<p>Poly(A) polymerase (PAP) is the enzyme catalyzing the synthesis of the adenine tail to the 3’-end of mRNA. This A-tail is present on the majority of the primary RNA transcripts of protein-coding genes, and is important for mRNA stability, export to the cytoplasm and translation. Therefore, PAP is a key regulator of eukaryotic gene expression. This thesis describes the heterogeneity of PAP and the functional significance of multiple isoforms of PAP. </p><p>PAP exists in many different isoforms generated by three different mechanisms, gene duplication, alternative mRNA processing and post-translational modification. In HeLa cell extracts three different forms of PAP being 90, 100 and 106 kDa in size have been detected, where the 106 kDa isoform is a phosphorylated version of the 100 kDa species. It is shown that the N-terminal region of PAP contains a region required for catalysis, while the C-terminal end is important for the interaction with the cleavage and polyadenylation specificity factor (CPSF). Interestingly, it was found that also the extreme N-terminal end is important for the interaction with CPSF. This region is post-translationally modified by phosphorylation. Five alternatively spliced forms of PAP mRNAs are encoded by the PAPOLA gene while one unique species is encoded by the PAPOLG gene. The analysis showed that the exact structure of the alternatively spliced C-terminal end of PAP played an important role for catalytic efficiency. Thus, the C-terminal end contains a region important for modulating the catalytic efficiency of PAP.</p><p>Aminoglycoside antibiotics inhibit PAP activity, most likely by displacement of catalytically important divalent metal ions. Data shows that different aminoglycosides inhibit PAP activity by different mechanisms suggesting that the binding sites for the different aminoglycosides do not completely overlap. It is concluded that aminoglycosides interfere with enzymes important for housekeeping functions in mammalian cell, which may explain some of the toxic side effects caused by aminoglycoside antibiotics in clinical practice.</p>

<p>Primary hyperparathyroidism (pHPT) due to parathyroid tumours with hypersecretion of parathyroid hormone and hypercalcaemia is a common disease with incompletely understood etiology affecting more than 1 % of the population, primarily postmenopausal women. In secondary hyperparathyroidism (sHPT), parathyroid tumours develop in response to calcium and vitamin D deficiency generally in patients with uraemia. HPT is usually treated by surgical removal of enlarged parathyroid glands.</p><p>The aim of this thesis was to examine the Wnt/β-catenin signalling pathway in parathyroid tumours.</p><p>Aberrantly accumulated β-catenin was found in all analysed pHPT and sHPT tumours, with a stabilising homozygous mutation (Ser37Ala) in 7.3% of the pHPT tumours. Truncation of the APC protein was not found. MYC, a β-catenin target gene was overexpressed in a substantial fraction of pHPT and sHPT parathyroid tumours. </p><p>A parathyroid tumour cell line (sHPT-1) was established from a hyperplastic gland removed at operation of a patient with sHPT. The cells produced parathyroid hormone and grew with a doubling time of approximately 72 hours. Stabilised nonphosphorylated transcriptionally active β-catenin was expressed. Efficient transfection of siRNA against β-catenin decreased expression of cyclin D1 and MYC, and inhibited cell growth with ensuring cell death. </p><p>The Wnt coreceptor LRP5 was found expressed with an internal deletion of 142 amino acids (LRP5Δ) in 86% and 100% of pHPT and sHPT tumours, respectively. Stabilising mutation of β-catenin and expression of LRP5Δ was mutually exclusive. Expression of LRP5Δ was required to maintain the nonphosphorylated transcriptionally active ß-catenin level, MYC expression, parathyroid cell growth in vitro, and tumour growth in transplanted SCID mice. Wnt3 ligand and LRP5Δ strongly activated transcription, and LRP5Δ was insensitive to inhibition by DKK1.</p><p>Aberrant accumulation of β-catenin by stabilising mutation or expression of LRP5Δ appears as a common pathogenic pathway for hyperparathyroid disease. LRP5Δ in particular presents a potential target for therapeutic intervention.</p>

