Hepatitis delta virus (HDV) is the smallest known human RNA pathogen. It requires the human hepatitis B virus (HBV) for virion production and transmission, and is hence closely associated with HBV in natural infections. HDV RNA encodes only two viral proteins - the small and the large delta antigens. Due to its limited coding capacity, HDV needs to exploit host factors to ensure its propagation. However, few human proteins are known to interact with the HDV RNA genome. The current study has identified several host proteins interacting with an HDV-derived RNA promoter by multiple approaches: mass spectrometry of a UV-crosslinked ribonucleoprotein complex, RNA affinity chromatography, and screening of a library of purified RNA-binding proteins. Co-immunoprecipitation, both in vitro and ex vivo, confirmed the interactions of eEF1A1, p54nrb, PSF, hnRNP-L, GAPDH and ASF/SF2 with both polarities of the HDV RNA genome. In vitro transcription assays suggested a possible involvement of eEF1A1, GAPDH and PSF in HDV replication. At least three of these proteins, eEF1A1, GAPDH and ASF/SF2, have also been shown to associate with potato spindle tuber viroid (PSTVd) RNA. Because HDV’s structure and mechanism of replication share many similarities with viroids, subviral helper-independent plant pathogens, I transfected human hepatocytes with RNA derived from PSTVd. Here, I show that PSTVd RNA can replicate in human hepatocytes. I further demonstrate that a mutant of HDV, lacking the delta antigen coding region (miniHDV), can also replicate in human cells. However, both PSTVd and miniHDV require the function of the small delta antigen for successful replication. Our discovery that HDV and PSTVd RNAs associate with similar RNA-processing pathways and translation machineries during their replication provides new insight into HDV biology and its evolution.

In the presented study, we demonstrate that the alternative splicing of caspase 9 was dysregulated in a large percentage of NSCLC tumors and cell lines. These findings led to the hypothesis that survival pathways activated by oncogenic mutation regulated this mechanism. Indeed, the oncogenic PI3-Kinase/Akt pathway was demonstrated to regulate the alternative splicing of caspase 9. Further mechanistic studies demonstrate that multiple Akt isoforms can regulate the alternative splicing of caspase 9 in NSCLC. Akt was additionally shown to mediate the exclusion of the exon 3,4,5,6 cassette of caspase 9 via the phospho-state of the RNA trans-factor, SRp30a. Mutagenesis studies identified serine 199, serine 201, serine 227, and serine 234 as critical residues regulating the alternative splicing of caspase 9, as well as playing a role in the anchorage-independent growth of A549 cells. Since dysregulation of this splicing mechanism correlated with NSCLC tumors/cell lines and constitutively active Akt, oncogenic factors for NSCLC known to activate the PI3-Kinase/Akt pathway were examined in HBEC-3KT cells. In contrast to k-ras V12 expression, the overexpression/mutation of EGFR affected the alternative splicing of caspase 9 in a pro-oncogenic manner, dramatically lowering the caspase 9a/9b mRNA ratio. Stable downregulation of caspase 9b by shRNA blocked the ability of E746-A750 del EGFR expressing HBEC-3KTs to induce anchorage-independent growth, suggesting a role for caspase 9b as a cooperative oncogenic factor. These findings were further corroborated by the ability of caspase 9b expression to completely block the inhibition of clonogenic colony formation by erlotinib. Therefore, this study demonstrates that oncogenic factors activating the PI3-Kinase/Akt pathway regulate the alternative splicing of caspase 9, to produce caspase 9b, via a coordinated mechanism involving the phosphorylation of SRp30a. In additional studies, we demonstrate that the PI3-Kinase/PKCι pathway, a pathway important for cancer cell survival and transformation of lung epithelial cells, regulates the alternative splicing of Bcl-x pre-mRNA via modulation of SAP155 expression to produce an anti-apoptotic phenotype in NSCLC. Therefore, these studies link oncogenic mechanisms in NSCLC to the therapeutically relevant and distal target mechanisms of caspase 9 and Bcl-x pre-mRNA splicing.

