Os genes eucarióticos, em sua maioria, são divididos em exons e introns, requerendo processamento do RNAm para remover as sequências intrônicas e juntar os exons (splicing). As bordas exon/intron são definidas por sítios de splice que normalmente são reconhecidos com alta fidelidade, gerando os mesmos RNAms processados a cada vez. Apesar desse reconhecimento preciso, tem sido observada a junção de exons de maneiras alternativas (splicing alternativo), foco de muitos estudos recentes devido à sua importância em vários processos biológicos. Este processamento alternativo do RNAm pode ser principalmente de três tipos: exclusão de exon, no qual um exon pode ser incluído ou não no RNAm maduro; uso alternativo de sítios de splice, resultando em exons mais longos ou mais curtos e retenção de intron, o tipo menos estudado, no qual uma sequência intrônica é mantida no RNAm maduro. Um dos aspectos cruciais no entendimento de splicing alternativo é conhecer os mecanismos que levam à geração de diferentes transcritos. Coerente com a importância dos sítios de splice no splicing de RNAms, a retenção de intron parece ser causada por falha no reconhecimento daqueles que são sub-ótimos. Como os sítios de splice são reconhecidos aos pares ao se estabelecer uma ponte através de exons ou introns, dependendo de qual é mais curto, uma falha no reconhecimento de um exon ou de um intron leva a diferentes tipos de splicing alternativo (exclusão de exon ou retenção de intron, respectivamente). Desta forma, acredita-se que a ocorrência de retenção de intron esteja também associada a uma falha no reconhecimento de introns curtos. Embora estudos de introns retidos individuais tenham abordado estas questões, poucas análises sistemáticas de grandes quantidades de dados foram conduzidas sobre as características gerais que levam à retenção de intron. Para este fim, realizamos uma análise de bioinformática de sequências do genoma e transcriptoma (RNAm) humanos armazenadas em formato de computador. Para realizar as análises computacionais, desenvolvemos um sistema de anotação de splicing alternativo completo. Particionamos os eventos de retenção de intron identificados em sequências expressas pelo nosso sistema de anotação em dois grupos, com base na abundância relativa das duas isoformas (um grupo de eventos com <50% e outro com >50% de transcritos retendo o intron) e comparamos características relevantes. Verificamos que uma maior frequência de retenção de intron em humano está associada a sítios de splice mais fracos, genes com introns mais curtos e maior nível de expressão gênica, e menor densidade de um conjunto de elementos inibitórios exônicos e do promotor de splicing intrônico GGG. Os dois grupos apresentaram eventos conservados em camundongo, nos quais os introns retidos também eram curtos e apresentavam sítios de splice mais fracos. Embora nossos resultados tenham confirmado que sítios de splice mais fracos estão associados à retenção de intron, eles mostram que uma fração não-desprezível dos eventos não pode ser explicada apenas por esta característica. Nossa análise sugere que elementos reguladores em cis provavelmente têm um papel na regulação da retenção de intron e também revelou características previamente desconhecidas que parecem influenciar sua ocorrência. Estes resultados salientam a importância de considerar o compromisso entre estas características na regulação da frequência relativa de retenção de intron. / Most eukaryotic genes are split in exons and introns, requiring mRNA processing to remove intervening sequences and join exons (splicing). Exon/intron borders are defined by splice sites that are normally recognized with high fidelity, yielding the same processed mRNA each time. Notwithstanding such precise recognition, alternative joining of exons has been observed (alternative splicing) and is the focus of many recent studies, due to its importance in several biological processes. This alternative mRNA processing can be mainly of three types: exon skipping, whereby an exon may be included or not in the mature mRNA; alternative use of splice sites, resulting in longer or shorter exons and intron retention, the least studied type whereby an intronic sequence is maintained in the mature mRNA. One of the key aspects in understanding alternative splicing is to know the mechanisms that lead to the generation of different transcripts. Coherent with the importance of splice sites in mRNA splicing, intron retention seems to be caused by failure in the recognition of those that are sub-optimal. As splice sites are recognized in pairs by bridging either exons or introns, depending on which is the shortest, failure to recognize an exon or an intron leads to different types of alternative splicing (exon skipping or intron retention, respectively). This way, the occurrence of intron retention is believed to be associated to failure in recognition of short introns also. Although studies on individual retained introns have addressed such issues, few systematic surveys of large amounts of data have been conducted on the general features leading to intron retention. To this end, we performed a bioinformatics analysis of human genome and transcriptome (mRNA) sequences stored in computer format. To perform the computational analyses we developed a complete alternative splicing annotation system. We partitioned intron retention events identified in expressed sequences by our annotation system in two groups based on the relative abundance of both isoforms (one group of events with <50% and another with >50% of transcripts retaining the intron) and compared relevant features. We found that a higher frequency of intron retention in human is associated to weaker splice sites, genes with shorter intron lengths and higher expression level, and lower density of a set of exonic inhibitory elements and the intronic splicing enhancer GGG. Both groups of events presented conserved events in mouse, in which the retained introns were also short and presented weaker splice sites. Although our results confirmed that weaker splice sites are associated to intron retention, they showed that a non-negligible fraction of events can not be explained by this feature alone. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating intron retention and also revealed previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of intron retention.

