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Almost every precursor mRNA (pre-mRNA) in a eukaryotic organism undergoes splicing, in some cases resulting in the formation of more than one splice variant, a process called alternative splicing. RNA-Seq provides a major opportunity to capture the state of the transcriptome, which includes the detection of alternative spicing events. Alternative splicing is a highly regulated process occurring in a complex machinery called the spliceosome. In this dissertation, I focus on identification of different splice variants and splicing factors that are produced during Arabidopsis and soybean embryo development. I developed several data analysis pipelines for the detection and the functional characterization of active splice variants and splicing factors that arise during embryo development. The main goal of this dissertation was to identify transcriptional changes associated with specific stages of embryo development and infer possible associations between known regulatory genes and their targets. We identified several instances of exon skipping and intron retention as products of alternative splicing. The coding potential of the splice variants were evaluated using CodeWise. I developed CodeWise, a weighted support vector machine classifier to assess the coding potential of novel transcripts with respect to RNA secondary structure free energy, conserved domains, and sequence properties. We also examined the effect of alternative splicing on the domain composition of resulting protein isoforms. The majority of splice variants pairs encode proteins with identical domains or similar domains with truncation and in less than 10% of the cases alternative splicing results in gain or loss of a conserved domain. I constructed several possible regulatory networks that occur at specific stages of embryo development. In addition, in order to gain a better understanding of splicing regulation, we developed the concept of co-splicing networks, as a group of transcripts containing common RNA-binding motifs, which are co-expressed with a specific splicing factor. For this purpose, I developed a multi-stage analysis pipeline to integrate the co-expression networks with de novo RNA binding motif discovery at inferred splice sites, resulting in the identification of specific splicing factors and the corresponding cis-regulatory sequences that cause the production of splice variants. This approach resulted in the development of several novel hypotheses about the regulation of minor and major splicing in developing Arabidopsis embryos. In summary, this dissertation provides a comprehensive view of splicing regulation in Arabidopsis and soybean embryo development using computational analysis. / Ph. D.

The human proteome is exponentially derived from a limited number of genes via alternative splicing, where one gene gives rise to multiple proteins. Alternatively spliced gene products, although crucial for normal physiology, are also linked to an increasing number of pathologies. Consequently, a growing focus is currently being placed on elucidating the extrinsic cues and ensuing signaling mechanisms which direct changes in gene splicing to yield functionally distinct proteins. Of note is the dysregulation of the vascular endothelial growth factor (VEGF) receptor, Flt1 and its soluble splice variants, sFlt1_v1 and sFlt1_v2, in the pregnancy-related disorder, preeclampsia. Preeclampsia is characterized by proteinuria and hypertension and is responsible for almost 600,000 maternal and fetal yearly deaths, worldwide. Here, we examined the impact of endothelial mitogens VEGF and FGF2 (fibroblast growth factor 2), both of which are upregulated in preeclampsia, on Flt1 transcript variants in umbilical vein endothelial cells. We tested the hypothesis that VEGF modulates the expression of Flt1 variants via the signaling kinase Akt and its impact on SR proteins. VEGF was observed to induce expression of overall Flt1 mRNA, principally as variants Flt1 and sFlt1_v1. Conversely, FGF2 induced a shift in splicing toward sFlt1_v2 without significant increase in overall Flt1. Based on inhibitor studies, the VEGF and FGF2 signals were transduced via ERK, but with the involvement of different upstream components. We mapped predicted SR protein binding to Flt1 pre-mRNA and identified two candidate proteins, SRSF2 and SRSF3, that may be involved in VEGF- or FGF2-induced Flt1 pre-mRNA splicing. Examination of SRSF2 and SRSF3 relative mRNA expression levels, following inhibition of VEGF- and FGF2-activated kinases, indicates that FGF2 significantly downregulates SRSF3 mRNA levels via PKC-independent activation of ERK. Additionally, our data suggest that FGF2 may impact Flt1 and sFlt1_v1 via SR protein kinases Akt and SRPK, while conversely regulating sFlt1_v2 levels via Clk. We did not find evidence of VEGF-induced Flt1 variant splicing via SR protein kinase activation or SRSF2 and SRSF3 mRNA levels. Thus, VEGF and FGF2 signals were tranduced via related but distinct mechanisms to differentially influence Flt1 pre-mRNA splicing. These findings implicate VEGF and FGF2 and their related intracellular signaling mechanisms in soluble Flt1 regulation. / Ph. D.

