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Les gradients morphogénétiques contrôlent l'émergence de polarités axiales au cours du développement. Bien que la dynamique d'établissement de ces gradients soit bien comprise, la précision des mécanismes d'activation agissant en aval restent à élucider. Nous abordons cette question avec le gradient de Bicoid qui fournit rapidement une réponse transcriptionnelle robuste dans l'embryon de drosophile. Cette robustesse survient malgré le challenge imposé par de fréquentes mitoses dépourvues de transcription. Un calcul théorique intégrant les paramètres physiques de Bicoid (concentration, diffusion) indique que la mesure précise de concentration de Bicoid ne peut être effectuée à chaque interphase en 5-6mn. Il a donc été proposé que l'acquisition rapide de cette robustesse repose sur une mémorisation de l'état transcriptionnel au cours des divisions. Pour tester cette hypothèse, j'ai adapté à l'embryon de drosophile le système MS2 d'étiquetage des ARN dans les cellules vivantes et démontré qu'il permettait de suivre la dynamique transcriptionnelle dans un organisme pluricellulaire vivant. De manière inattendue, le rapporteur MS2 s'exprime aussi postérieurement ce qui m'a empêché de tester l'hypothèse de mémorisation. J'ai montré que cette expression postérieure est due à la présence de sites de fixation pour le facteur de transcription Zelda dans la cassette MS2. Un nouveau rapporteur MS2, dépourvu de ces sites récapitule l'expression endogène et fournit un outil de choix pour tester l'hypothèse de mémorisation. Ce travail ouvre de nouvelles perspectives pour comprendre la dynamique transcriptionnelle sur laquelle repose l'émergence des patrons d'expression développementaux. / Morphogen gradients provide concentration-dependent positional information along polarity axes. Although the dynamics of these gradients is well described, precision and noise in the activation processes acting downstream remain unclear. To address this question, we study the response to the Bicoid gradient that elicits very rapidly a robust transcriptional response in young fly embryos. This robustness occurs despite the challenge imposed by frequent mitoses during which transcription is interrupted suggesting that nuclei measure the Bicoid concentration during the 5-6 mn interphases. Modeling using statistical mechanics and Bicoid physical parameters do not account for accurate measurement of Bicoid concentration in such a short period. It was proposed that rapid robustness of the Bicoid response relies on a memorization process allowing nuclei to recall Bicoid concentration from previous cycles. To understand how the Bicoid system resists to the challenge imposed by mitosis, I have adapted the MS2 RNA-tagging approach to fly embryos and shown that it can be used to quantify transcription dynamics in a living multicellular organism. Unexpectedly, the MS2 reporter was also expressed in the posterior of the embryo making it impossible to directly test the memorization hypothesis. I have shown that this posterior expression is due to binding sites for the transcription factor Zelda unexpectedly localized in the MS2 cassette. A newly engineered MS2 reporter removing those sites faithfully reproduces the endogenous expression providing a powerful tool to test the memory hypothesis. This work opens new avenue to decipher the transcription dynamics underlying pattern formation.

<p>Post-transcriptional regulation plays an important role in governing various processes in all organisms. The development of the early embryo of <italic>Drosophila melanogaster</italic> is governed solely by post-transcriptional mechanisms; therefore, further insights into post-transcriptional regulation can be gained by studying the <italic>Drosophila </italic> embryo. This thesis addresses the actions of the translational repressor, Pumilio, in regulating two mRNAs during early embryogenesis. First, we examined the ability of Pumilio to regulate the mRNA stability of <italic>bicoid</italic>, a gene required for <italic>Drosophila </italic> head development. <italic>bicoid</italic> mRNA contains the canonical Pumilio recognition site, termed the Nanos response element (NRE), within the 3'UTR. Interestingly, we show that Pumilio binds to the NRE both in vitro and in vivo; however, no physiological significance is associated with this interaction. Furthermore, in <italic> pumilio</italic> mutant embryos <italic>bicoid</italic> mRNA stability and translation are unaltered, demonstrating that Pumilio does not regulate <italic>bicoid</italic> mRNA. Second, Pumilio has been shown to negatively regulate <italic>Cyclin B</italic>, the cyclin necessary for mitotic entry, in the somatic cytoplasm of the embryo and this repression is alleviated by the PNG Kinase complex through currently unidentified mechanisms. We further investigated the actions of Pumilio in regulating <italic>Cyclin B</italic> and discovered that the canonical partner of Pumilio, Nanos, is not involved in repressing somatic <italic>Cyclin B</italic>. Furthermore, we show that the 3'UTR of <italic>Cyclin B</italic> is not required for the regulation by Pumilio and the PNG Kinase complex. Lastly, through genetic analyses, we conclude that Pumilio may actually act upstream of the PNG Kinase complex to regulate <italic>Cyclin B</italic>.</p> / Dissertation