No description available.

Les carcinomes hépatocellulaires (CHC) mutés CTNNB1 ont des caractéristiques phénotypiques propres en termes de polarité et de métabolisme (absence de stéatose). Nous avons émis l’hypothèse que ce phénotype pouvait être secondaire à l’activation du gène suppresseur de tumeurs LKB1 qui code une Ser/Thr kinase multitâches.Nous avons tout d’abord montré qu’il existait effectivement un dialogue complexe entre les voies Wnt/β-Caténine et LKB1 dans le foie. Les mutations de CTNNB1 sont en effet capables d’induire l’expression protéique de LKB1 dans des lignées hépatomateuses humaines, et les CHC mutés CTNNB1 présentent une expression protéique accrue de LKB1 et une signature transcriptionnelle d’activation de LKB1. De plus, dans deux modèles murins d’invalidation hépatospécifique de Lkb1, LKB1 est apparu comme requis pour l’activation complète du programme transcriptionnel de β-Caténine mais de façon dépendante du stade de développement et du contexte nutritionnel. Enfin, la signalisation LKB1 est apparue comme nécessaire à la survie des hépatocytes activés pour β-Caténine dans deux modèles murins différents.Nous avons aussi caractérisé les rôles métaboliques de LKB1 dans le foie. L’invalidation hépatospécifique de Lkb1 induisait une augmentation progressive de la masse grasse corporelle avec utilisation préférentielle des glucides comme substrat énergétique. Il existait une activation de la néoglucogenèse hépatique avec hyperglycémie et une lipogenèse accrue avec accumulation hépatocytaire de lipides. Enfin, nous avons mis en évidence une activation paradoxale de la signalisation AKT dans les hépatocytes, même à jeun, et une dépendance énergétique aux acides aminés. Enfin, nous avons identifié une nouvelle isoforme protéique de LKB1 délétée de son domaine N-Terminal et d’une partie de son domaine kinase. D’expression tissulaire préférentiellement musculaire et myocardique, cette isoforme catalytiquement inactive se comportait comme dominant positif sur l’activation de l’AMPK par la forme conventionnelle mais comme dominant négatif dans l’activité polarisation induite par LKB1. Enfin, elle était capable d’induire, en l’absence de la forme conventionnelle, la prolifération cellulaire et la tumorigenèse chez la souris nude. Elle pourrait exercer des rôles métaboliques particuliers dans les tissus fortement oxydatifs et des rôles oncogéniques dans certains contextes. / CTNNB1-Mutated hepatocellular carcinomas (HCC) share a specific polarity and metabolic phenotype without steatosis. We hypothesized that such phenotype could imply the tumor suppressor gene LKB1 that encodes for a multi-Task Ser/Thr kinase.We first demonstrated that a complex crosstalk indeed exists in the liver between LKB1 and the Wnt/β-Catenin pathway. LKB1 proteic expression was controlled by mutant β-Catenin in hepatomatous cell line and CTNNB1-Mutated HCCs had an enhanced LKB1 proteic expression as well a transcriptomic signature of LKB1 activation. In two mouse model of liver-Specific invalidation of Lkb1, we showed that LKB1 was required for full activation of the β-Catenin transcriptomic program, but it depended on the developmental stage and nutritional context. At least, LKB1 appeared to be required for the survival of β-Catenin activated liver cells in two other mouse models.Then, we wanted to caracterize the metabolic roles of LKB1 in the liver. Liver-Specific invalidation of Lkb1 progressively raised the body fat mass and we observed that carbohydrates were preferred as whole-Body energetic fuel. In the liver, gluconeogenesis and lipogenesis were enhanced, resulting in mild hyperglycemia and lipid accumulation in the hepatocytes. At least, we identified an aberrant activation of the AKT signaling in the liver, even during fasting, and an energetic dependence towards amino acids.At least, we identified a novel LKB1 proteic isoform that is deleted of its N-Terminal domain and part of its kinase domain. Highly expressed in the muscle and in the heart, this catalytically inactive isoform however acted as a positive dominant towards AMPK activation by full length LKB1 but as a negative dominant towards LKB1-Induced cell polarization. This isoform is also able to enhance cell proliferation and to induce tumors in a xenograft model, even when expressed alone. It could play specific metabolic roles in oxidative tissues and could be oncogenic in some contexts.

