RNA-binding proteins play a central role in the post-transcriptional regulation of gene expression; however, little is known about the endogenous transcripts to which they bind. Here, I have used the ultra-violet cross-linking and immuno-precipitation (CLIP) technique to identify RNA targets directly bound to two RNA-binding proteins: Acinus and hnRNP A1. Acinus (apoptotic chromatin condensation inducer in the nucleus) contains a region that is homologous to the RNA binding domain of the Drosophila splicing regulator sex-lethal, and a serine and arginine rich region similar to that seen in the SR family of proteins, which function extensively in splicing. Furthermore it is a component of the multi-protein spliceosome complex, and I have demonstrated it can directly bind polyadenylated RNA. I have shown that Acinus displays a diffuse nuclear localisation pattern, however, overexpression of an epitope-tagged protein results in its accumulation in enlarged nuclear speckles. Together these results suggest a role in pre-mRNA splicing. Acinus is cleaved during apoptosis by caspase-3, resulting in a truncated protein with chromatin condensation inducing activity (Sahara et al., 1999). Accordingly, I have demonstrated that overexpression of epitope-tagged Acinus results in an increased number of cells exhibiting an apoptotic phenotype. The proteolytic fragment contains the RNA binding region, and to determine if the role of Acinus in apoptosis is mediated by RNA interactions I utilised CLIP to identify in vivo RNA targets. I have identified several mRNA targets of Acinus and found that the binding sites in those mRNA targets predominantly map to constitutively expressed exons. This is in agreement with the exon junction complex, of which Acinus is a component, being deposited on mRNAs after splicing. These results may indicate that Acinus is a core RNA binding factor of the exon junction complex. To complement this approach, I also performed CLIP with a known alternative splicing regulator, hnRNP A1. In this manner, the binding site preferences could be compared between the two proteins. As expected, the majority of hnRNP A1 binding sites are located in introns, corresponding with their identified role of antagonizing pre-mRNA splicing by binding intronic splicing elements. Interestingly, a number of the CLIP tags are located in, or adjacent to, alternatively spliced events suggesting a role for hnRNP A1 in the regulation of alternative splicing of these specific pre-mRNAs. In addition to pre-mRNA splicing hnRNP A1 also functions in the cellular stress response. Upon environmental stresses it relocates to the cytoplasm and accumulates in cytoplasmic foci known as stress granules (Guil et al., 2006). Here I show some of the targets identified by CLIP are regulated by hnRNP A1 in times of cellular stress. In summary, I have identified two novel subsets of RNAs, bound by Acinus or hnRNP A1 in vivo. I have shown these proteins exhibit distinct binding preferences, which correspond to their biological function. This work is consistent with hnRNP A1 acting as an alternative splicing regulator, and provides evidence for a dual role of Acinus in mRNA splicing and apoptosis. This study also demonstrates the power of the CLIP technique, as identification of in vivo RNA targets allows greater understanding of the mechanisms by which RNA-binding proteins exert their regulatory control.

Human Rhinoviruses (HRVs) utilize Internal Ribosome Entry Sites (IRES) to drive viral protein synthesis. IRESs are specialized RNA elements present within the 5’ UTR of mRNAs that recruit ribosomes independently of the 5’ m7G cap structure. hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1), a multifunctional RNA binding protein, is required for the IRES-dependent translation of many specific RNAs within the cell cytoplasm. The phosphorylation of hnRNP A1 is required for its cytoplasmic accumulation. I have identified and validated the role of HK2 in hnRNP A1 cellular localization by immunofluorescence microscopy, by analysis of HRV infection and by siRNA-based screening. These studies show that decreased HK2 protein levels lead to decreased cytoplasmic accumulation of hnRNPA1 during osmotic shock and HRV infection, to a decrease in HRV-infected cells and to decreased caspase activation in osmotically stressed and HRV-infected cells. Thus, HK2 may regulate hnRNP A1 cytoplasmic localization following HRV infection.

Les protéines hnRNP A1 sont impliquées dans l'épissage alternatif. Un mode d'action proposé implique la formation d'homodimères entre molécules hnRNP A1 causant un réarrangement dans la structure de l'ARN pré-messager. Cette modulation de l'ARN permettrait le rapprochement de sites d'épissage 5' et 3' d'exons situés de par et d'autres d'un exon alternatif. Le domaine riche en résidus glycines est responsable, en grande partie, de l'interaction entre les deux protéines hnRNP A1. Comme la protéine hnRNP H contient aussi un domaine riche en résidus glycines, nous avons postulé que cette dernière pouvait moduler l'épissage alternatif de la même manière que hnRNP A1. Afin de vérifier cette hypothèse, nous avons utilisé un ARN pré-messager constitué de deux sites d'épissage 5' (distal et proximal) en compétition pour un seul site d'épissage 3'. En présence de sites de liaison pour hnRNP H, nous observons que le choix du site d'épissage 5' est déplacé vers le site distal. Nous avons confirmé le rôle des protéines hnRNP H dans la sélection des sites d'épissage 5' in vitro et avons déterminé que le domaine riche en résidus glycines (GRD) est important pour l'activité d'épissage de ce régulateur. Nous avons ensuite exploré la possibilité que des combinaisons de sites de liaison pour hnRNP H et hnRNP A1 puissent activer l'utilisation du site d'épissage 5' distal. Nous avons observé que des combinaisons hétérotypiques peuvent reproduire cette activité d'épissage. Finalement, nous avons utilisé la technologie BRET ("bioluminescence resonance energy transfer") pour démontrer que des interactions homotypiques entre protéines hnRNP H et hétérotypiques entre molécules hnRNP A1 et hnRNP H peuvent se former dans les cellules vivantes. Notre étude suggère que les protéines hnRNP H et hnRNP A1 peuvent changer la conformation de l'ARN pré-messager et affecter le choix du site d'épissage.

