Résumé: Les cellules germinales mâles remodèlent leur chromatine pour compacter leur noyau afin de protéger leur matériel génétique et assurer un transit optimal vers le gamète femelle. Il a été démontré que tous les spermatides de plusieurs mammifères, incluant l’homme et la souris, présentaient ce mécanisme de remodelage de la chromatine. Celui-ci est caractérisé par une augmentation transitoire de cassures d’ADN dont une quantité importante sont bicaténaires. Ce remodelage chromatinien a été étudié et semble être conservé chez plusieurs espèces, allant de l’algue à l’humain. Dans le contexte de la recherche fondamentale sur le phénomène de la spermiogenèse, il devient parfois très difficile d’investiguer certains aspects importants en vertu de l’impossibilité de réaliser des manipulations génétiques simples. Il est donc impératif de développer un nouveau modèle d’étude plus permissif afin de palier à ces difficultés encourues. Comme le processus de maturation des spores chez la levure à fission présente de grandes similitudes avec la spermiogenèse des mammifères, l’utilisation d’un modèle d’étude basé sur la sporulation de la levure à fission Schizosaccharomyces pombe a été proposée comme modèle comparatif de la spermatogenèse murine. À la suite de la synchronisation de la méiose de la souche S. pombe pat1-114, des analyses d’électrophorèse en champ pulsé (PFGE) et de qTUNEL ont permis de déterminer la présence de cassures bicaténaires transitoires de l’ADN lors de la maturation post-méiotique des ascospores nouvellement formés (t>7h). Des analyses par immunobuvardages dirigés contre le variant d’histones H2AS129p suggère la présence d’un remodelage chromatinien postméiotique dix heures suivant l’induction de la méiose, corroborant le modèle murin. Enfin, des analyses protéomiques couplées à l’analyse par spectrométrie de masse ont permis de proposer l’endonucléase Pnu1 comme candidat potentiellement responsable des cassures bicaténaires transitoires dans l’ADN des ascospores en maturation. En somme, bien que le processus de maturation des spores soit encore bien méconnu, quelques parallèles peuvent être tracés entre la maturation des ascospores de la levure à fission et la spermiogenèse des eucaryotes supérieurs. En identifiant un modèle simple du remodelage chromatinien au niveau de la spermiogenèse animale, on s’assurerait ainsi d’un outil beaucoup plus malléable et versatile pour l’étude fondamentale des événements survenant lors de la spermiogenèse humaine. / Abstract : The male germ cells undergo a major chromatin remodeling process in order to protect their genetic material and ensure optimal transit to the female gamete. It has been demonstrated that all spermatids from several mammals, including humans and mice, require this structural transition in order to reach their full maturity and fertilizing potential. This mechanism is characterized by a transient surge in DNA breaks, including a significant number of double-stranded breaks. This feature has been studied and seems conserved in many species, ranging from algae to humans. In the context of basic research on the phenomenon of spermiogenesis, it is sometimes very difficult to investigate important aspects due to the impossibility of carrying out simple genetic manipulations. A more flexible model to overcome the incurred difficulties is therefore needed. Since the process of ascospore maturation of the fission yeast presents great similarities with mammal spermiogenesis, the use of a model based on the sporulation of the fission yeast Schizosaccharomyces pombe has been proposed as a comparative model to the murine spermatogenesis. Following synchronization of meiosis in the S. pombe diploid strain pat1-114, pulsed field gel electrophoresis and qTUNEL assay were used to determine the presence of transient double-stranded breaks in DNA during the post-meiotic maturation of newly formed ascospores (t> 7h). Analyses by immunoblotting directed against the histone variant H2AS129p suggests the presence of a post-meiotic chromatin remodeling to t=10h, that may share similarities with higher eu karyotes. Finally, proteomic analyzes coupled with mass spectrometry allowed us to propose the Pnu1 endonuclease as a potential candidate responsible for the transient DNA double-stranded breaks during ascospore morphogenesis. In sum mary, although the spore maturation process is still under investigation, some parallels can be drawn between the maturation of ascospores of fission yeast s and higher eukaryotic spermio genesis. Thus, identifying a simple eukaryotic model for chromatin remodeling in animal spermiogenesis would ensure a flexible genetic tool to decipher the molecular events occurring during human spermiogenesis.