Salinity and oxygen availability have long been recognised as important factors influencing animal physiology and therefore species distribution. The maintenance of appropriate cellular ion levels is critical for many essential physiological processes, but at the same time is energetically expensive. Since hypoxia is likely to impose aerobic limitations for ATP generation, the maintenance of salt and water homeostasis could be at risk during hypoxia. The amphidromous inanga (Galaxias maculatus) is well known for its salinity tolerance and its life cycle that involves several salinity related migrations. During these migrations inanga also frequently encounters hypoxic waters, and therefore must maintain energy homeostasis when aerobic metabolism may be compromised. The present study has investigated behavioural, physiological, biochemical and molecular mechanisms by which inanga tolerate changes in salinity and hypoxia. After 14 days of acclimation to salinities ranging from freshwater to 43‰, inanga showed physiological acclimation. This was evident by no changes in metabolic rates or energy expenditures through this salinity range. Energy balance seemed to be tightly and efficiently controlled by changes in the proportion of protein and lipids used as energy substrate. No mortalities and only minor changes in plasma osmolality also indicated salinity acclimation. The remarkable osmoregulatory capacity of inanga was also evidenced after a seawater challenge. The osmotic balance of inanga was only disrupted during the first 24 hours after the challenge, evidenced by an increase in plasma osmolality and plasma Na+, and a decrease in muscle water content. These physiological changes were correlated with changes at the molecular level. Different isoforms of the catalytic subunit of the Na+,K+-ATPase (NKA) were isolated, partially sequenced and identified in inanga. Phylogenetic analysis grouped inanga isoforms (α-1a, α-1b, α-1c) with their respective homologues from salmonids. Patterns of mRNA expression were also similar to salmonids, with α-1a being downregulated and α-1b being up-regulated following seawater challenge. Previous to this study, NKA isoform switching was reported to occur only in salmonids and cichlids. The presence of NKA subunits that change with environmnetal salinity in inanga indicates that this isoform switching phenomenon is much more widespread among teleost lineages than previously thought. Aiming to elucidate the hypoxia tolerance of inanga, oxygen consumption rate as a function of decreasing external PO2 was evaluated. At no point did inanga regulate oxygen consumption, suggesting that this species is an oxyconformer. This is the first robust demonstration of the existence of oxyconforming in fish. Evaluation of the scaling relationship between oxygen consumption and fish size in normoxia, showed that the exponent of this relationship fell within the range previously reported for fish. However, in hypoxic conditions the scaling relationship was less clear suggesting different size-related mechanisms for tolerating hypoxia. Analysis of the aerobic and anaerobic metabolism of small and large fish, showed that smaller inanga were able to sustain aerobic metabolism for longer than larger inanga, which instead relied on anaerobic metabolism for extending their survival. This knowledge is likely to be of value for the conservation of this iconic fish species, by incorporating these size related differences in hypoxia tolerance in streams management. In light of the unusual oxyconforming response of inanga, a study examining the behavioural responses of this species to declining dissolved oxygen was performed. Inanga did not display a behaviour that might reduce energy expenditure during oxygen limitation; instead swimming activity and speed were elevated relative to normoxia. As hypoxia deepened inanga leaped out of the water, emersing themselves on a floating platform. Once emersed, fish exhibited an enhanced oxygen consumption rate compared to fish that remained in hypoxic water. Although this emersion behaviour was hypothesised to be of physiological advantage, both aquatic hypoxia and emersion resulted in similar physiological and biochemical consequences in inanga. While in hypoxic water oxygen availability seemed to be the limiting factor, in air failure of the circulatory system was hypothesised to be the cause of a similar metabolic signature to that found in aquatic hypoxia. Overall, inanga seemed to be not particularly well adapted to tolerate aquatic hypoxia. In light of the increasing likelihood of anthropogenic-induced hypoxia in inanga habitats, this is likely to have negative consequences for the future of inanga populations in the wild. Although this study provides the mechanisms behind the exceptional salinity tolerance of inanga, its susceptibility to hypoxia is likely to impose further constraints for the osmoregulatory processes that guarantee inanga survival during life cycle migrations. The results of the present study are relevant for understanding and managing the fishery of this economically- and culturally important fish species.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 3 uppsatser.