Variability of transgene expression levels resulting from gene silencing is considered as ahindrance to the successful application of plant genetic engineering. Towards alleviatinggene silencing, I decided to screen for novel genes involved in transgene silencing and toinvestigate how these genes regulate plant development. Genes encoding putative chromatinremodeling factors, especially those including a SET domain, were selected as candidatetargets. A bioinformatic analysis of the Arabidopsis SET genes (AtSET) was performed andthese genes were classified into 6 groups based on the domain architecture. RNA interference (RNAi) vectors were constructed for ~ 20 AtSET genes and wereintroduced into both wild type lines and transgenic lines silenced for a GFP reporter gene.Surprisingly, altered developmental phenotypes were only observed for three constructs,raising questions as to the effectiveness of the RNAi approach for the chosen Arabidopsissystem. To assess this situation, I targeted a phytoene desaturase (PDS) gene using the sameRNAi approach. Inactivation of PDS renders plant a readily identifiable phenotype. Whereasthe RNAi penetrance in Arabidopsis can be very high, the expressivity of RNAi in varioustissues and among different plants can vary dramatically. Contradictory to previous reports,I found that there is correlation between transcript level and silencing phenotype. Possiblereasons for this discrepancy are discussed. No apparent correlation between transgene copynumber and RNAi phenotypes was observed. Among the three RNAi constructs that caused an abnormal development inArabidopsis, K-23 which targets SuvR3 has the highest expressivity and could reactivate asilenced GFP locus. SuvR3 RNAi lines were selfed for six generations and were screenedfor morphological phenotypes. Abnormal number of flower organs, loss of viability of malegametophytes, and decreased seedling germination percentage were found in SuvR3 RNAilines. A progressive increase in both severity and frequency of abnormal phenotypes wereseen in subsequent generations, suggesting an epigenetic regulatory mechanism involvedwith SuvR3. Alternative splicing of SuvR3 was also observed in most of Arabidopsis tissues.One of the protein isoforms, SuvR3, lacks 16 amino acids within the highly conserved SETdomain. Possible effects of isoform interaction are proposed.

Les organismes vivants sont en intime relation avec leur environnement et sont constamment influencés par de nombreux facteurs chimiques et physiques. Parmi les facteurs physiques présents dans notre environnement, les forces mécaniques, y compris la gravité, les radiations, dont les ultraviolets, et les champs électromagnétiques constituent les trois pôles principaux de nos travaux de doctorat. Des outils biologiques, cellulaires et moléculaires ont été développés afin dévaluer le rôle des RhoGTPases dans les altérations morphologiques, prolifératives et phénotypiques induites par la perte du vecteur gravité au cours de vols spatiaux. Au cours du vol de la capsule spatiale inhabitée FOTON-M3, nous avons pu mettre en évidence que la suppression de Rac1 par ARN interférentiel permettait de contrecarrer les effets délétères de la microgravité sur larchitecture du cytosquelette suggérant que cette molécule de signalisation participe à la réception et à la réactivité à la gravité. RhoA et Cdc42 ne semblent pas impliqués. Nous avons également développé un modèle expérimental dinduction de flux calcique par des peptides mimétiques de la matrice extracellulaire activant les intégrines destiné à être expérimenté au cours de vols paraboliques. Au cours de nos travaux visant à évaluer les effets biologiques des champs électromagnétiques, nous avons observé que les EMF de très basse fréquence (450µT-50Hz) naffectent ni les signaux calciques induits par des concentrations élevées de sérum ou des peptides mimétiques de la matrice extracellulaire, ni lexpression des gènes régulés par les UV-B. Ils sont cependant capables de soutenir les oscillations calciques induites par une concentration sub-optimale de sérum, sans toutefois réguler de manière évidente les voies de