<p dir="ltr">Tomato, being a tropical species, is sensitive to temperatures below 10°C, thus limiting its growth to warmer regions and greenhouses. Understanding the cold response pathways in tomato will help improve its climate resiliency through breeding and biotechnology. Reportedly, plant genes undergo alternative splicing (AS) in response to various environmental stresses, however, the scope and dynamics of alternative splicing events in response to cold are unknown in tomato. To fill this knowledge gap, a fine-scale time-series cold (4°C) experiment was performed followed by RNA-sequencing of shoot and root tissues in tomato. Computational analysis revealed that various AS events occur within the first 20 minutes of temperature reduction and later on. Many AS genes were common between shoots and roots, however, the majority of the changes were organ-specific. Circadian rhythm and photosynthesis were the most significant among the various impacted biological processes, highlighting their importance in cold stress response. This study will help us gain insights into cold response pathways of tomato and other commercially important, closely related Solanaceae species.</p>

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.

La caséine [bêta] (CN-[bêta]) et la caséine [alpha]s1 (CN-[alpha]s1) du lait de jument possèdent un taux variable de phosphorylation et sont de bons modèles d’étude de l’influence du degré de phosphorylation et de la séquence peptidique sur la chélation de caséinophosphopeptides (CPP) avec des minéraux d’intérêt nutritionnel. Avant d’envisager une telle étude, la structure des caséines doit être déterminée précisément. Notre travail a été consacré à la caractérisation de variants post-transcriptionnels et post-traductionnels de CN-[alpha]s1 et de CN-[bêta]. Après fractionnement chromatographique et analyse par spectrométrie de masse, la CN-[alpha]s1 entière, trois variants d’épissage alternatif des exons 7 et 14 de la CN-[alpha]s1 et quatre variants délétés du résidu Gln91, résultat de l’utilisation d’un site d’épissage cryptique, ont été identifiés dans le lait équin. Nous avons montré que le degré de phosphorylation de ces isoformes varie de 2 à 8 groupes phosphates. Au total, 36 isoformes différentes de CN-[alpha]s1 ont été caractérisées. La cartographie bidimensionnelle de la CN-[bêta] a été établie avec précision après avoir isolé par chromatographie chacun des variants de phosphorylation (possédant de 3 à 7 groupes phosphates) et après avoir caractérisé les formes de CN-[bêta] modifiées par désamidation non enzymatique du résidu Asn135. Des CPP trypsiques de chaque variant de phosphorylation ont été préparés avec une technique récente de chromatographie d’affinité au dioxyde de titane, ce qui a permis de localiser par spectrométrie de masse en tandem les sites phosphorylés de la CN-[bêta] (Ser9, Ser10, Thr12, Ser18, Ser23, Ser24, Ser25) et de montrer que la phosphorylation de la CN-[bêta] n’est pas aléatoire mais séquentielle / Equine [bêta]-casein ([bêta]-CN) and [alpha]s1-casein ([alpha]s1-CN) have a variable phosphorylation degree and are good models for the study of the influence of phosphorylation degree and peptide sequence on chelation of caseinophosphopeptides (CPP) with minerals of nutritional interest. Before considering such study, structure of caseins must be precisely determined. Our work has been devoted to the characterization of post-transcriptional and post-translational variants of [alpha]s1-CN and [bêta]-CN. Concerning [alpha]s1-CN, the full-length protein, three alternative splicing variants involving exons 7 and 14 and four variants involving cryptic splice site resulting in deletion of residue Gln91 have been identified in mare’s milk after chromatographic fractionation and mass spectrometric analysis. The phosphorylation degree of these variants varies between 2 and 8 phosphate groups. Finally, 36 isoforms of [alpha]s1-CN have been identified. Isolation of each phosphorylation variant (having 3 to 7 phosphate groups) of [bêta]-CN by chromatography, and characterization of modified forms of [bêta]-CN by non enzymatic deamidation of residue Asn135 permits the establishment of bidimensional cartography of [bêta]-CN with precision. After hydrolysis by trypsin, CPP of each phosphorylation variant have been prepared by affinity chromatography to titanium dioxide, a recent technology, which allowed to locate by mass tandem spectrometry the phosphorylated sites of [bêta]-CN (Ser9, Ser10, Thr12, Ser18, Ser23, Ser24, Ser25). It was shown that the phosphorylation of [bêta]-CN is not a random process but follows a sequential way

