There are two classes of transposable elements: DNA transposons and retrotransposons. DNA transposons spread in the genome by “cut and paste” mechanism. In contrast, retrotransposons use copy and paste strategy involving RNA and retrotranscriptase mediated mechanism; these include long interspersed nuclear elements-1 (LINE-1, L1) and short interspersed nuclear elements (SINE). In mammals, in order to maintain genome integrity both types of transposons are tightly repressed. However, some copies of retrotransposons are still active in germ cells contributing to natural variation. Surprisingly, recent reports indicate that also somatic cells support L1 reactivation in early development, in particular in the brain leading to mosaicism. However, whether L1 retrotransposition is a part of other cell lineage developmental programs and its functional significance in the context of cell differentiation remain to be elucidated. To address this question, I investigated whether L1 retrotransposition was occurring during in vitro osteogenic and adipogenic differentiation of bone marrow derived human mesenchymal stem cells (hMSCs). Interestingly, clinical observations have revealed loss of bone density in HIV-infected individuals treated with nucleoside analogs that inhibit HIV retrotranscriptase, as well as the endogenous one encoded by L1s. This observation made us to hypothesize that transposable elements played a positive role in post-natal bone homeostasis. I found that while adipogenesis is “retrotransposition free”, osteogenic differentiation is a “retrotransposition-prone” process and its inhibition blocks its genetic program. Indeed, L1 DNA content does not change during adipogenic differentiation and that of retrotranscriptase does not have any effect on the acquisition of a terminally differentiated phenotype. In contrast, soon after MSCs commitment into pre-osteoblasts, L1 retrotransposable elements increase their expression and actively transpose. Inhibition of retrotransposition and knock down of L1 mRNA strongly impairs matrix deposition. Moreover, I forced L1 expression in in vitro adipogenesis, by directly delivering L1 mRNA to the cells. Interestingly, overexpression of L1 elements was detrimental for in vitro adipogenesis. Then, I performed loss of function experiments in osteogenesis by directly targeting and degrading the L1 endogenous transcript. This experiment confirmed the positive role of L1 reactivation in the osteogenic context, suggesting also a possible role for L1 RNA, distinct from retrotransposition.

Ribonucleases (RNases) H1 and H2 are endonucleases that hydrolyze the RNA strand of RNA-DNA hybrids forming at the chromosomal level as well as extra-chromosomal hybrids. Extra-chromosomal RNA-DNA hybrids can frequently occur in cells as intermediate structures in the process of reverse transcription and generation of cDNA by retrotransposition. It is known that mutations in RNase H2 are found in Aicardi-Goutières syndrome (AGS) patients. AGS is a rare but severe immune-mediated neurodevelopmental disorder. Currently, the mechanism by which defects in RNase H2 cause AGS is still unclear. We hypothesized that defects in RNases H, including those associated with AGS can trigger the accumulation of extra-chromosomal RNA-DNA hybrids. Thus, we speculate that increased stability of such free RNA-DNA hybrid structures could be a likely trigger for stimulating the autoimmune system, mimicking a viral infection in AGS patients. RNase H2 protein subunits of human and yeast Saccharomyces cerevisiae RNase H2 proteins have conserved amino acid sequences. Based on the similarity between human and yeast RNase H2, we thought to utilize S. cerevisiae as a research model to generate and study several AGS-related mutants. Initially, we set up an assay to detect retrotransposition activity in the budding yeast by introducing a recombinant DNA which includes a Ty1 retrotransposable element fused to an inactive his3 marker gene. To test whether the retrotransposition assay works in our yeast strains, we treated yeast cells with phosphonoformic acid (PFA) or knocked out DBR1 gene coding for the RNA lariat debranching enzyme. Both approaches strongly reduced the frequency of retrotransposition in our strains, demonstrating that the system was working as expected. Next, we examined whether yeast cells with defective forms of RNases H or AGS-orthologous mutants of RNase H2 had altered retrotransposition activity compared with cells with wild-type RNases H. Results showed that the retrotransposition activity was repressed in the absence of both types of RNase H. In addition, AGS-related mutants showed decreased retrotransposition frequencies when RNase H1 was also knocked-out. These findings are relevant to uncover the mechanism of the AGS.