Orientador: Daniel Carvalho Pimenta / Resumo: O veneno de Crotalus durissus terrificus (Cdt), baseado no critério do perfil da cromatografia de exclusão molecular, pode ser descrito como sendo composto de quatro principais toxinas: Giroxina, Crotamina, Crotoxina e Convulxina. A crotoxina é uma neutoroxina, é um heterodímero não covalente, composta por duas subunidades: fosfolipase A2 (PLA2) e crotapotina (Ctp). A crotapotina constitui o componente da crotoxina que apresenta atividade anti-inflamatória além de ser chaperona de PLA2. Esta molécula é constituída por três cadeias peptídicas ligadas por pontes dissulfeto. Além disso, já foram descritas isoformas para a crotapotina. O objetivo deste estudo foi desenvolver um método cromatográfico para isolar a crotapotina, separar suas cadeias e analisá-las por LC/MS e LC-MS/MS para análise proteômica e/ou seqüenciamento de novo e avaliação da possível existência de um padrão de variação nas substituições de aminoácidos. O método C8-RP-HPLC foi capaz de separar os componentes do veneno de Cdt que puderam ser identificados por espectrometria de massas, de acordo com a sua massa molecular. A crotapotina foi isolada, reduzida e alquilada e submetida à outra separação cromatográfica RP-HPLC (C18) para isolamento das subunidades alquiladas. Conforme descrito na literatura, a cadeia α da crotapotina é composta por 40 resíduos de aminoácidos, enquanto que a cadeia β possui 35 resíduos e a cadeia γ 14, pelo que as subunidades podem ser identificadas pelas suas massas moleculares. As a... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The Crotalus durissus terrificus venom (Cdt), based on molecular size chromatography, can be described as being composed of four main toxins: Giroxin, Crotamine, Crotoxin and Convulxin. Crotoxin is a neutoroxin, a non-covalent heterodimer composed of two subunits: phospholipase A2 (PLA2) and crotapotin (Ctp). Crotapotin is the component of crotaxin that has anti-inflammatory activity besides being a PLA2 chaperone. This molecule consists of three peptide chains linked by disulfide bonds. In addition, isoforms for crotapotin have been described. The objective of this study was to develop a chromatographic methodology to isolate a crotapotin, separate its chains and analyze by LC/MS and LC-MS/MS for proteomic analysis and/or de novo sequencing and evaluation of the possibility of a variation pattern amino acid substitutions. The C8-RPHPLC method was able to separate the Cdt venom components that could be identified by mass spectrometry, according to their molecular mass. The crotapotin was isolated, reduced and alkylated and subjected to another RP-HPLC (C18) chromatographic separation for isolation of the alkylated subunits. As described in the literature, the α chain of crotapotin is composed of 40 amino acid residues, while the β chain has 35 residues and the γ chain, 14, and thus the subunits can be identified by their molecular masses. The analyzes of isolated chains of crotapotin showed the presence of more than one molecule per fraction, indicating the presence of isofor... (Complete abstract click electronic access below) / Mestre

A proteína do retardo mental do X frágil (FMRP), codificada pelo gene do Retardo Mental do X Frágil (do inglês, Fragile Mental Retardation 1, FMR1) associa-se a RNA e transita entre o núcleo celular, grânulos citoplasmáticos e polirribossomos. No SNC, tem um importante papel como reguladora traducional atuando na maturação e eliminação sináptica. A exclusão do éxon 14 de transcritos do FMR1, associada ao uso do terceiro sítio de splicing do éxon 15 do FMR1, acarreta mudança da fase de leitura dos códons subsequentes, produzindo potencialmente isoformas da FMRP com nova região C-terminal, sem o sinal de localização nuclear e o domínio RGG, principal efetor de sua associação a RNAs. Sua importância funcional ainda não foi estudada. Neste trabalho, avaliamos por RT-qPCR a expressão dos transcritos que incluem e excluem o éxon 14 do Fmr1 no SNC de ratos e identificamos o córtex cerebral no décimo nono dia embrionário (E19) e no segundo dia pós-natal (P2) como tecido e fases do desenvolvimento em que são observados transcritos do Fmr1 com junção entre o éxon 13 e o terceiro sítio de splicing do éxon 15. Demonstramos que transcritos com essa junção exônica associam-se à proteína 4E de iniciação da tradução de eucarioto (eIF4E), indicando sua estabilidade no citoplasma. Geramos um anticorpo que identifica proteína de fusão com nova região C-terminal da FMRP. Paralelamente, a triagem por elementos em cis (transcritos) e fatores proteicos em trans trouxeram candidatos a inibirem o splicing do éxon 14 do FMR1 / Fragile X Mental Retardation Protein (FMRP), encoded by the Fragile Mental Retardation 1 (FMR1) gene, is an RNA-binding protein with nucleus-to-cytoplasm shuttling, and polyribosome association. In the central nervous system (CNS), FMRP is a translation regulator with important roles in synaptic maturation and elimination. In primary FMR1 transcripts, exon 14 skipping followed by selection of the exon 15 third splicing acceptor site, shifts the open reading frame of the downstream codons creating a putative FMRP isoform with a novel