Trypanosoma cruzi é o agente causador da Doença de Chagas, que segundo a OMS, atinge oito milhões de pessoas principalmente na América Latina, causando danos à saúde pública, juntamente com um impacto econômico negativo. Durante o processo de infecção, uma variedade de eventos celulares ocorre apenas pelo simples contato do parasito com a célula hospedeira, levando a modificações no metabolismo celular e alterações morfológicas. O parasita é capaz de modular respostas celulares e imunológicas da célula hospedeira para sua própria sobrevivência. Além do que, pode alterar compartimentos celulares como o número e tamanho de nucléolos, sugerindo que a presença do parasita poderia estar interferindo na maquinaria nuclear. Porém, pouco se conhece sobre a organização nuclear da célula hospedeira quando infectada por Trypanosoma cruzi. O objetivo deste estudo foi de investigar pela primeira vez os compartimentos nucleares das células hospedeiras durante o curso da infecção por T. cruzi. Células LLC-MK2 foram infectadas com T. cruzi e reações de imunofluorescência indireta foram realizadas utilizando anticorpos e marcadores específicos para proteínas nucleares. As análises das imagens de microscopia confocal e quantificação das fluorescências pelo ImageJ mostraram padrões distintos nos compartimentos nucleares quando comparadas com células não infectadas. Corpos de Cajal e Speckles sofrem alterações quando a célula está infectada e isso depende do ciclo celular do parasita. Neste trabalho também foi investigado através de quantificação de imagem e immunoblotting o comportamento das Ribonucleoproteínas A1 e A2B1 durante a parasitemia. Estas análises demonstram que o T. cruzi pode modular a célula hospedeira quando infectada a favor de sua sobrevivência, promovendo alterações na dinâmica dos compartimentos nucleares durante o seu ciclo celular. Esse estudo inédito poderá auxiliar a compreender a biologia do parasita e sua interação com a célula hospedeira e desta maneira contribuir na busca de possíveis alvos terapêuticos / Trypanosoma cruzi is the causal agente of Chagas disease, that affects about eight million people mostly in Latin America according to the WHO, causing damage to public health and a negative economic impact. During infection, a variety of signaling processes occur after contact of the parasite to the host cell, what can lead to metabolic modifications as well morphological alterations in both cells. The parasite can modulate host cell cellular and immunological responses for its own survival. In addiction, the presence of T. cruzi can modify the nuclear compartments such as nucleoli, suggesting that the presence of the parasite could be interfering with the nuclear machinery. However, little is know about the nuclear organization when the host cell is infected with Trypanosoma cruzi. This study aimed to investigate for the first time the nuclear compartment of host cells infected by T. cruzi using specific antibodies and fluorescent markers for nuclear compartments, in order to investigate the morphological and functional changes in the nucleus of the host cell. Using LLC-MK2 cells infected with T. cruzi, we performed indirect immunofluorescence using distinct nuclear antibodies. Confocal microscopy analysis of infected cells showed pattern variations in the nuclear compartments when compared to uninfected cells. Cajal bodies and Speckles suffer alterations when the cell is infected and it is related to the parasite life cycle. In this work we also investigated by image quantification and immunoblotting the behavior of Ribonucleoproteins A1 and A2B1 during infection. These evidences support the idea that T. cruzi can modulate host cell response to ensure its own survival during the infection, promoting changes in the dynamics of the nuclear compartments. This unpublished data may help to understand the biology of the parasite and its interaction with the host cell and thus contributing to seek for potential therapeutic targets