signalisation contrôlant la prolifération. Lirradiation par les UV-B dun grand nombre de cellules, primaires, immortalisées et tumorales induit, par épissage alternatif du préARNm du VEGF-A, lexpression dun nouveau variant, le VEGF111. Celui-ci est constitué de la combinaison des exons 1-4 et de lexon 8. Cette nouvelle forme de VEGF-A contient donc les sites de fixation aux VEGF-R1 et R-2 et est pro-angiogène in vitro sur les cellules endothéliales et les cellules souche embryonnaires et in vivo chez la souris. Labsence des exons 6 et 7 codant pour la liaison aux protéines de la matrice extracellulaire lui confère une diffusibilité tissulaire. Une de ses caractéristiques remarquable est sa résistance à la dégradation en raison de labsence du site de clivage par la plasmine et les MMPs. Ce nouveau variant est également induit par diverses substances génotoxiques dont les agents chimiothérapeutiques. Les mécanismes régulant lexpression du VEGF111 dépendent des voies de signalisation ATM/ATR, p53 et MAPKinases. La double personnalité de ce nouveau facteur pro-angiogène, néfaste par son induction potentielle au cours de traitements anti-cancéreux mais bénéfique par son utilisation dans le traitement de pathologies ischémiques particulièrement pertinente en cas dactivités protéolytiques élevées, ouvre un champ considérable dinvestigations. ----------------------------------------------------------------------------------------------------- Living organisms interact with their environment and are constantly influenced by various chemical and physical factors. Among the physical factors present in our environment, mechanical forces, including gravity, radiations, among which ultraviolet radiations, and electromagnetic fields constitute the three main poles of our research. Biological, cellular and molecular tools have been developed with the aim to evaluate the role of RhoGTPases in the morphological, proliferative and phenotypic alterations induced by the loss of gravitational field experienced during space flight. During the flight of the unmanned FOTON-M3 capsule, we have demonstrated that the suppression of Rac1 by small interference RNA was able to counteract the deleterious effects of microgravity on the cytoskeleton architecture. This suggests that this signaling molecule participates to the reception and reaction to gravity. RhoA and Cdc42 do not seem to be implicated. We have also developed an experimental model of induction of intracellular calcium ions fluxes by mimetic peptides of the extracellular matrix activating integrins to be used in parabolic flights. During our investigations aimed at evaluating the biological effects of electromagnetic fields, we observed that EMF of very low-frequency (450µT-50Hz) do not affect neither the calcium signals induced by high concentrations of serum or extracellular matrix mimetic peptides, nor the expression of genes regulated by UV-B. They are however able to sustain calcium oscillations induced by a sub-optimal concentration of serum but without disturbing the cellular proliferation rate. Irradiation by UV-B of a large number of cells, primary, immortalized and tumoral, induces, by alternative splicing of the VEGF-A pre-mRNA, the expression of a new variant, the VEGF111. This isoform is made of a combination of exons 1-4 and exon 8. This new VEGF-A variant contains therefore the binding sites to VEGF-R1 and R-2 and proved to be proangiogenic in vitro for endothelial and ES cells and in vivo in mice. The absence of exons 6 and 7 coding for the heparin binding sites confers it with tissue diffusibility. One of its striking characteristics is its resistance to degradation due to the absence of the cleavage site by plasmin and MMPs. This new variant is also induced by a series of genotoxic agents, including chemotherapeutic drugs. The mechanisms controlling the VEGF111 expression depend on the ATM/ATR, p53 and MAPKinases signaling pathways. The dual faces of VEGF111, detrimental by its potential induction during anti-cancer therapy but beneficial by its use for managing ischemic pathologies, mostly relevant when associated with high proteolytic activities, opens a considerable field of investigations.