LINE-1 retrotransposons, also known as "jumping genes", are repetitive sequences capable of copying, pasting, and reinserting themselves into the genome. These events were documented at high frequency in various types of cancers, including colorectal cancer (CRC). Furthermore, the expression of proteins encoded by these elements, such as L1ORF1p, has been linked to cancer aggressiveness, stemness, and lower patient survival rates. Colorectal cancer stem cells (CCSC), constitute a small subset of cells endowed with pluripotency and self-renewal abilities. They play roles in tumorigenesis, cancer aggressiveness, drug resistance, cancer recurrence, and metastasis. Conventional chemotherapeutics primarily target bulk tumor cells and tend to spare cancer stem cell populations. Consequently, targeting CCSC is expected to significantly increase complete remission and survival rates in CRC patients. Here, I have characterized specific aspects of a novel repurposed drug that effectively targets CCSC, reactivates the expression of transposable elements and, consequently, triggers an innate immune response. Further, I tested an in silico drug screening approach to identify compounds with high predicted affinity for the RNA binding domains of L1ORF1p, a key protein for the LINE1 retrotransposition event to occur, from a virtual drug library. Two lead compounds, both FDA-approved drugs, were identified and evaluated for their capacity to block L1ORF1p nuclear translocation, a needed step to complete the LINE1 lifecycle, as well as their capacity to decrease LINE-1 retrotransposition levels. In addition, I established a protocol for the isolation, culture, propagation, and cryopreservation of patient-derived normal colonic organoids. This protocol is crucial to the establishment of a colonic organoid biobank, representing a powerful resource to assess cancer-selective toxicity of putative CCSC-targeting compounds. Together, this thesis emphasizes the importance of transposable elements in CRC and contributes to the establishment of a gold standard ex vivo disease-modeling system for the discovery of new therapeutic agents.

Le génome humain est constitué d'environ 45% d'éléments transposables, et l'élément LINE-1 (L1), qui représente 17% de la masse totale, est le seul élément actif connu de notre génome capable de rétrotransposer. Les protéines de L1, ORF1p et ORF2p, peuvent mobiliser divers ARN en trans, tel que Alu, le snRNA U6 ou encore d'autres ARNm cellulaires. C'est, en partie pour ces raisons que l'élément L1 est considéré comme un acteur majeur de la plasticité de notre génome.Dans un premier temps, nous avons élaboré un nouveau système, la lignée stable inductible Trex, qui permettra d'étudier la rétrotransposition de L1 à partir d'une localisation chromosomique. Cette lignée stable présente une intégration d'un élément L1 marqué avec T7 et Flag-HA pour ORF1p et ORF2p, respectivement. Ce système nous permettra dans un avenir proche de purifier les partenaires protéiques d'ORF2p selon le protocole de double purification sur colonne d'affinité Flag suivi de HA, et de les identifier par spectrométrie de masse (MS/MS). Dans un deuxième temps, nous nous sommes intéressés aux séquences chimères U6-L1 présentes au niveau du génome humain. Nous avons entamé ainsi une étude in silico, qui nous a conduit à la découverte d'une nouvelle unité répétée présente dans les génomes de primates, que l'on a appelé ‘'RSU6''. / The human génome is composed of about 45% of mobile elements. LINE-1 (L1, which represents 17% of the total mass, is the only active element, capable of retrotransposition in our génome. L1 proteins, ORF1p and ORF2p, can mobilise other RNA in trans, such Alu, snRNA U6 or other cellular mRNA. This is one of the reasons why L1 element is considered as the major actor of genome plasticity. First, we have developed a new system, the stable Trex cell line, which will allow us to study L1 retrotransposition from a chromosomal location. This stable cell line has integrated a marqued L1 (with ORF1-T7 and ORF2- Flag-HA) into the genome. This new system will enable us to purify cellular cofactors of ORF2p, according to the double affinity protocol (Flag and HA), and to identify them by mass spectrometry. Second, we were intersted in the chimeric sequences U6-L1 present in the human genome. We have done an in silico analyses which allowed us to identify a new repeated unit in the primate genome that we called ‘'RSU6''.