Master of Science / Department of Computing and Information Sciences / Doina Caragea / As genomes are sequenced, a major challenge is their annotation -- the identification of genes and regulatory elements, their locations and their functions. For years, it was believed that one gene corresponds to one protein, but the discovery of alternative splicing provided a mechanism for generating different gene transcripts (isoforms) from the same genomic sequence. In the recent years, it has become obvious that a large fraction of genes undergoes alternative splicing. Thus, understanding alternative splicing is a problem of great interest to biologists. Supervised machine learning approaches can be used to predict alternative splicing events at genome level. However, supervised approaches require large amounts of labeled data to produce accurate classifiers. While large amounts of genomic data are produced by the new sequencing technologies, labeling these data can be costly and time consuming. Therefore, semi-supervised learning approaches that can make use of large amounts of unlabeled data, in addition to small amounts of labeled data are highly desirable. In this work, we study the usefulness of a semi-supervised learning approach, co-training, for classifying exons as alternatively spliced or constitutive. The co-training algorithm makes use of two views of the data to iteratively learn two classifiers that can inform each other, at each step, with their best predictions on the unlabeled data. We consider three sets of features for constructing views for the problem of predicting alternatively spliced exons: lengths of the exon of interest and its flanking introns, exonic splicing enhancers (a.k.a., ESE motifs) and intronic regulatory sequences (a.k.a., IRS motifs). Naive Bayes and Support Vector Machine (SVM) algorithms are used as based classifiers in our study. Experimental results show that the usage of the unlabeled data can result in better classifiers as compared to those obtained from the small amount of labeled data alone. In addition to semi-supervised approaches, we also also study the usefulness of graph based transductive learning approaches for predicting alternatively spliced exons. Similar to the semi-supervised learning algorithms, transductive learning algorithms can make use of unlabeled data, together with labeled data, to produce labels for the unlabeled data. However, a classification model that could be used to classify new unlabeled data is not learned in this case. Experimental results show that graph based transductive approaches can make effective use of the unlabeled data.

Les ARN hélicases DDX5 et DDX17 sont des protéines « multi-tâches », elles sont impliquées dans de nombreuses étapes de la régulation du métabolisme des ARNs dont la transcription, l’épissage et la dégradation des ARNs. Lors de processus biologiques complexes tels que la myogénèse, les programmes d’expression génique sont profondément modifiés. Durant mon travail de thèse, j’ai contribué à montrer que DDX5 et DDX17 sont des protéines orchestratrices de la différenciation en coordonnant de manière directe et dynamique plusieurs niveaux de régulation génique. DDX5 et DDX17 contrôlent l’activité du facteur de transcription MyoD, régulateur majeur de la myogénèse ainsi que des microARNs spécifiques du muscle miR-1 et miR-206. Ceux-ci ciblent et régulent en retour l’expression de DDX5 et DDX17 mettant en place une boucle de rétro-contrôle négative induisant la diminution d’expression de ces deux protéines au cours de la différenciation. Enfin, cette diminution d’expression permet la mise en place d’un programme d’épissage participant à l’acquisition de phénotypes morphologiques des cellules différenciées. D’un point de vue mécanistique, il apparaît qu’un sous-groupe des événements d’épissage régulés durant la différenciation est contrôlé par la coopération de DDX5 et DDX17 avec le facteur d’épissage hnRNP H/F. D’autre part, DDX5 a aussi été impliqué dans un contexte pathologique du muscle. Cette hélicase interagit avec la mutation responsable de la Dystrophie Myotonique de type 1 (DM1). Durant ma thèse, j’ai produit des résultats préliminaires suggérant un rôle de DDX5 dans la mise en place des défauts d’épissage observés dans cette pathologie / RNA helicases DDX5 and DDX17 are “multi-tasks” proteins involved in nearly all aspects of RNA metabolism such as transcription, splicing and RNA degradation. During complex biological processes like myogenesis, gene expression programs are deeply modified. During my PhD, I contributed to show that DDX5 and DDX17 are orchestrators of differentiation by dynamically and directly orchestrating several layers of gene expression. DDX5 and DDX17 control the activity of the transcription factor MyoD, master regulator of myogenesis, as well as the expression of miR1/206, muscle-specific micro-RNAs. During myogenesis, these miRNAs downregulate the protein expression of DDX5 and DDX17 in a negative feedback loop, contributing to the switch of splicing programs observed in differenciated cells. Mechanistically, this splicing subprogram appear to be in part regulated by DDX5 and DDX17 in cooperation with hnRNP H/F splicing factors. Moreover DDX5 has been involved in a pathological muscular pathology : Myotonic Dystrophy type 1 (DM1). This helicase interact with the DM1 pathological mutation. During my PhD, I produced preliminary results suggesting a role for DDX5 in the establishment of the splicing defects observed in DM1