L'épissage alternatif des pré-ARN messagers est un mécanisme qui permet de générer une très grande diversité protéique chez les eucaryotes supérieurs. La sélection des sites d'épissage permet ainsi de produire certains isoformes protéiques plutôt que d'autres dans des conditions précises. Cette modulation implique généralement la participation d'une multitude de facteurs aux propriétés parfois synergiques et/ou antagonistes. Dans le cas du pré-ARN messager hnRNP A1, au moins trois éléments distincts renforcent l'exclusion de l'exon 7B. Par contre, l'élément intronique conservé de 38 nt (CE9) situé en aval de l'exon 7B permet la répression du site d'épissage 3', ce qui entraînerait l'inclusion de l'exon 7B. La portion 5' de l'élément CE9 est liée par la protéine SRp30c et cette interaction est importante pour permettre l'activité de CE9 in vitro. Afin de déterminer les composantes essentielles à l'activité de répression de SRp30c, des sites de liaison de haute affinité pour cette protéine ont été identifiés à l'aide de la procédure"SELEX". Les résultats obtenus indiquent que plusieurs sites de haute affinité reproduisent l'activité de l'élément CE9 complet dans un essai d'épissage où deux sites d'épissage 3' sont en compétition pour un seul site d'épissage 5'. De plus, les résultats suggèrent une contribution de la portion 3' de CE9, en plus de la partie 5', pour la liaison de la protéine SRp30c. En utilisant la séquence complète de CE9 pour effectuer une chromatographie d'affinité, la protéine hnRNP UPTB a été isolée et identifiée par spectrométrie de masse. Cependant, nous avons été surpris de constater que la protéine recombinante PTB agit comme activateur du site d'épissage 3' en diminuant l'activité de répression de CE9. Ces résultats suggèrent donc un nouveau rôle pour la protéine PTB, c'est-à-dire comme anti-répresseure de l'activité d'inhibition de SRp30c. PTB pourrait donc être un nouveau facteur capable de contrôler l'épissage alternatif du pré-ARN messager de hnfP A1.

During cellular stress, the regulation of protein synthesis is a key adaptive mechanism used by cells to survive. In response to various stresses, heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), an RNA binding protein principally found within the nucleus, is phosphorylated and consequently accumulates in the cytoplasm. Among other roles, cytoplasmic hnRNP A1 functions as an auxiliary translation factor for internal ribosome entry site (IRES)-mediated translation of specific mRNA, including the anti-apoptotic protein B-cell lymphoma-extra large (Bcl-xL). To identify which kinases control the cytoplasmic accumulation of hnRNP A1, an RNAi-based kinome-wide screen was performed in hypertonically stressed U2OS cells, from which AMPK-related kinase 5 (ARK5) was identified as a potential regulator of hnRNP A1’s localization. Here we show that ARK5 directly phosphorylates hnRNP A1 and that the inhibition of ARK5 expression blocks the stress induced cytoplasmic accumulation of hnRNP A1, modulates expression of Bcl-xL protein and increases cell viability. Our data points to a novel role for ARK5 and provides further insight into the mechanisms regulating cellular stress response.

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La SLA est une maladie neurodégénérative fatale se déclenchant tardivement. Elle est caractérisée par la perte des neurones moteurs supérieurs et inférieurs. Jusqu’à présent, aucun traitement ne permet de ralentir ou de guérir la maladie de façon robuste. De récentes découvertes portant sur TDP-43 et hnRNP A1 y ont identifié des mutations reliées à des cas de SLA. Comme les deux possèdent de multiples fonctions dans le métabolisme de l’ARN, l’impact de ces mutations devient difficile à définir. Notre hypothèse est que TDP-43 régule hnRNP A1 et que les mutations causant la SLA dérégulent ce mécanisme, aboutissant ainsi à un impact majeur sur la vulnérabilité des neurones moteurs. Nos résultats démontrent que TDP-43 lie l’ARNm de hnRNP A1, mais n’affecte pas sa stabilité. En revanche, TDP-43 réprime l’expression de hnRNP A1. Ce mécanisme pourrait être appliqué in vivo où le ratio protéique hnRNP A1B/A1 augmente chez les souris âgées et davantage chez les TDP-43A315T dans la région cervicale et lombaire de la moelle épinière. Cette différence n’est pas causée par un défaut de l’épissage alternatif. Aussi, la mutation TDP-43A315T serait davantage responsable de cette différence que la surexpression de TDP-43 (résultats obtenus en culture). L’impact d’une telle augmentation sur la cellule pourrait être la formation d’agrégats puisque la forme hnRNP A1B possède quatre domaines de fibrillation de plus que hnRNP A1. Nos résultats pourraient donc fournir un mécanisme potentiel de la formation d’inclusions cytoplasmiques reconnues comme étant une des caractéristiques pathologiques principales de la SLA. / ALS is a fatal and late onset disease characterized by the selective loss of lower and upper motor neurons. Yet, there is no way to robustly slow or cure the disease. Recent discoveries concern TDP-43 and hnRNP A1 where mutations have been identified in ALS cases. Both have multiple functions in RNA metabolism, making the impact of mutations difficult to define. Our hypothesis is that TDP-43 regulates hnRNP A1 and that the ALS causative mutations deregulate this mechanism, having a major impact on the vulnerability of motor neurons. Our results demonstrate that TDP-43 binds hnRNP A1 mRNA, but does not affect its stability. In contrast, TDP-43 represses the expression of hnRNP A1. This mechanism could be applied in vivo where hnRNP A1B/A1 protein ratio increases in aged mice and even more in TDP-43A315T mice in the cervical and lumbar region of the spinal cord. This difference is not caused by a defect in alternative splicing. Also, the TDP-43A315T mutation would be more responsible for this difference than the overexpression of TDP-43 (result from cell culture). The impact of that increased on the cell could be the formation of aggregates since the shape of hnRNP A1B has four more areas of fibrillation than hnRNP A1. Our findings could thus provide a potential mechanism for the formation of cytoplasmic inclusions recognized as one of the main pathological features of ALS.