Nuclear precursor of mature messenger RNA (pre-mRNA) splicing is one of the most highly regulated processes in eukaryotic organisms. In addition to its role in the removal of constitutive or alternative introns present in the pre-mRNA, splicing is also highly integrated into other layers of gene expression. This study investigates the potential role of the nuclear branchpoint binding protein (BBP) outside of the pre-mRNA splicing cycle. More specifically, we were interested in the biological relevance of its association with two cytoplasmic proteins Smy2 and Syh1. Smy2 and Syh1 belong to the GYF family of poly-proline binding proteins, and their roles in cell biology have not been well elucidated. Here we report that Smy2 and Syh1 act redundantly in: (i) limiting pre-mRNA accumulation when yeast cultures reach high cell density, potentially through promoting pre-mRNA decay in the cytoplasm; (ii) restricting Ty1 retrotransposition, apparently by limiting the Ty1 transcript abundance; (iii) limiting the accumulation of BBP-associated yet intronless TDA1 mRNA. With the presence of UACUAAC motif and BBP association as common features of these Smy2/Syh1 sensitive substrates, we tested if BBP interaction is required for Smy2/Syh1 function in RNA metabolism. Interestingly, we found that deletion of BBP C-terminal region (bbp∆C), which largely reduces or abolishes its association with Smy2, does not lead to similar phenotypes as observed in smy2∆ syh1∆ deletion mutant cells. In addition, mutagenesis of the TACTAAC BBP-binding site within the TDA1 coding region does not seem to affect TDA1 mRNA abundance or its sensitivity to the smy2∆ syh1∆ deletions. Therefore, we concluded that while the two BBP-binding proteins Smy2 and Syh1 impact the levels of certain cellular RNAs, this phenomenon is not strictly dependent upon BBP-Smy2 interaction and may be independent of BBP contribution. A model is proposed for Smy2 and Syh1 function in RNA metabolism based on our observations and interactions between these proteins with other factors implicated in RNA stability or translation.

No description available.

Les rétrotransposons L1 sont les seuls éléments transposables autonomes et actifs chez l'Homme et constituent 20% de notre ADN. Ils prolifèrent via un intermédiaire ARN et un processus couplé de réverse transcription et d'intégration, appelé rétrotransposition, et médié par une particule ribonucléoprotéique (RNP). Les L1s sautent de façon active dans les cellules germinales, les cellules souches embryonnaires et l'embryon précoce, ce qui provoque parfois de nouvelles maladies génétiques. Cependant ils sont considérés comme éteints dans la plupart des tissus somatiques. Dans le but d'explorer l'importance et les conséquences de la rétrotransposition des L1s chez l'Homme, nous avons développé une approche de cartographie des L1s actifs dans le génome humain, en combinant amplification sélective des sites d'insertion et séquençage à haut-débit. Nous avons utilisé cette stratégie afin d'obtenir la cartographie différentielle des L1s dans deux lignées cellulaires humaines apparentées. Ainsi, nous avons découvert plusieurs insertions de L1 présentes uniquement dans la lignée fille mais absente dans la lignée parentale, démontrant pour la première fois que les éléments L1 endogènes humains sont capables de mobilité dans des lignées de cellules somatiques en culture. D'autre part, afin d'éclaircir les déterminants qui dictent l'intégration des L1s, nous avons développé un test direct de réverse transcription in vitro à partir de RNP L1 natives partiellement purifiées de cellules humaines. Ceci nous a permis de montrer que la réverse transcriptase du L1 participe à la sélection du site d'insertion, ajoutant une couche additionnelle de spécificité après l'endonucléase L1. En conclusion, notre travail met en lumière la flexibilité de la machinerie des L1s, une propriété qui a certainement participé à l'efficacité de l'invasion des génomes de mammifères par ces éléments génétiques mobiles. / L1 retrotransposons are the only autonomous and active transposable elements in humans and comprise as much as 20% of our DNA. They proliferate via an RNA intermediate and a coupled reverse transcription and integration process, called retrotransposition and mediated by an L1-encoded ribonucleoprotein particle (RNP). L1s are actively jumping in germ cells, embryonic stem cells and in the early embryo, occasionally leading to de novo genetic diseases, but are considered silent in most somatic tissues. To comprehensively map active L1 elements in the human genome and to further explore the importance and consequences of L1 retrotransposition in humans, we combined selective amplification of L1 insertion sites and high-throughput sequencing. We applied this strategy to obtain a differential map of L1 insertions in two related human cultured cell lines and to question the possibility that endogenous L1 elements could be jumping in somatic cultured cells. We discovered several L1 insertions only present in the daughter cell line but absent in the parental cell line, demonstrating for the first time that retrotransposition of endogenous L1s takes place in a human somatic cell line. To get insights into the determinants of L1 integration, we have also developed a novel reverse transcription assay using partially purified native L1 RNPs. This enabled us to show that the L1 reverse transcriptase participates to insertion site selection, adding a second layer of specificity beyond the L1 endonuclease. Finally our work highlights the flexibility of the L1 machinery, which certainly participates to the efficient spreading of L1 elements within mammalian genomes.