L'inactivation du chromosome X correspond au silence transcriptionnel de l'un des deux chromosomes X dans les cellules des mammifères femelles. Il s'agit d'un mécanisme de compensation du dosage du chromosome X qui assure un taux d'expression des gènes liés aux chromosomes X équivalent entre organismes mâles (XY) et femelles (XX). Elle débute par une accumulation de l'ARN Xist (X inactive specific transcript) sur le chromosome X qui sera inactivé (Xi). Elle est suivie très rapidement par des modifications des histones qui assurent l'établissement, le maintien et la transmission de l'état transcriptionnel inactif de la chromatine. L'ARN Xist comprend plusieurs régions d'éléments répétés et notamment la région des A-repeats, essentielle pour la mise en place de l'inactivation. Mes recherches se sont portées sur l'étude de cette région singulière : sa structure et ses interactions protéiques. La technique de FRET (Fluorescence Resonance Energy Transfer) appliquée à l'ARN nous a permis de confirmer la structure de cette région parmi 3 modèles possibles. Elle se structure en deux tiges-boucles formée par l'appariement 2 à 2 de 4 répétitions successives. Dans une seconde partie, j'ai caractérisé l'interaction de cette région avec certains de ses partenaires protéiques in vitro. La région des A-repeats interagit notamment de manière directe avec les protéines PTB, KSRP et ASF/SF2. Les 2 premières protéines pourraient avoir un rôle dans la stabilité de l'ARN tandis qu'ASF/SF2 serait impliquée dans la maturation de l'ARN X / X-chromosome inactivation is the transcriptional silencing of one of the two X chromosomes in female mammal cells. This mechanism of dosage compensation ensures an equal level of the X-linked genes expression between males (XY) and females (XX). It initiates with the accumulation of the Xist RNA (X inactive specific transcript) on the futur inactive X chromosome (Xi). It is followed by the apposition of epigenetic marks such as histone modifications, that ensure establishment, maintenance and transmission of the inactive state of the chromatin. Xist RNA comprises a number of repeated regions and, in particular to its 5' end the A region, absolutely necessary for the establishment of the X-inactivation. My research was focused on the study of this singular region: its structure and its protein interactions. The FRET method (Fluorescence Resonance Energy Transfer) applied to RNA allowed us to ascertain that the RNA is structured in two long stem-loop structures each including four repeats. In a second part, I characterized the in vitro interaction of this region with some of its protein partners. The A region interacts directly with PTB, KSRP and ASF/SF2 proteins. The first two proteins may have a role in RNA stability whereas ASF/SF2 could be involved in the splicing process

<p>Viruses depend on their hosts for the production and spread of new virus particles. For efficient virus replication, the viral genes have adapted the strategy of being recognized and processed by the cellular biosynthetic machineries. Viruses therefore provide an important tool to study the cellular machinery regulating gene expression. In this thesis, we have used two model DNA viruses; herpes simplex virus (HSV) and adenovirus, to study RNA processing at the level of pre-mRNA splicing in mammalian cells. </p><p>During a lytic infection, HSV cause an almost complete shut-off of host cell gene expression. Importantly, HSV infection cause inhibition of pre-mRNA splicing which is possibly advantageous to the virus, as only four HSV genes contain introns. </p><p>The HSV immediate early protein, ICP27, has been shown to modulate several post-transcriptional processes such as polyadenylation and pre-mRNA splicing. We have studied the role of ICP27 as an inhibitor of pre-mRNA splicing.</p><p>We show that ICP27 inhibits pre-mRNA splicing <i>in vitro</i> in the absence of other HSV proteins. We further show that ICP27 inhibits splicing at the level of spliceosome assembly. Importantly, ICP27 induced inhibition of splicing can be reversed, either by the addition of purified SR proteins or by the addition of an SR protein specific kinase, SRPK1. We propose that SR proteins are prime candidates as mediators of the inhibitory effect of ICP27 on pre-mRNA splicing. </p><p>In order to learn more about how splicing is organized in the cell nucleus <i>in vivo</i>, we investigated how cellular splicing factors are recruited to sites of transcription and splicing in adenovirus infected cells using confocal microscopy. Our results showed that the SR proteins, ASF/SF2 and SC35, are efficiently recruited to sites in the nucleus where adenovirus genes are transcribed and the resulting pre-mRNAs are processed. Our results demonstrate that only one of the two RNA recognition motifs (RRMs) present in the ASF/SF2 protein is required for its recruitment to active sites of splicing. The arginine/serine rich (RS) domain in ASF/SF2 is redundant and insufficient for the translocation of the protein to active viral polymerase II genes in adenovirus infected cells.</p>