C-terminus, which lacks the nuclear localization signal and the major RNA binding domain, RGG box. The relevance of such isoform is as yet unknown. In the present study, we assessed, by RT-qPCR, the expression of rat Fmr1 transcripts in the CNS, relative to the inclusion of exon 14. We identified the cerebral cortex in the nineteenth embryonic day (E19) and the second postnatal day (P2) as the most prominent sources of transcripts bearing a splicing junction between exon 13 and the third splicing acceptor site in exon 15. Those transcripts are associated with the eukaryotic translation initiation factor 4E (eIF4E), indicating its cytoplasmic stability. We generated an antibody that recognizes a fusion protein carrying the novel FMRP C-terminus. Concurrently, a search for ci (transcript) and trans (protein) elements identified putative inhibitors of FMR1 exon 14 splicing

Submitted by LAUDICÉIA ALVES DE OLIVEIRA null (laudiceias2me@hotmail.com) on 2017-08-24T14:12:10Z No. of bitstreams: 1 Dissertação Laudicéia Alves de Oliveira CEVAP_UNESP.pdf: 2169254 bytes, checksum: 473bc1036ce9b9cddf2749344ac2b4c6 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-08-25T14:32:15Z (GMT) No. of bitstreams: 1 oliveira_la_me_bot.pdf: 2169254 bytes, checksum: 473bc1036ce9b9cddf2749344ac2b4c6 (MD5) / Made available in DSpace on 2017-08-25T14:32:15Z (GMT). No. of bitstreams: 1 oliveira_la_me_bot.pdf: 2169254 bytes, checksum: 473bc1036ce9b9cddf2749344ac2b4c6 (MD5) Previous issue date: 2017-07-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O veneno de Crotalus durissus terrificus (Cdt), baseado no critério do perfil da cromatografia de exclusão molecular, pode ser descrito como sendo composto de quatro principais toxinas: Giroxina, Crotamina, Crotoxina e Convulxina. A crotoxina é uma neutoroxina, é um heterodímero não covalente, composta por duas subunidades: fosfolipase A2 (PLA2) e crotapotina (Ctp). A crotapotina constitui o componente da crotoxina que apresenta atividade anti-inflamatória além de ser chaperona de PLA2. Esta molécula é constituída por três cadeias peptídicas ligadas por pontes dissulfeto. Além disso, já foram descritas isoformas para a crotapotina. O objetivo deste estudo foi desenvolver um método cromatográfico para isolar a crotapotina, separar suas cadeias e analisá-las por LC/MS e LC-MS/MS para análise proteômica e/ou seqüenciamento de novo e avaliação da possível existência de um padrão de variação nas substituições de aminoácidos. O método C8-RP-HPLC foi capaz de separar os componentes do veneno de Cdt que puderam ser identificados por espectrometria de massas, de acordo com a sua massa molecular. A crotapotina foi isolada, reduzida e alquilada e submetida à outra separação cromatográfica RP-HPLC (C18) para isolamento das subunidades alquiladas. Conforme descrito na literatura, a cadeia α da crotapotina é composta por 40 resíduos de aminoácidos, enquanto que a cadeia β possui 35 resíduos e a cadeia γ 14, pelo que as subunidades podem ser identificadas pelas suas massas moleculares. As análises das cadeias isoladas de crotapotina mostraram a presença de mais de uma molécula por fração, indicando a presença de isoformas no veneno. Análises proteômicas e sequenciamento de novo por LC-MS/MS elucidaram a existência de variações de resíduos de aminoácidos em tais cadeias. Estudos de atividade biológica poderão elucidar as diferenças que tais isoformas apresentam em suas características intrínsecas. / The Crotalus durissus terrificus venom (Cdt), based on molecular size chromatography, can be described as being composed of four main toxins: Giroxin, Crotamine, Crotoxin and Convulxin. Crotoxin is a neutoroxin, a non-covalent heterodimer composed of two subunits: phospholipase A2 (PLA2) and crotapotin (Ctp). Crotapotin is the component of crotaxin that has anti-inflammatory activity besides being a PLA2 chaperone. This molecule consists of three peptide chains linked by disulfide bonds. In addition, isoforms for crotapotin have been described. The objective of this study was to develop a chromatographic methodology to isolate a crotapotin, separate its chains and analyze by LC/MS and LC-MS/MS for proteomic analysis and/or de novo sequencing and evaluation of the possibility of a variation pattern amino acid substitutions. The C8-RPHPLC method was able to separate the Cdt venom components that could be identified by mass spectrometry, according to their molecular mass. The crotapotin was isolated, reduced and alkylated and subjected to another RP-HPLC (C18) chromatographic separation for isolation of the alkylated subunits. As described in the literature, the α chain of crotapotin is composed of 40 amino acid residues, while the β chain has 35 residues and the γ chain, 14, and thus the subunits can be identified by their molecular masses. The analyzes of isolated chains of crotapotin showed the presence of more than one molecule per fraction, indicating the presence of isoforms in the venom. Protein analyzes and de novo sequencing by LC-MS / MS elucidated a existence of variations of amino acid residues in such chains. Studies of biological activity are to elucidate how the differences that such isoforms present in their intrinsic characteristics.