Comment les cellules établissent leurs formes et organisations internes est un problème biologique fondamental. Au cours de cette thèse, j’ai étudié le développement de la forme cellulaire et de la polarité chez la cellule de levure fissipare. Ces études sont fondées sur l’exploration de la façon dont les petites spores symétriques de levures se développent et s’organisent pour briser la symétrie pour la définition de leur tout premier axe de polarité. Dans une première partie, j’ai étudié les couplages entre la mécanique de surface de la paroi cellulaire des spores et la stabilité de domaines de polarité de Cdc42 qui contrôlent les aspects spatio-temporelles de la brisure de symétrie de ces spores. Dans une seconde partie, j’ai étudié les mécanismes par lesquels ces domaines de polarité contrôlent leur taille et l'adapte à la géométrie de la cellule, un processus vraisemblablement pertinents pour comprendre comment des domaines fonctionnels corticaux s’adaptent à la taille des cellules. Globalement, ces nouvelles recherches focalisant sur la façon dont les cellules développent dynamiquement leur forme et polarité de novo, permettent de mettre en évidence des couplages complexes dans la morphogenèse qui ne peuvent pas être testés en regardant les cellules à « l’état stationnaire» ou avec des outils génétiques. / How cells establish their proper shapes and organization is a fundamental biological problem. In this thesis, I investigated the dynamic development of cellular form and polarity in the rod-shape fission yeast cell. These studies are based on monitoring how small symmetric fission yeast spores grow and self-organize to break symmetry for the definition of their very first polarity axis. In a first part, I studied interplays between surface mechanics of the spore cell wall and the stability of Cdc42-based polarity domains which control spatio-temporal aspects of spore symmetry breaking. In a second part, I studied mechanisms by which these polarity domains control their width and adapt it to cell surface geometry, a process likely relevant to understand how functional cortical domains scale to cell size. Overall these novel investigations focusing on how cells dynamically develop their form and polarity de novo highlight complex feedbacks in morphogenesis that cannot be evidenced by looking at cells at “steady state” or with genetics.

The major aims of this thesis were to investigate the influence of i) antisense gene location relative to the target gene locus (?????location effect?????), ii) double-stranded RNA (dsRNA) formation, and iii) over-expression of host-encoded proteins on antisense RNA-mediated gene regulation. To test the location effect hypothesis, strains were generated which contained the target lacZ gene at a fixed location and the antisense lacZ gene at various genomic locations including all arms of the three fission yeast chomosomes and in close proximity to the target gene locus. A long inverse-PCR protocol was developed to rapidly identify the precise site of antisense gene integration in the fission yeast transformants. No significant difference in lacZ suppression was observed when the antisense gene was integrated in close proximity to the target gene locus, compared with other genomic locations, indicating that target and antisense gene co-localisation is not a critical factor for efficient antisense RNA-mediated gene suppression in vivo. Instead, increased lacZ down-regulation correlated with an increase in the steady-state level of antisense RNA, which was dependent on genomic position effects and transgene copy number. In contrast, convergent transcription of an overlapping antisense lacZ gene was found to be very effective at inhibiting lacZ gene expression. DsRNA was also found to be a central component of antisense RNA-mediated gene silencing in fission yeast. It was shown that gene suppression could be enhanced by increasing the intracellular concentration of non-coding lacZ RNA, while expression of a lacZ panhandle RNA also inhibited beta-galactosidase activity. In addition, over-expression of the ATP-dependent RNA-helicase, ded1, was found to specifically enhance antisense RNA-mediated gene silencing. Through a unique overexpression screen, four novel factors were identified which specifically enhanced antisense RNA-mediated gene silencing by up to an additional 50%. The products of these antisense enhancing sequences (aes factors), all have natural associations with nucleic acids which is consistent with other proteins which have previously been identified to be involved in posttranscriptional gene silencing.