The aim of this thesis was to study the evolution of reproductive systems and reproductive traits in the fungal genus Neurospora. More specifically, I have investigated the evolutionary forces shaping the genes involved in sexual reproduction, focusing on mating-type (mat) and pheromone receptor (pre) genes. Neurospora contains species exhibiting three different mating systems, i.e., heterothallism (self-incompatibility), homothallism (self-compatibility) and pseudohomothallism (partial self-incompatibility). First, a robust phylogeny of Neurospora was established. The phylogenetic analyses revealed multiple independent transitions in reproductive life style during the evolutionary history of the genus. We argued for a heterothallic ancestor of the genus, although our subsequent ancestral reconstruction analyses favored a homothallic ancestor. To be able to settle the ancestral mating system, we zoomed in on the structural architecture of the mat-locus in four homothallic species of Neurospora, thought to have arisen from independent transitions. Our results led us to suggest two different genetic mechanisms (translocation and unequal crossover) to explain the transitions in mating system from heterothallism to homothallism. We pointed out that the mating-system transitions in Neurospora are unidirectional, and suggested that transposable elements might be driving the transitions. In conclusion, we suggest a heterothallic ancestor for Neurospora, and that at least six transitions to homothallism and two transitions to pseudohomothallism have occurred in its evolutionary history. Further, we used the phylogeny of Neurospora as a framework to test if the evolution of pre-genes (pre-1 and pre-2) in hetero- and homothallic Neurospora is dependent on mating systems and/or even the homothallic clades themselves (i.e., mating-system and/or switch-dependent). The molecular evolution results suggest that pre-1 and pre-2 are overall functional in both homothallic and heterothallic Neurospora. The molecular evolution of pre-1 seems to be independent of mating-system or homothallic clade, and we detected signs for positive selection in the C-terminal tail. For pre-2 we found no support for mating-system dependent evolution, but indications for switch-dependent evolution. In this study we also included expression analyses of both pre- as well as mat-genes, with the prospect to assess functionality and regulation. During this thesis work, we also performed a phylogenetic study were we found that reproductive genes might be more permeable to introgression than other genes, which is in contrast to theoretical expectations. In the last study, we confirmed the co-existence of two alternative splice variants of the pheromone receptor gene pre-1 in Neurospora crassa, and performed expression profiles studies using quantitative RT-PCR. I hope this thesis work will further strengthen Neurospora as a model for research in evolutionary genetics.

The concept of the gene has been constantly challenged by new discoveries in the life sciences. Recent challenging observations include the high frequency of alternative splicing events and the common transcription of non-protein-coding-RNAs (ncRNAs) from the genome. The latter has long been considered noise in biological systems. Multiple lines of evidence from genomic studies indicate that alternative splicing and ncRNA play important roles in expanding proteome diversity in eukaryotes. Here, the aim is to find the link between alternative splicing and ncRNAs by studying the expression profile of the spliceosomal snRNAs (U snRNA). Spliceosomal snRNAs are essential for pre-mRNA splicing in eukaryotes. They participate in splice site selection, recruitment of protein factors and catalyzing the splicing reaction. Because of this, both the abundance and diversity of U snRNAs were expected to be large. In our study we deeply analyzed the U snRNA population in primates using a combination of bioinformatical, biochemical and high throughput sequencing approaches. This transcriptome profiling has revealed that human, chimpanzee and rhesus have similar U snRNA populations, i.e. the vast majority of U snRNAs originate from few well-defined gene loci and the heterogeneity observed in U snRNA populations was largely due to the presence of SNPs at these loci. It seems that the gene loci that could potentially encode a significantly heterogeneous population of U snRNAs are mostly silent. Only few minority transcripts were detected in our study, and among them three U1-like snRNAs might play a role in the regulation of alternative splicing by recognizing non-canonical splicing sites. Mutations of U snRNA have been shown to impact the splicing process. Therefore, our study provides a reference to study the biological significance of SNPs in U snRNA genes and their association with diseases.