Retrogenes are a group of functional genes produced by gene retroduplication events during evolution. It has been observed that many retrogenes have formed since the evolutionary divergence of Anopheles mosquitoes from the Aedes lineage as a result of developing heteromorphic sex chromosomes. It has been further observed that these retroduplications predominately occur from parent genes on the heteromorphic X chromosome to autosomes and have a predisposition to have enriched expression in testis. In order to investigate the nature of this male-biased expression in testis, we utilized bioinformatic techniques to identify retrotransposition events and assign them relative ages based on evolutionary branches of divergence. This list of parent genes and retrogenes were then analyzed and a total of twenty-five gene pairs were selected for further examination. Available gene expression data in the form of RNA-seq and DNA microarray were used in tandem with gene annotation data to computationally investigate gene pairs in An. coluzzii. These pairs were further investigated experimentally by means of RT-PCR conducted on dissected head, thorax, abdomen, and reproductive organs in both male and female Anopheles coluzzii Mopti strain. Testis and male accessory glands (MAGs) were also investigated by this method in An. coluzzii. Available expression data support previously observed testis enriched expression of retrogenes and provides evidence for the predominate expression of retrogenes occurring in postmeiotic cells suggesting retrogene involvement in sperm development. Experimental evidence revealed a small group of five retrogenes which exhibit the expected male-biased expression in male testis with little to no expression in female ovaries, although a shared expression in the heads of both sexes was observed. Of the five retrogenes, four carry out energy related functions involving mitochondria, suggesting contribution to energy requirements of developing sperm. Testis and MAG experiments in An. coluzzii revealed a predisposition for retrogenes to be expressed in testis while parent genes tended to have higher expression in MAGs, and this phenomenon is partially supported by DNA microarray expression data. Overall, these results suggest further investigation of retrogenes in An. coluzzii may reveal unique functions in male mosquito fertility that are exploitable in genetic approaches to mosquito control. / Master of Science in Life Sciences / Malaria is a potentially deadly disease which effects thousands of people every year. Malaria around the world is spread by multiple species of mosquitoes in a genus called Anopheles. Controlling the populations of these disease spreading mosquitoes is essential to preventing the spread of malaria. Current insecticide-based approaches used to stop mosquitoes are becoming less effective overtime as mosquitoes become resistant. A potential way to develop new techniques for mosquito control is through research involving mosquito reproductive genetics. Understanding the genes involved in how mosquitoes reproduce could improve future techniques designed to reduce or prevent mosquitos from reproducing. This research focuses on a group of genes called retrogenes which have formed over the evolution of these mosquitoes via the duplication from a separate parent gene. In mosquitoes these retrogenes are understood to be involved in male reproduction. The retrogenes involved in male mosquito reproduction could have important functions in male sexual reproduction and sterility. These important genes could be manipulated to interrupt whatever important functions these genes have in reproduction. In this research we first computationally identified retrogenes and their parent genes and categorized them by age. We then utilized available annotation and expression data to analyze the potential significance of retrogenes to male fertility and found that multiple retrogenes tended to be expressed during sperm development. Lastly, we conducted gene expression experiments using dissected head, thorax, abdomen, and reproductive organs in both male and female Anopheles mosquitoes. Results revealed unique patterns of expression that suggest male specific roles of five retrogenes in testes and head expression in both males and females suggesting a possible role in mating behavior. These results provide evidence that retrogenes do have functional roles in male fertility specifically related to the maturation and development of sperm.