Submitted by Izabel Franco (izabel-franco@ufscar.br) on 2016-10-10T13:11:28Z No. of bitstreams: 1 DissJLO.pdf: 1924288 bytes, checksum: 2b2ce6a9b82a3dfb41ddb5f343fde1b7 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-20T19:39:32Z (GMT) No. of bitstreams: 1 DissJLO.pdf: 1924288 bytes, checksum: 2b2ce6a9b82a3dfb41ddb5f343fde1b7 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-20T19:39:39Z (GMT) No. of bitstreams: 1 DissJLO.pdf: 1924288 bytes, checksum: 2b2ce6a9b82a3dfb41ddb5f343fde1b7 (MD5) / Made available in DSpace on 2016-10-20T19:39:46Z (GMT). No. of bitstreams: 1 DissJLO.pdf: 1924288 bytes, checksum: 2b2ce6a9b82a3dfb41ddb5f343fde1b7 (MD5) Previous issue date: 2014-02-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The genus Anastrepha (Tephritidae) has several species of great economic importance due to their impact in fruticulture. We are particularly interested in the evolutionary history of Anastrepha fraterculus, the most relevant species in the closely related group of species fraterculus, which has undergone recent divergence and holds the majority of species of economic importance in the genus. To better understand the differentiation process and identification in the group, we need to find molecular and morphological markers that are involved with the differences between species. Reproductive genes have, in general, been very informative in this regard due to their rapid evolutionary rates, although few of them have been studied and characterized in this species so far. Therefore, the present study focuses on the exuperantia gene (exu), which participates in both oogenesis (localization of bicoid and oskar mRNAs) and spermatogenesis, since exu embryos from mutant mothers are unviable and males are sterile. Thus, the first step was to use Next generation sequencing strategies (RNA-seq) to structurally characterize and define expression patterns of this gene between sexes in the cephalic and reproductive tissues of A. fraterculus. A. fraterculus has similar structural and expression patterns to Drosophila melanogaster in reproductive tissues, in which the transcripts differ between sexes for the 5’ and 3’ untranslated regions (UTRs). We describe for the first time the expression of exu in cephalic tissues, involving a new isoform that is common to both sexes. All these alternative spliced transcripts share a common coding region, resulting in the same protein. We used the exu coding region, along with sequences from several Diptera to investigate the molecular evolution of exu in Cyclorrhapha. This group has experienced an enormous adaptive radiation, associated with molecular and morphological changes, and by comparing the dN/dS ratio between Cyclorrhapha and other Diptera we found that exu was subjected to positive selection in Cyclorrhapha for at least two sites in the coding region. One of the sites is present in the RNA exonuclease-like domain of exu. The second site is located in a not characterized region that is conserved and under purifying selection in Diptera, suggesting that it may be an important region of the protein. The adaptive changes found in exu may reflect an evolutionary gain that allowed its co-option for a new function the gene performs in Cyclorrhapha: the localization of bicoid in the anterior region of the oocyte, since bcd is a gene exclusive of Cyclorrhapha. / O gênero Anastrepha (Tephritidae) é de grande importância econômica devido ao seu impacto na fruticultura nacional. Estudamos aqui a história evolutiva de Anastrepha fraterculus, a espécie mais relevante do grupo fraterculus, o qual sofreu divergência recente e contém a maioria das espécies de importância econômica do gênero. Para entender melhor o processo de especiação nesse grupo, e auxiliar no processo de identificação taxonômica, precisamos estabelecer marcadores morfológicos e moleculares envolvidos com as diferenças entre as espécies. Genes envolvidos com a reprodução têm se mostrado bastante informativos para estes propósitos, devido às rápidas taxas evolutivas que apresentam, embora poucos tenham sido estudados e caracterizados nessas espécies até o momento. Nesse sentido, esse trabalho tem como foco o gene exuperantia (exu), que participa tanto da ovogênese (localização dos mRNAs bicoid e oskar) quanto da espermatogênese, uma vez que embriões formados a partir de fêmeas mutantes exu são inviáveis e machos mutantes exu são estéreis. Assim, o primeiro passo foi caracterizar estruturalmente e definir padrões de expressão desse gene entre os sexos nos tecidos cefálicos e reprodutivos em A. fraterculus. Utilizando sequenciamento de próxima geração (RNA-seq), identificamos um padrão estrutural e de expressão semelhante àquele de Drosophila melanogaster em tecidos reprodutivos: os transcritos diferem nas regiões não traduzidas (UTRs) 5’ e 3’ entre os sexos. Pela primeira vez identificamos a expressão de exu em tecidos cefálicos, envolvendo uma nova isoforma que é igual nos dois sexos. Em todos os casos, as regiões codificadoras são iguais, resultando na sequência proteica. Utilizamos essa região codificadora de exu junto com sequências de outras espécies de Diptera para investigar a evolução molecular de exu em Cyclorrhapha, que sofreu uma grande radiação adaptativa associada com alterações morfológicas e moleculares. Comparando a relação dN/dS entre Cyclorrhapha e outros Diptera, encontramos dois sítios sob seleção positiva em Cyclorrhapha, um deles presente no domínio semelhante à RNA exonuclease de exu. O segundo está presente em uma região não caracterizada para domínios proteicos, mas que é bem conservada e está sob seleção purificadora em Diptera, sugerindo ser uma região importante da proteína. As mudanças adaptativas encontradas em exu podem refletir um ganho evolutivo que permitiu sua co-optação para uma nova função em Cyclorrhapha: a de localização de bicoid na região anterior do ovócito, visto que bcd é um gene exclusivo de Cyclorrhapha.