In eukaryotes the genome adopts a non-random spatial organisation, which is important for gene regulation. However, very little is known about the driving forces behind nuclear organisation. In the simple model eukaryote fission yeast, Schizosaccharomyces pombe, it has been known for a long time that transcriptionally repressed heterochromatin localise to the nuclear membrane (NM); the centromeres attaches to spindle pole body (SPB), while the telomeres are positioned at the NM on the opposite side of the nucleus compared to the SPB. Studies presented in this thesis aimed at advancing our knowledge of nuclear organisation in Schizosaccharomyces pombe. We show that the heterochromatic mating-type region localises to the NM in the vicinity of the SPB. This positioning was completely dependent on Clr4, a histone methyl transferase crucial for the formation of heterochromatin. Additional factors important for localisation were also identified: the chromo domain protein Swi6, and the two boundary elements IR-L and IR-R surrounding this locus. We further identify two other chromo domain proteins; Chp1 and Chp2, as crucial factors for correct subnuclear localisation of this region. From these results we suggest that the boundary elements together with chromodomain proteins in balanced dosage and composition cooperate in organising the mating-type chromatin. Gene regulation can affect the subnuclear localisation of genes. Using nitrogen starvation in S. pombe as a model for gene induction we determined the subnuclear localisation of two gene clusters repressed by nitrogen: Chr1 and Tel1. When repressed these loci localise to the NM, and this positioning is dependent on the histone deacetylase Clr3. During induction the gene clusters moved towards the nuclear interior in a transcription dependent manner. The knowledge gained from work presented in this thesis, regarding nuclear organisation in the S. pombe model system, can hopefully aid to a better understanding of human nuclear organisation.

The major aims of this thesis were to investigate the influence of i) antisense gene location relative to the target gene locus (?????location effect?????), ii) double-stranded RNA (dsRNA) formation, and iii) over-expression of host-encoded proteins on antisense RNA-mediated gene regulation. To test the location effect hypothesis, strains were generated which contained the target lacZ gene at a fixed location and the antisense lacZ gene at various genomic locations including all arms of the three fission yeast chomosomes and in close proximity to the target gene locus. A long inverse-PCR protocol was developed to rapidly identify the precise site of antisense gene integration in the fission yeast transformants. No significant difference in lacZ suppression was observed when the antisense gene was integrated in close proximity to the target gene locus, compared with other genomic locations, indicating that target and antisense gene co-localisation is not a critical factor for efficient antisense RNA-mediated gene suppression in vivo. Instead, increased lacZ down-regulation correlated with an increase in the steady-state level of antisense RNA, which was dependent on genomic position effects and transgene copy number. In contrast, convergent transcription of an overlapping antisense lacZ gene was found to be very effective at inhibiting lacZ gene expression. DsRNA was also found to be a central component of antisense RNA-mediated gene silencing in fission yeast. It was shown that gene suppression could be enhanced by increasing the intracellular concentration of non-coding lacZ RNA, while expression of a lacZ panhandle RNA also inhibited beta-galactosidase activity. In addition, over-expression of the ATP-dependent RNA-helicase, ded1, was found to specifically enhance antisense RNA-mediated gene silencing. Through a unique overexpression screen, four novel factors were identified which specifically enhanced antisense RNA-mediated gene silencing by up to an additional 50%. The products of these antisense enhancing sequences (aes factors), all have natural associations with nucleic acids which is consistent with other proteins which have previously been identified to be involved in posttranscriptional gene silencing.

Comment les cellules établissent leurs formes et organisations internes est un problème biologique fondamental. Au cours de cette thèse, j’ai étudié le développement de la forme cellulaire et de la polarité chez la cellule de levure fissipare. Ces études sont fondées sur l’exploration de la façon dont les petites spores symétriques de levures se développent et s’organisent pour briser la symétrie pour la définition de leur tout premier axe de polarité. Dans une première partie, j’ai étudié les couplages entre la mécanique de surface de la paroi cellulaire des spores et la stabilité de domaines de polarité de Cdc42 qui contrôlent les aspects spatio-temporelles de la brisure de symétrie de ces spores. Dans une seconde partie, j’ai étudié les mécanismes par lesquels ces domaines de polarité contrôlent leur taille et l'adapte à la géométrie de la cellule, un processus vraisemblablement pertinents pour comprendre comment des domaines fonctionnels corticaux s’adaptent à la taille des cellules. Globalement, ces nouvelles recherches focalisant sur la façon dont les cellules développent dynamiquement leur forme et polarité de novo, permettent de mettre en évidence des couplages complexes dans la morphogenèse qui ne peuvent pas être testés en regardant les cellules à « l’état stationnaire» ou avec des outils génétiques. / How cells establish their proper shapes and organization is a fundamental biological problem. In this thesis, I investigated the dynamic development of cellular form and polarity in the rod-shape fission yeast cell. These studies are based on monitoring how small symmetric fission yeast spores grow and self-organize to break symmetry for the definition of their very first polarity axis. In a first part, I studied interplays between surface mechanics of the spore cell wall and the stability of Cdc42-based polarity domains which control spatio-temporal aspects of spore symmetry breaking. In a second part, I studied mechanisms by which these polarity domains control their width and adapt it to cell surface geometry, a process likely relevant to understand how functional cortical domains scale to cell size. Overall these novel investigations focusing on how cells dynamically develop their form and polarity de novo highlight complex feedbacks in morphogenesis that cannot be evidenced by looking at cells at “steady state” or with genetics.

