investigated the roles of enhancer derived RNAs (eRNAs). eRNAs are lncRNAs transcribed from enhancers that have been suggested to regulate transcription through different mechanisms, including enhancer-promoter looping, RNA polymerase elongation, and chromatin remodeling. However, no coherent model of eRNA function has yet emerged. Using MCF7 breast cancer cells as a model system, we sought to determine how estrogen (E2) induced eRNAs participate in estrogen receptor alpha (ERα) mediated transcription regulation at the single allele level. Using single molecule fluorescent in situ hybridization (smFISH), we revealed that upon E2 induction eRNAs are induced with similar kinetics as target mRNAs, but are localized exclusively in the nucleus, mostly chromatin associated, and are less abundant than mRNAs. Surprisingly, we found that eRNAs are rarely co-transcribed with their target loci, indicating that active gene transcription does not require the continuous synthesis or accumulation of eRNAs at the enhancer. Furthermore, using sub-diffraction-limit distance measurements, we demonstrated that co-transcription of eRNAs and mRNAs rarely occurs within a closed enhancer-promoter loop. Moreover, we revealed that basal eRNA transcription does not require ERα or the histone methyltransferase MLL1, which activates the enhancer through H3K4 mono-methylation. Altogether, our findings showed that eRNAs may play a role during promoter activation, but are not required to sustain mRNA transcription or stabilize enhancer-promoter looping interactions.