Les ARNm codent pour les protéines, tandis qu'un grand nombre d'ARNs nommés longues ARNs non codants (ARNlnc) ne sont pas traduites en protéines. Les deux types d’ARNs existent en isoforms qui se distinguent à cause de l’épissage alternatif. Certains des ARNlnc jouent des rôles importants dans la croissance et différentiation cellulaire. Cependant, leurs fonctions dans la cytotoxicité de la chimiothérapie anti-cancéreuse médicamenteuse utilisant le 5-fluorouracile (5-FU) sont encore inconnues. Pendant mes travaux j'ai trouvé que le traitement par le 5-FU cause l’accumulation des ARNlnc. Ce phénomène est parfois, sous forme d’ARN double brin (ARNds) formé par une paire de transcrits chevauchant, corrélé négativement avec le niveau de la protéine codée par l'ARNm. Cette inhibition potentielle de la traduction des régulateurs du cycle cellulaire clés et les gènes essentiels en formant des l'ARNds peut éventuellement empêcher la progression du cycle cellulaire. Nos analyses prometteuses devraient inspirer des études approfondies des ARNlnc dans la cytotoxicité du 5-FU chez la levure et l’homme afin d’'améliorer la chimiothérapie. J'ai trouvé que la surexpression de RRP6, peut conduire à une résistance accrue au traitement par le 5-FU. Je démontre ensuite que l’ARNlnc MUT1312 forme des ARNds avec RRP6 qui sont négativement corrélés avec le niveau de la protéine Rrp6. Par ailleurs, la surexpression de MUT1312 pendant la mitose et associé avec une diminution d’Rrp6. Ainsi, mon étude suggère que MUT1312 soit impliqué dans la régulation de Rrp6 pendant la differentiation cellulaire. Mes recherches de MUT477/SWI4 indiquent la function importante de la méiose induite à long ARN non codantes en tant que forme d'ARN double brin potentiellement réguler la traduction. J'ai trouvé que SUT200 pourrait inhiber la transcription de CDC6 durant la méiose par read-through. Un cas comparable est MUT1465 et CLN2. J’ai fait un criblage in silico pour trouver des facteurs de transcription qui activent des MUTs durant la méiose. J’ai trouvé que la plupart des MUTs sont induites par Ndt80. MUT1465 est parmi eux : il pourrait être induite par Ndt80 ce qui inhiberait l’expression de CLN2 après l’initiation de la méiose. J’ai trouvé que la répression de certains MUTs par le complexe Ume6/Rpd3 en mitose est différemment régulée entre JHY222 et SK1. MUT100 qui ne possède pas l'élément USR1 fixé par Ume6, et qui est donc une cible indirecte, est déréprimé dans JHY22 ume6 mais pas dans SK1 ume6. Pour la régulation de l'étude de isoforme méiose, Nous avons trouvé que le complexe histone déacétylase Rpd3/Sin3/Ume6, empêche également l'induction de l'isoforme longue de BOI1 dans la mitose par liaison directe de liaison Ume6 à sa cible de URS1. Orc1 est importante pour la réplication de l'ADN. J’ai démontré que mORC1 est une cible directe de l'activateur Ndt80 et que son motif de fixation (MSE) est nécessaire pour l'induction de l’isoforme mORC1 et du gene méiotique SMA2 transcrit de façon divergente. J’ai trouvé qu'une souche incapable d’induire mORC1, contient des niveaux anormalement élevés d’Orc1 pendant la gamétogenèse, ce qui corréle mORC1 avec la baisse de la protéine Orc1. En conclusion, mes études au cours du doctorat révèlent des nouvelles cibles et ainsi offrent des nouvelles perspectives de l’amélioration de la chimiothérapie par le 5-FU. Les mécanismes incluent la formation d'un ARN double brin avec son ARNm anti-sens pour potentiellement inhiber la traduction de l'ARNm, et inhibition en aval de l'ARNm par transcription read-through d’une ARNlnc. Mon travail a également révélé un mécanisme de régulation des ARNlnc et les isoforms d’ARN pendent la croissance et la différentiation cellulaire. / RNAs are molecules with important functions in diverse cellular processes. mRNAs encode