Duplicação genica é uma das principais forças levando a evolução dos genomas eucarioto. O impacto de duplicações gênicas/genômicas vem sendo investigado a muito tempo em humanos e outros primatas. Um segundo mecanismo de duplicação gênica, a retrotransposição baseada em RNA maduros, vem sendo menos estudada devido ao seu potencial menor de gerar cópias funcionais. No entanto, recentemente, publicações descreveram retrocópias funcionais em humanos, roedores e mosca de fruta. Nesta tese, para investigar sobre retrocópias causando variabilidade genética no genoma de primatas, nós desenvolvemos a implementamos os métodos para detectar estas inserções. Utilizando nove genomas e transcriptomas publicamente disponíveis (sete primatas e dois roedores) nós confirmamos um número similar, porém, com origem independente, de retrocópias em primatas e roedores. Nós também encontramos um enriquecimento de retrocópias no genoma de Platyrrhini, possivelmente explicado pela expansão de L1PA7 e L1P3 nestes genomas. Posteriormente, nós analisamos a ortologia de retrocópias no genoma de primatas e encontramos 127 eventos específicos à linhagem humana. Nós também exploramos dados do projeto 1000 Genomes para detectar retrocópias polimórficas (retroCNVs germinativos) e encontramos 17 eventos, presentes no genoma referência humano, mas ausentes em mais de um indivíduo. Similarmente, nós investigamos novas retroduplicações de mRNAs no genoma humano, detectando 21 eventos ausentes do genoma referência. Finalmente, investigamos a existência de retroCNVs somáticos e descrevemos sete possíveis retrocópias somáticas. Apesar de sua possível insignificância, nós encontramos que algumas retrocópias compartilhadas entre todos os primatas, espécie específicas, e polimórficas podem ser expressas per se ou como transcritos quiméricos com genes hospedeiros. Sobretudo, nós encontramos que retrocópias são um fator importante da variabilidade genética inter-espécie, intra-espécie e intra-indivíduo e podem estar influenciando a evolução de mamíferos ao criar reservatórios de duplicações potencialmente funcionais. / Gene duplication is a major driving force of evolution in eukaryotic genome. The impact of gene/genomic duplication has long been investigated in human and other primates. A second mechanism of gene duplication, retrotransposition, which is based on mature RNA, has been traditionally less studied due to their lower potential to generate functional copies. Recently, however, publications described functional retrocopies in humans, murines and drosophila. Here, to gain insights of the genetic variability arising from retrocopies on primate genomes, we developed and implemented the methods to detect these insertions. Using nine publicly available reference genomes and transcriptomes (seven primates and two rodents) we described a similar number independently arisen retrocopies in primates and rodents. We also found an enrichment of retrocopies in Platyrhinni genomes, putatively explained by the expansion of L1PA7 and L1P3 in these genomes. Next, we evaluated the orthology of retrocopies in primate genomes and found 127 events specific to human lineage. We also explored 1000 Genomes Project data to detect polymorphic events (germinative retroCNVs) on human populations and found 17 events, present on the reference genome, absent in more than one individual. Conversely, we also investigated new insertions of mRNA retroduplications in the human genome, detecting 21 events absent to the human reference genome. Finally, we evaluated the existence of somatic retroCNVs and described seven putative somatic retrocopies. Despite their putative insignificance, we found that some of these shared, specie-specific and polymorphic events may be expressed per se and as chimeric transcripts within host genes. Taken together, we found that retrocopies are a great factor of genetic variation interspecie, intraspecie e intraindividual and may be affecting mammal evolution by creating reservoirs of potentially functional duplications