Primary hyperparathyroidism (pHPT) due to parathyroid tumours with hypersecretion of parathyroid hormone and hypercalcaemia is a common disease with incompletely understood etiology affecting more than 1 % of the population, primarily postmenopausal women. In secondary hyperparathyroidism (sHPT), parathyroid tumours develop in response to calcium and vitamin D deficiency generally in patients with uraemia. HPT is usually treated by surgical removal of enlarged parathyroid glands. The aim of this thesis was to examine the Wnt/β-catenin signalling pathway in parathyroid tumours. Aberrantly accumulated β-catenin was found in all analysed pHPT and sHPT tumours, with a stabilising homozygous mutation (Ser37Ala) in 7.3% of the pHPT tumours. Truncation of the APC protein was not found. MYC, a β-catenin target gene was overexpressed in a substantial fraction of pHPT and sHPT parathyroid tumours. A parathyroid tumour cell line (sHPT-1) was established from a hyperplastic gland removed at operation of a patient with sHPT. The cells produced parathyroid hormone and grew with a doubling time of approximately 72 hours. Stabilised nonphosphorylated transcriptionally active β-catenin was expressed. Efficient transfection of siRNA against β-catenin decreased expression of cyclin D1 and MYC, and inhibited cell growth with ensuring cell death. The Wnt coreceptor LRP5 was found expressed with an internal deletion of 142 amino acids (LRP5Δ) in 86% and 100% of pHPT and sHPT tumours, respectively. Stabilising mutation of β-catenin and expression of LRP5Δ was mutually exclusive. Expression of LRP5Δ was required to maintain the nonphosphorylated transcriptionally active ß-catenin level, MYC expression, parathyroid cell growth in vitro, and tumour growth in transplanted SCID mice. Wnt3 ligand and LRP5Δ strongly activated transcription, and LRP5Δ was insensitive to inhibition by DKK1. Aberrant accumulation of β-catenin by stabilising mutation or expression of LRP5Δ appears as a common pathogenic pathway for hyperparathyroid disease. LRP5Δ in particular presents a potential target for therapeutic intervention.

Non-coding RNAs (ncRNAs) have emerged as highly diverse and powerful key players in the cell, the range of capabilities spanning from catalyzing essential processes in all living organisms, e.g. protein synthesis, to being highly specific regulators of gene expression. To fully understand the functional significance of ncRNAs, it is of critical importance to identify and characterize the repertoire of ncRNAs in the cell. Practically every genome-wide screen to identify ncRNAs has revealed large numbers of expressed ncRNAs and often identified species-specific ncRNA families of unknown function. Recent years' advancement in high-throughput sequencing techniques necessitates efficient and reliable methods for computational identification and annotation of genes. A major aim in the work underlying this thesis has been to develop and use computational tools for the identification and characterization of ncRNA genes. We used computational approaches in combination with experimental methods to study the ncRNA repertoire of the model organism Dictyostelium discoideum. We report ncRNA genes belonging to well-characterized gene families as well as previously unknown and potentially species-specific ncRNA families. The complicated task of de novo ncRNA gene prediction was successfully addressed by developing a method for nucleotide composition-based gene prediction using maximal-scoring partial sums and considering overlapping dinucleotides. We also report a substantial heterogeneity among human spliceosomal snRNAs. Northern blot analysis and cDNA cloning, as well as bioinformatical analysis of publicly available microarray data, revealed a large number of expressed snRNAs. In particular, U1 snRNA variants with several nucleotide substitutions that could potentially have dramatic effects on splice site recognition were identified. In conclusion, we have by using computational approaches combined with experimental analysis identified a rich and diverse ncRNA repertoire in the eukaryotes D. discoideum and Homo sapiens. The surprising diversity among the snRNAs in H. sapiens suggests a functional involvement in recognition of non-canonical introns and regulation of messenger RNA splicing.