<p>We have constructed two adenovirus-based gene expression vector systems permitting regulated protein expression. They are based on the tetracycline-regulated Tet-ON- and the progesterone antagonist RU 486-regulated gene expression systems, which were rescued into E1-deficient adenovirus vectors. The vectors function in a number of cell types representing a broad species-variety and the regulation of protein expression was shown to be tightly controlled in cells not permissive for virus replication. Furthermore, the adenovirus-Tet-ON system was shown to perform in mice after intramuscular administration.</p><p>The novel adenovirus-vector systems were then used to study the effects of overexpression of selected proteins on adenovirus replication during a lytic infection, with focus on regulation of adenovirus alternative splicing. Expression of adenovirus transcription units is to a large extent temporally regulated at the level of alternative pre-mRNA splicing, where viral splice site usage shifts from proximal to distal splice site selection as infection proceeds. This makes adenovirus an appropriate model for mechanistic studies of regulated splicing. We show that overexpression of the essential host cell splicing factor ASF/SF2 inhibits this shift by promoting usage of proximal splice sites. As a consequence, the virus displayed a markedly inhibited growth. Interestingly, mRNA expression from the adenovirus major late promoter was almost completely lost as a consequence of ASF/SF2 overexpression. Collectively, the cellular splicing factor ASF/SF2 prevents adenovirus from entering the late phase of infection. This strongly argues for a need for the virus to block the splicing enhancer activity of ASF/SF2 for establishment of a lytic infection. Further, from analysis of the strict inhibition of late region 1 late pre-mRNA splicing we propose that the temporal regulation of alternative splicing is merely a consequence of fitness rather than profoundly deleterious effects of an unregulated expression. During our studies we noted that in 293 cells, which are used for growth of E1-deficient Ad vectors, an unwanted background reporter gene expression was evident in our vector systems. We therefore introduced an additional regulatory element, functioning as a transcriptional road-block, and showed that this methodological innovation represents a way to overcome the potentially deleterious effects of background reporter gene expression. This modified viral vector system should make it possible to reconstruct recombinant viruses expressing highly toxic proteins.</p><p>In conclusion, this work presents a new <i>in vivo </i>model system to study proteins involved in RNA splicing and other gene regulatory mechanisms.</p>

We have constructed two adenovirus-based gene expression vector systems permitting regulated protein expression. They are based on the tetracycline-regulated Tet-ON- and the progesterone antagonist RU 486-regulated gene expression systems, which were rescued into E1-deficient adenovirus vectors. The vectors function in a number of cell types representing a broad species-variety and the regulation of protein expression was shown to be tightly controlled in cells not permissive for virus replication. Furthermore, the adenovirus-Tet-ON system was shown to perform in mice after intramuscular administration. The novel adenovirus-vector systems were then used to study the effects of overexpression of selected proteins on adenovirus replication during a lytic infection, with focus on regulation of adenovirus alternative splicing. Expression of adenovirus transcription units is to a large extent temporally regulated at the level of alternative pre-mRNA splicing, where viral splice site usage shifts from proximal to distal splice site selection as infection proceeds. This makes adenovirus an appropriate model for mechanistic studies of regulated splicing. We show that overexpression of the essential host cell splicing factor ASF/SF2 inhibits this shift by promoting usage of proximal splice sites. As a consequence, the virus displayed a markedly inhibited growth. Interestingly, mRNA expression from the adenovirus major late promoter was almost completely lost as a consequence of ASF/SF2 overexpression. Collectively, the cellular splicing factor ASF/SF2 prevents adenovirus from entering the late phase of infection. This strongly argues for a need for the virus to block the splicing enhancer activity of ASF/SF2 for establishment of a lytic infection. Further, from analysis of the strict inhibition of late region 1 late pre-mRNA splicing we propose that the temporal regulation of alternative splicing is merely a consequence of fitness rather than profoundly deleterious effects of an unregulated expression. During our studies we noted that in 293 cells, which are used for growth of E1-deficient Ad vectors, an unwanted background reporter gene expression was evident in our vector systems. We therefore introduced an additional regulatory element, functioning as a transcriptional road-block, and showed that this methodological innovation represents a way to overcome the potentially deleterious effects of background reporter gene expression. This modified viral vector system should make it possible to reconstruct recombinant viruses expressing highly toxic proteins. In conclusion, this work presents a new in vivo model system to study proteins involved in RNA splicing and other gene regulatory mechanisms.