Le virus T lymphotropique humain HTLV-1 est l’agent étiologique de la leucémie-lymphome T de l’adulte (ATLL) et de nombreuses maladies inflammatoires. HTLV-1 est associée à de nombreuses modifications quantitatives de l’expression des gènes cellulaires. À ce jour, ces modifications ont été décrites essentiellement à l’échelle transcriptionnelle à travers notamment les effets de l’oncoprotéine virale Tax, et plus récemment HBZ. Outre leurs impacts sur les niveaux d’activité des promoteurs, certains facteurs apparaissent jouer également un rôle dans la régulation de l’épissage alternatif. Ce mécanisme essentiel à la diversité du transcriptome et du protéome cellulaire, apparait étroitement couplé à la transcription et ses dérégulations sont de plus en plus décrites dans les phénomènes cytotoxiques et pathogènes tels que les infections et les cancers. Dans ce contexte, mon travail s’est intéressé à caractériser les profils d’expression des exons des cellules T CD4+ infectées ou non, et transformée ou non par HTLV-1 in vivo. Dans une seconde étude, j’ai abordé les aspects mécanistiques des modifications d’épissage alternatif par HTLV-1. Mes données montrent que, outre ses effets sur la régulation quantitative de l’expression des gènes cellulaires, l’activation de la voie NF-kB par l’oncogène Tax est impliquée dans la reprogrammation de l’épissage alternatif de nombreux gènes. Ces données révèlent un nouveau degré de complexité dans les mécanismes de dérégulation de l’expression des gènes cellulaires par HTLV-1 et ouvre de nouvelles perspectives d’investigations dans la compréhension des processus leucémogènes associés à l’infection par le virus HTLV-1 / Reprogramming cellular gene transcription sustains HTLV-1 viral persistence that ultimately leads to the development of adult T-cell leukemia/lymphoma (ATLL). We hypothesized that besides these quantitative transcriptional effects. HTLV-1 quantitatively modifies the pattern of cellular gene expression. Exon expression analysis shows that patients’ untransformed and malignant HTLV-1+ CD4+ T-cells exhibit multiple alternate exon usage (AEU) events. These affect either transcriptionally modified or unmodified genes, culminate in ATLL, and unveil new functional pathways involved in cancer and cell cycle. A total of 486 exon modifications occurred in untransformed infected CD4+ cells were detected in ATLL arguing for a role of AEUs in HTLV-1 leukemogenesis. Unsupervised hierarchical clustering of array data permitted to isolate exon expression patters of 3977 exons that discriminate uninfected, infected, and transformed CD4+ T-cells. Exposing cells to splicing inhibitors revealed that Sudemycin E reduces cell viability of HTLV-1 transformed cells without affecting primary control CD4+ cells and HTLV-1 negative cell lines, suggesting that the huge excess of AEU might provides news targets for treating ATLL. Taken together, these data reveal that HTLV-1 significantly modifies the structure of cellular transcripts and unmask new putative leukemogenic pathways and possible therapeutic targets