proteins, while a large number of RNAs called long noncoding RNAs (lncRNAs) are not translated into proteins. Both types of RNAs exist in various isoforms due to alternative splicing.Some of lncRNA play important roles in cell growth and differentiation. However, their functions in the cytotoxicity of the drug anticancer chemotherapy using 5-fluorouracil (5-FU) are still unknown. During my research I found that treatment with 5-FU causes accumulation of lncRNA. Acuumulated antisense lncRNA form double stranded RNA with the mRNAs , negatively correlated with the level of the protein encoded by the mRNA. This potential inhibition of translation of key cell cycle regulators and essential genes by forming dsRNA may possibly prevent the progression of the cell cycle. My results suggest that lncRNA are likely to play an important role in the cytotoxicity of 5-FU. Our promising testing should inspire in-depth studies of lncRNA in the cytotoxicity of 5-FU in yeast and humans to improve chemotherapy.Rrp6 is a 3'-5 'exoribonuclease, which plays an important role in the regulation and modification of rRNA, mRNA and lncRNA. I found that overexpression of RRP6, the homologue of the yeast EXOSC10 gene in mammals, can lead to increased resistance to treatment with 5-FU. I found that the lncRNA MUT1312 form dsRNA with RRP6 that are negatively correlated with the level of Rrp6 protein. Furthermore, overexpression of MUT1312 during mitosis and associated with a decrease of Rrp6. Thus, my study suggests that MUT1312 may involved in the regulation of Rrp6 during cell differentiation. I further explored the function of the double-stranded RNA in meiosis. My research about SWI4/MUT477 indicates the important function of meiosis induced long noncoding RNA as a form of double-stranded RNA potentially regulate translation. Another aspect of the function of lncRNA is to regulate the transcription of downstream mRNA. I found SUT200 could inhibit transcription of CDC6 during meiosis by read-through. A similar case is CLN2/MUT1465. I did an in silico screening to find transcription factors that activate MUTs during meiosis. I found that most MUTs are induced by Ndt80. MUT1465 is among them: it could be induced by Ndt80 which inhibit the expression of CLN2 after initiation of meiosis. I found that repression of certain MUTs by the Ume6 / Rpd3 complex in mitosis is regulated differently between JHY222 and SK1. MUT100 which does not have the Ume6 binding site URS1 element, and is therefore an indirect target is derepressed in JHY22 ume6 but not in SK1 ume6. For the study about regulation of meiosis isoform, we have found that the histone deacetylase complex Rpd3 / Sin3 / Ume6 prevents the induction of long isoform BOI1 in mitosis by direct binding Ume6 binding to its target URS1.Orc1 is important for DNA replication. I have demonstrated that mORC1 is a direct target of the Ndt80 activator and its binding motif (MSE) is required for induction of isoform mORC1 and meiotic gene SMA2 divergently transcribed. I found that a strain incapable of inducing mORC1 contains abnormally high levels of Orc1 during gametogenesis, which correlates with mORC1 declining Orc1 protein. Since eukaryotic genes often encode multiple transcripts with 5'-UTR of variable length, the findings are likely relevant to gene expression during development and disease in higher eukaryotes. In conclusion, my studies during PhD reveal new targets and thus offer new prospects for improving chemotherapy with 5-FU. Mechanisms include (1) the formation of a double strand with its antisense mRNAs to potentially inhibit translation of mRNA, and (2) downstream inhibition of mRNA transcription read-through of a lncRNA. My work also revealed a lncRNA regulatory mechanism and RNA isoforms dangling growth and cell differentiation.