This thesis was done in collaboration with Sorbonne University as part of a double degree Cotutelle. / During development, cell differentiation frequently occurs upon signaling from concentration or activity gradients of molecules called morphogens. These molecules control in a dose-dependent manner the expression of sets of target genes that determine cell identity. A simple paradigm to study morphogens is the Bicoid gradient, which determines antero-posterior patterning in fruit fly embryos. The Bicoid transcription factor allows the rapid step-like expression of its major target gene hunchback, expressed only in the anterior half of the embryo. The general goal of my thesis was to understand how the information contained in the Bicoid morphogen gradient is rapidly interpreted to provide the precise expression pattern of its target. Using the MS2 system to fluorescently tag specific RNA in living embryos, we were able to show that the ongoing transcription process at the hunchback promoter is bursty and likely functions according to a two-state model. At each nuclear interphase, transcription is first observed in the anterior and it rapidly spreads towards the posterior, as expected for a Bicoid dose-dependent activation process. Surprisingly, it takes only 3 minutes from the first hints of transcription at the anterior to reach steady state with the setting of a sharp expression border in the middle of the embryo. Using modeling taking into account this very fast dynamics, we show that the presence of only 6 Bicoid binding sites (known number of sites in the hunchback promoter) in the promoter, is not sufficient to explain the establishment of a sharp expression border in such a short time. Thus, either more Bicoid binding sites or inputs from other transcription factors could help reconcile the model to the data. To better understand the role of transcription factors other than Bicoid in this process, I used a two-pronged strategy involving synthetic MS2 reporters combined with the analysis of the hunchback MS2 reporter in various mutant backgrounds. I show that the pioneer factor Zelda and the Hunchback protein itself are also critical for hunchback expression, maternal Hunchback acting at nuclear cycle 11-12, while zygotic Hunchback is acting later at nuclear cycle 13-14. The synthetic reporter approach indicate that in contrast to Hunchback and Caudal, Bicoid is able to activate transcription on its own when bound to the promoter. However, the presence of 6 Bicoid binding sites only leads to stochastic activation of the target loci. Interestingly, the binding of Hunchback to the Bicoid-dependent promoter reduces this stochasticity while Caudal might act as a posterior repressor gradient. Confronting these experimental data to theoretical models is ongoing and should allow to better understand the role of transcription factors, other than Bicoid, in hunchback expression at the mechanistic level. / Thesis / Doctor of Philosophy (PhD) / Have you ever wondered how a single cell can become a full grown organism? Well it starts when an egg and sperm fuse together. As time passes this single cell divides over and over again until an organism is formed. During this developmental process, somehow the cells know exactly where they are and what they need to become so that they form the organism. However, we don’t fully understand this process and this is what we hope to answer with our research: How do the cells know where they are and what they need to become during development? We study this process in the fruit fly. Although fruit flies might not look a lot like us, during early embryonic development we are quite similar, so we can try to answer these questions in fruit flies and what we find might be relevant to other organisms like us. During development, the first element that an embryo needs to know is the orientation of its body, where the head and tail, the left and right and the back and front of the body will be. We concentrate on studying how the head to tail axis, which we call the anterior-posterior axis, is formed. To know where the head is going to be, the embryo releases proteins called morphogens that broadcast instructions to other genes so that cells know where they are and what they should become. We study a morphogen called Bicoid. Its concentration is high in the anterior, the region that will become the head of the embryo, and lower as you move towards the posterior where the tail will form. Bicoid activates a gene called hunchback, which ends up dividing the embryo in two large parts, the top and the bottom. However, Bicoid’s message fades away during each cell division and needs to be read again at the beginning of each new nuclear cycle. So how is the message read and how long does this process take? This last question is particularly critical during the period of very fast cell division. My thesis tries to answer this question. We found out that it takes 3 minutes for a nuclei to read the Bicoid concentration, activate hunchback and express it correctly. However, in contrast to what was believed before, or namely, that only Bicoid was involved in this process, we found out that other players are involved in helping relay this message. This way hunchback can accurately divide the body in two parts exactly in the middle and without mistake in such a short period of time.

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