Duplicação genica é uma das principais forças levando a evolução dos genomas eucarioto. O impacto de duplicações gênicas/genômicas vem sendo investigado a muito tempo em humanos e outros primatas. Um segundo mecanismo de duplicação gênica, a retrotransposição baseada em RNA maduros, vem sendo menos estudada devido ao seu potencial menor de gerar cópias funcionais. No entanto, recentemente, publicações descreveram retrocópias funcionais em humanos, roedores e mosca de fruta. Nesta tese, para investigar sobre retrocópias causando variabilidade genética no genoma de primatas, nós desenvolvemos a implementamos os métodos para detectar estas inserções. Utilizando nove genomas e transcriptomas publicamente disponíveis (sete primatas e dois roedores) nós confirmamos um número similar, porém, com origem independente, de retrocópias em primatas e roedores. Nós também encontramos um enriquecimento de retrocópias no genoma de Platyrrhini, possivelmente explicado pela expansão de L1PA7 e L1P3 nestes genomas. Posteriormente, nós analisamos a ortologia de retrocópias no genoma de primatas e encontramos 127 eventos específicos à linhagem humana. Nós também exploramos dados do projeto 1000 Genomes para detectar retrocópias polimórficas (retroCNVs germinativos) e encontramos 17 eventos, presentes no genoma referência humano, mas ausentes em mais de um indivíduo. Similarmente, nós investigamos novas retroduplicações de mRNAs no genoma humano, detectando 21 eventos ausentes do genoma referência. Finalmente, investigamos a existência de retroCNVs somáticos e descrevemos sete possíveis retrocópias somáticas. Apesar de sua possível insignificância, nós encontramos que algumas retrocópias compartilhadas entre todos os primatas, espécie específicas, e polimórficas podem ser expressas per se ou como transcritos quiméricos com genes hospedeiros. Sobretudo, nós encontramos que retrocópias são um fator importante da variabilidade genética inter-espécie, intra-espécie e intra-indivíduo e podem estar influenciando a evolução de mamíferos ao criar reservatórios de duplicações potencialmente funcionais. / Gene duplication is a major driving force of evolution in eukaryotic genome. The impact of gene/genomic duplication has long been investigated in human and other primates. A second mechanism of gene duplication, retrotransposition, which is based on mature RNA, has been traditionally less studied due to their lower potential to generate functional copies. Recently, however, publications described functional retrocopies in humans, murines and drosophila. Here, to gain insights of the genetic variability arising from retrocopies on primate genomes, we developed and implemented the methods to detect these insertions. Using nine publicly available reference genomes and transcriptomes (seven primates and two rodents) we described a similar number independently arisen retrocopies in primates and rodents. We also found an enrichment of retrocopies in Platyrhinni genomes, putatively explained by the expansion of L1PA7 and L1P3 in these genomes. Next, we evaluated the orthology of retrocopies in primate genomes and found 127 events specific to human lineage. We also explored 1000 Genomes Project data to detect polymorphic events (germinative retroCNVs) on human populations and found 17 events, present on the reference genome, absent in more than one individual. Conversely, we also investigated new insertions of mRNA retroduplications in the human genome, detecting 21 events absent to the human reference genome. Finally, we evaluated the existence of somatic retroCNVs and described seven putative somatic retrocopies. Despite their putative insignificance, we found that some of these shared, specie-specific and polymorphic events may be expressed per se and as chimeric transcripts within host genes. Taken together, we found that retrocopies are a great factor of genetic variation interspecie, intraspecie e intraindividual and may be affecting mammal evolution by creating reservoirs of potentially functional duplications