The aim of this thesis was to identify genetic factors involved in frontotemporal lobar degeneration (FTLD), a neurodegenerative disorder clinically characterised by a progressive change in personality, behaviour and language. FTLD is a genetically complex disorder and a positive family history is found in up to 40% of the cases. In 10-20% of the familial cases the disease can be explained by mutations in the gene encoding the microtubule associated protein tau (MAPT). In the first study we describe the clinical and neuropathological features of a Finnish family with FTLD caused by a mutation in MAPT. We also provide evidence that the pathogenic mechanism of this mutation is through altered splicing of MAPT transcripts. Recently, mutations in the gene encoding progranulin (PGRN) were identified as a major cause of FTLD. In the second study we describe a Swedish family with FTLD caused by a frameshift mutation in PGRN. We provide a clinical and neuropathological description of the family, as well as evidence that the pathogenicity of this mutation is through nonsense-mediated decay of the mutant mRNA transcripts and PGRN haploinsufficiency. In the third study we describe a novel PGRN splice site mutation and a previously described PGRN frameshift mutation, found in a mutation screen of 51 FTLD patients. We describe the clinical and neuropathological characteristics of the mutation carriers and demonstrate that haploinsufficiency is the pathogenic mechanism of the two mutations. In the fourth study we investigate the prevalence of PGRN and MAPT gene dosage alterations in 39 patients with FTLD. No gene dosage alterations were identified, indicating that variations in copy number of the PGRN and MAPT genes are not a common cause of disease, at least not in this FTLD patient collection.

Magnocellular neurosecretory cells (MNCs) are neuroendocrine cells with somata located in the hypothalamus and nerve terminals in the posterior pituitary. They receive neuronal inputs from the brain and release vasopressin and oxytocin into the blood to regulate many important functions such as water balance, lactation, and parturition. The process of hormone release depends on Ca2+ influx mediated by voltage-gated Ca2+ channels (VGCCs) on the plasma membranes of neuroendocrine cells. To better understand the cellular and molecular components that are involved in regulating secretory vesicle exocytosis, this thesis work was conducted to investigate the expression and function of different subtypes of VGCCs in MNCs and pituicytes (the glial cells surrounding MNC nerve terminals).<p> Molecular biology, immunohistochemistry and cellular biology were used to detect expression and alternative splicing of different VGCC subtypes in MNCs, neurons, and pituicytes. First, the presence of CaV2.2 and CaV2.3 channels were detected on the pituicytes in situ. When the pituicytes were isolated and cultured for 14 days, more VGCC subtypes were expressed including CaV1.2 channels. Regulation of VGCC expression was measured in normal and dehydrated rats, and CaV1.2 channels were found to be selectively up-regulated in pituicytes after 24 hours of dehydration.<p> Second, two splice variants of CaV2.1 channels (CaV2.1Ä1 and Ä2) that lack a large portion of the synprint (synaptic protein interaction) site were detected in the rat brain. To determine whether the splice variants were expressed in MNCs, we did immunocytochemistry using two antibodies (the selective and the inclusive antibody) that recognized the carboxyl-terminus of channels and the synprint site, respectively, in different cell types. We found that vasopressin MNCs, but not the oxytocin MNCs, and one type of endocrine cell (the melanotropes of the pituitary gland) expressed the synprint site deleted variants, whereas the hippocampal neurons mainly expressed the full-length isoform. The splice variants were properly distributed on the plasma membrane of the somata and nerve terminals of the MNCs, suggesting the synprint site is not essential for CaV2.1 channel targeting into the nerve terminals of neuroendocrine cells.<p> Third, expression and distribution of CaV2.2 channels were studied in the MNCs. All CaV2.2 isoforms we detected contained the full-length synprint site. To test the importance of the CASK/Mint1 binding site for CaV2.2 channel targeting, we over-expressed a peptide that inhibits the interaction between CaV2.2 channels and CASK/Mint1 in differentiated PC12 cells (a neuroendocrine cell line). We found that the distribution of CaV2.2 channels in the growth cones of PC12 cells were significantly decreased, suggesting that the CASK/Mint1 interaction is important for CaV2.2 channel targeting into the neuroendocrine terminals.<p> In conclusion, these results provide insights of VGCC expression in neuroendocrine cells, and also give rise to a better understanding of the molecular components that are involved in forming the exocytotic machinery in these cells.