In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions, we have analyzed the checkpoint in the fission yeast Schizosaccharomyces pombe using a single-molecule DNA combing assay, which allows us to unambiguously separate the contribution of origin and fork regulation towards replication slowing, and allows us to investigate the behavior of individual forks. Moreover, we have interrogated the role of forks interacting with individual sites of damage by using three damaging agents—MMS, 4NQO and bleomycin—that cause similar levels of replication slowing with very different frequency of DNA lesions. We find that the checkpoint slows replication by inhibiting origin firing, but not by decreasing fork rates. However, the checkpoint appears to facilitate replication of damaged templates, allowing forks to more quickly pass lesions. Finally, using a novel analytic approach, we rigorously identify fork stalling events in our combing data and show that they play a previously unappreciated role in shaping replication kinetics in response to DNA damage.

Les cellules dans la nature se développent dans un large éventail de formes, suivant divers modèles de croissance. Malgré l'importance de ces processus fondamentaux, la façon dont les cellules régulent leur croissance et leur morphogenèse est encore mal comprise. Dans cette thèse, j'ai exploré ces aspects, avec une approche principalement biomécanique, en concentrant mes investigations sur des cellules à paroi à croissance de pointe et en exploitant en particulier la levure fissipare Schyzosaccharomyces pombe. J'ai d'abord développé de nouvelles méthodes pour mesurer les paramètres mécaniques clés de la paroi cellulaire in vivo et à grande échelle, ce qui a permis les premières observations de la dynamique des parois cellulaires. Ceci a révélé que la paroi cellulaire est plus souple et très variable au niveau des pôles de croissance, et presque stable et plus rigide dans les sites non cultivés. Au cours de l'allongement, il existe une interaction entre la mécanique des parois et la croissance cellulaire, dont le contrôle actif permet l'expansion cellulaire tout en préservant l'intégrité des cellules. De plus, j'ai observé qu'il existe une forte corrélation entre la mécanique des parois cellulaires et la morphologie cellulaire, et des perturbations des propriétés de la paroi affectent directement l'établissement et la maintenance de la forme. Ensemble, mes résultats montrent que la régulation de la paroi est fondamentale dans la détermination de la dynamique cellulaire dans les cellules à parois épaissies. Globalement, cela suggère que l'observation dynamique de la mécanique de surface cellulaire est essentielle pour une compréhension complète des processus multifactoriels et complexes comme la croissance et la morphogenèse. / Cells in nature develop in a wide range of forms, following diverse growth patterns. Despite the importance of these fundamental processes, how cells regulate their growth and morphogenesis is still poorly understood. In this thesis, I explored these processes, focusing my investigations on tip growing walled cells and in particular, by exploiting the fission yeast Schyzosaccharomyces pombe, adopting a mainly biomechanical approach. To this aim, I first developed novel methods to measure key cell wall mechanical parameters in vivo and in large scale, which allowed the very first observations of cell wall dynamics. This revealed that the cell wall is softer and highly variable at growing poles, and almost stable and stiffer at non-growing sites. During elongation, there is an interplay between wall mechanics and cell growth, whose active control allows cell expansion while preserving cell integrity. In addition, I observed that there is a strong correlation between cell wall mechanics and cell morphology, and ectopic perturbations of wall properties directly affect shape establishment and maintenance. Together my results show that the regulation of wall mechanics is fundamental in the determination of cell dynamics in tip growing walled cells. Moreover, this suggests that dynamic observation of cell surface mechanics is crucial for a complete understanding of multifactorial and complex processes as growth and morphogenesis.

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