Os genes eucarióticos, em sua maioria, são divididos em exons e introns, requerendo processamento do RNAm para remover as sequências intrônicas e juntar os exons (splicing). As bordas exon/intron são definidas por sítios de splice que normalmente são reconhecidos com alta fidelidade, gerando os mesmos RNAms processados a cada vez. Apesar desse reconhecimento preciso, tem sido observada a junção de exons de maneiras alternativas (splicing alternativo), foco de muitos estudos recentes devido à sua importância em vários processos biológicos. Este processamento alternativo do RNAm pode ser principalmente de três tipos: exclusão de exon, no qual um exon pode ser incluído ou não no RNAm maduro; uso alternativo de sítios de splice, resultando em exons mais longos ou mais curtos e retenção de intron, o tipo menos estudado, no qual uma sequência intrônica é mantida no RNAm maduro. Um dos aspectos cruciais no entendimento de splicing alternativo é conhecer os mecanismos que levam à geração de diferentes transcritos. Coerente com a importância dos sítios de splice no splicing de RNAms, a retenção de intron parece ser causada por falha no reconhecimento daqueles que são sub-ótimos. Como os sítios de splice são reconhecidos aos pares ao se estabelecer uma ponte através de exons ou introns, dependendo de qual é mais curto, uma falha no reconhecimento de um exon ou de um intron leva a diferentes tipos de splicing alternativo (exclusão de exon ou retenção de intron, respectivamente). Desta forma, acredita-se que a ocorrência de retenção de intron esteja também associada a uma falha no reconhecimento de introns curtos. Embora estudos de introns retidos individuais tenham abordado estas questões, poucas análises sistemáticas de grandes quantidades de dados foram conduzidas sobre as características gerais que levam à retenção de intron. Para este fim, realizamos uma análise de bioinformática de sequências do genoma e transcriptoma (RNAm) humanos armazenadas em formato de computador. Para realizar as análises computacionais, desenvolvemos um sistema de anotação de splicing alternativo completo. Particionamos os eventos de retenção de intron identificados em sequências expressas pelo nosso sistema de anotação em dois grupos, com base na abundância relativa das duas isoformas (um grupo de eventos com <50% e outro com >50% de transcritos retendo o intron) e comparamos características relevantes. Verificamos que uma maior frequência de retenção de intron em humano está associada a sítios de splice mais fracos, genes com introns mais curtos e maior nível de expressão gênica, e menor densidade de um conjunto de elementos inibitórios exônicos e do promotor de splicing intrônico GGG. Os dois grupos apresentaram eventos conservados em camundongo, nos quais os introns retidos também eram curtos e apresentavam sítios de splice mais fracos. Embora nossos resultados tenham confirmado que sítios de splice mais fracos estão associados à retenção de intron, eles mostram que uma fração não-desprezível dos eventos não pode ser explicada apenas por esta característica. Nossa análise sugere que elementos reguladores em cis provavelmente têm um papel na regulação da retenção de intron e também revelou características previamente desconhecidas que parecem influenciar sua ocorrência. Estes resultados salientam a importância de considerar o compromisso entre estas características na regulação da frequência relativa de retenção de intron. / Most eukaryotic genes are split in exons and introns, requiring mRNA processing to remove intervening sequences and join exons (splicing). Exon/intron borders are defined by splice sites that are normally recognized with high fidelity, yielding the same processed mRNA each time. Notwithstanding such precise recognition, alternative joining of exons has been observed (alternative splicing) and is the focus of many recent studies, due to its importance in several biological processes. This alternative mRNA processing can be mainly of three types: exon skipping, whereby an exon may be included or not in the mature mRNA; alternative use of splice sites, resulting in longer or shorter exons and intron retention, the least studied type whereby an intronic sequence is maintained in the mature mRNA. One of the key aspects in understanding alternative splicing is to know the mechanisms that lead to the generation of different transcripts. Coherent with the importance of splice sites in mRNA splicing, intron retention seems to be caused by failure in the recognition of those that are sub-optimal. As splice sites are recognized in pairs by bridging either exons or introns, depending on which is the shortest, failure to recognize an exon or an intron leads to different types of alternative splicing (exon skipping or intron retention, respectively). This way, the occurrence of intron retention is believed to be associated to failure in recognition of short introns also. Although studies on individual retained introns have addressed such issues, few systematic surveys of large amounts of data have been conducted on the general features leading to intron retention. To this end, we performed a bioinformatics analysis of human genome and transcriptome (mRNA) sequences stored in computer format. To perform the computational analyses we developed a complete alternative splicing annotation system. We partitioned intron retention events identified in expressed sequences by our annotation system in two groups based on the relative abundance of both isoforms (one group of events with <50% and another with >50% of transcripts retaining the intron) and compared relevant features. We found that a higher frequency of intron retention in human is associated to weaker splice sites, genes with shorter intron lengths and higher expression level, and lower density of a set of exonic inhibitory elements and the intronic splicing enhancer GGG. Both groups of events presented conserved events in mouse, in which the retained introns were also short and presented weaker splice sites. Although our results confirmed that weaker splice sites are associated to intron retention, they showed that a non-negligible fraction of events can not be explained by this feature alone. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating intron retention and also revealed previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of intron retention.