Viruses depend on their hosts for the production and spread of new virus particles. For efficient virus replication, the viral genes have adapted the strategy of being recognized and processed by the cellular biosynthetic machineries. Viruses therefore provide an important tool to study the cellular machinery regulating gene expression. In this thesis, we have used two model DNA viruses; herpes simplex virus (HSV) and adenovirus, to study RNA processing at the level of pre-mRNA splicing in mammalian cells. During a lytic infection, HSV cause an almost complete shut-off of host cell gene expression. Importantly, HSV infection cause inhibition of pre-mRNA splicing which is possibly advantageous to the virus, as only four HSV genes contain introns. The HSV immediate early protein, ICP27, has been shown to modulate several post-transcriptional processes such as polyadenylation and pre-mRNA splicing. We have studied the role of ICP27 as an inhibitor of pre-mRNA splicing. We show that ICP27 inhibits pre-mRNA splicing in vitro in the absence of other HSV proteins. We further show that ICP27 inhibits splicing at the level of spliceosome assembly. Importantly, ICP27 induced inhibition of splicing can be reversed, either by the addition of purified SR proteins or by the addition of an SR protein specific kinase, SRPK1. We propose that SR proteins are prime candidates as mediators of the inhibitory effect of ICP27 on pre-mRNA splicing. In order to learn more about how splicing is organized in the cell nucleus in vivo, we investigated how cellular splicing factors are recruited to sites of transcription and splicing in adenovirus infected cells using confocal microscopy. Our results showed that the SR proteins, ASF/SF2 and SC35, are efficiently recruited to sites in the nucleus where adenovirus genes are transcribed and the resulting pre-mRNAs are processed. Our results demonstrate that only one of the two RNA recognition motifs (RRMs) present in the ASF/SF2 protein is required for its recruitment to active sites of splicing. The arginine/serine rich (RS) domain in ASF/SF2 is redundant and insufficient for the translocation of the protein to active viral polymerase II genes in adenovirus infected cells.

Hepatitis delta virus (HDV) is the smallest known human RNA pathogen. It requires the human hepatitis B virus (HBV) for virion production and transmission, and is hence closely associated with HBV in natural infections. HDV RNA encodes only two viral proteins - the small and the large delta antigens. Due to its limited coding capacity, HDV needs to exploit host factors to ensure its propagation. However, few human proteins are known to interact with the HDV RNA genome. The current study has identified several host proteins interacting with an HDV-derived RNA promoter by multiple approaches: mass spectrometry of a UV-crosslinked ribonucleoprotein complex, RNA affinity chromatography, and screening of a library of purified RNA-binding proteins. Co-immunoprecipitation, both in vitro and ex vivo, confirmed the interactions of eEF1A1, p54nrb, PSF, hnRNP-L, GAPDH and ASF/SF2 with both polarities of the HDV RNA genome. In vitro transcription assays suggested a possible involvement of eEF1A1, GAPDH and PSF in HDV replication. At least three of these proteins, eEF1A1, GAPDH and ASF/SF2, have also been shown to associate with potato spindle tuber viroid (PSTVd) RNA. Because HDV’s structure and mechanism of replication share many similarities with viroids, subviral helper-independent plant pathogens, I transfected human hepatocytes with RNA derived from PSTVd. Here, I show that PSTVd RNA can replicate in human hepatocytes. I further demonstrate that a mutant of HDV, lacking the delta antigen coding region (miniHDV), can also replicate in human cells. However, both PSTVd and miniHDV require the function of the small delta antigen for successful replication. Our discovery that HDV and PSTVd RNAs associate with similar RNA-processing pathways and translation machineries during their replication provides new insight into HDV biology and its evolution.

Hepatitis delta virus (HDV) is the smallest known human RNA pathogen. It requires the human hepatitis B virus (HBV) for virion production and transmission, and is hence closely associated with HBV in natural infections. HDV RNA encodes only two viral proteins - the small and the large delta antigens. Due to its limited coding capacity, HDV needs to exploit host factors to ensure its propagation. However, few human proteins are known to interact with the HDV RNA genome. The current study has identified several host proteins interacting with an HDV-derived RNA promoter by multiple approaches: mass spectrometry of a UV-crosslinked ribonucleoprotein complex, RNA affinity chromatography, and screening of a library of purified RNA-binding proteins. Co-immunoprecipitation, both in vitro and ex vivo, confirmed the interactions of eEF1A1, p54nrb, PSF, hnRNP-L, GAPDH and ASF/SF2 with both polarities of the HDV RNA genome. In vitro transcription assays suggested a possible involvement of eEF1A1, GAPDH and PSF in HDV replication. At least three of these proteins, eEF1A1, GAPDH and ASF/SF2, have also been shown to associate with potato spindle tuber viroid (PSTVd) RNA. Because HDV’s structure and mechanism of replication share many similarities with viroids, subviral helper-independent plant pathogens, I transfected human hepatocytes with RNA derived from PSTVd. Here, I show that PSTVd RNA can replicate in human hepatocytes. I further demonstrate that a mutant of HDV, lacking the delta antigen coding region (miniHDV), can also replicate in human cells. However, both PSTVd and miniHDV require the function of the small delta antigen for successful replication. Our discovery that HDV and PSTVd RNAs associate with similar RNA-processing pathways and translation machineries during their replication provides new insight into HDV biology and its evolution.

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