Les télomères garantissent la stabilité des extrémités chromosomiques. Une défaillance de protection entraine l’apparition de chromosomes dicentriques (c-à-d. possédant deux centromères) instables en mitose. La présence de chromosomes dicentriques est donc une source de mutagénèse et une menace pour la viabilité des cellules. Chez Saccharomyces cerevisiae, les dicentriques issus d’une fusion de télomères cassent préférentiellement à la fusion. Ce processus inexpliqué permet la régénération d’un caryotype normal et protège les chromosomes des conséquences néfastes d’une fusion accidentelle de leurs extrémités. Ce manuscrit explore les mécanismes moléculaires de cette voie de secours. La haute affinité de Rap1, pour ses sites consensus en tandem ou pour des séquences télomériques est suffisantes pour former un point chaud de cassure des chromosomes dicentriques. Une protéine hétérologue ayant aussi une haute affinité fixation pour sa séquence mime la présence de fusions de télomères, montrant que la forte affinité d’une protéine pour ses sites en tandem suffit à créer un point chaud. En l’absence de séquence télomérique interne, les chromosomes dicentriques cassent plutôt aux régions péricentromériques. Ces positions de cassure dépendent d’une force générée par les Condensines capable de relocaliser rapidement les centromères des chromosomes dicentriques au site de cytodiérèse avant leur cassure. De plus, le repliement des chromosomes dicentriques dépendant des Condensines est également nécessaire à une cassure préférentielle aux séquences fixant Rap1. En anaphase, ces séquences forment aussi un isolateur capable de séparer deux domaines chromosomiques. Ainsi, les télomères fusionnés sont secourus par un mécanisme qui favorise une capture des fusions et des régions péricentromériques par le septum dépendant de la conformation des chromosomes dirigées par les Condensines et par Rap1, Ces résultats suggèrent que les séquences télomériques fixant Rap1 bloquent l’extrusion de boucles par Condensine. De plus ce travail propose un nouvel outil pour l’étude de la condensation in vivo. Il montre également que la cassure des chromosomes dicentriques survient pendant la septation et que cytodiérèse n’est pas ralentie par la présence d’un pont de chromatine. / Telomeres ensure chromosome end stability. Failure to do so would lead to chromosome end fusions and the formation dicentric chromosomes (i.e. chromosomes with two centromeres) that are unstable in mitosis. Dicentrics are a threat to cell viability and a source of extensive mutagenesis. In Saccharomyces cerevisiae, dicentrics formed by telomere fusion preferentially break at the fusion. This unexplained process allows the recovery of a normal karyotype and protects the genome from the detrimental consequences of accidental telomere fusions. Here, I address the molecular basis of this rescue pathway. Simple tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. I also adress the mechanism allowing breakage at pericentromeric regions when dicentric do not bear telomeric sequences. During anaphase, Condensins generate forces sufficient to rapidly relocalize the centromeres to the bud neck and refold dicentrics prior their breakage by cytokinesis. This relocalisation is essential for breakage at pericentromeres. Moreover Condensin-dependent refolding is essential to the preferential breakage at telomere fusions, more generally at Rap1-bound arrays and which delimit insulated chromosomal domains. Thus, the rescue of fused telomeres results from a Condensin- and Rap1-driven chromosome conformation that favours fusion entrapment where the septum closes. These results suggest that Rap1-bound telomere sequences stall loop-extrusion by Condensins. In addition, this work provides a new and direct way to monitor Condensin activity on chromatin in live cells. It also shows that dicentric chromosomes are broken during septation and that cytokinesis is not delayed by chromatin bridges.

La terminaison de la transcription est essentielle, aussi bien pour assurer la formation de l’extrémité 3’ de transcrits fonctionnels que pour éviter les phénomènes d’interférence transcriptionnelle entre des régions transcrites adjacentes. Ceci est particulièrement important dans un génome compact comme celui de S. cerevisiae. La terminaison est aussi l’une des stratégies principales que la cellule emploie pour contrôler et limiter la transcription dite envahissante ou cachée. Chez S. cerevisiae, l’ARN polymérase II est responsable de la transcription des ARNm et de nombreuses classes d’ARN non codants tels que les sn(o)ARN et les CUT (Cryptic Unstable Transcripts). Ces derniers représentent une fraction importante des transcrits issus de la transcription cachée. Il existe deux voies canoniques de terminaison de la transcription par cette polymérase. Elles font intervenir le complexe de clivage et de polyadénylation, CPF-CF, notamment pour la terminaison des ARNm ou le complexe NNS pour la terminaison des sn(o)ARN et des CUT. Au cours de ma thèse j’ai étudié deux aspects de la terminaison de la transcription : 1) l’étude des motifs de recrutement du complexe NNS et 2) l’identification et la caractérisation d’une nouvelle voie de terminaison par le facteur Rap1. Les complexes CPF-CF et NNS agissent tous les deux en liant le transcrit naissant et l’ARN pol II. Le complexe NNS lie l’ARN naissant grâce à ses sous-unités Nrd1 et Nab3 qui reconnaissent des motifs spécifiques. Cependant, bien que la séquence de ces motifs soit maintenant connue, leur présence ne permet pas de définir de façon certaine un terminateur. En effet, le nombre de ces motifs varie beaucoup d’un terminateur à l’autre. Afin de mieux comprendre la structure des terminateurs ciblés par le complexe NNS et l’organisation des motifs liés par Nrd1 et Nab3, j’ai recherché les séquences impliquées dans la terminaison d’un CUT modèle en réalisant une mutagenèse aléatoire et j’ai identifié par SELEX des motifs de fixation optimale du dimère Nrd1-Nab3. Un second volet de ma thèse porte sur la caractérisation d’une nouvelle voie de terminaison de la transcription dépendante du facteur Rap1. Rap1 est important pour la structure des télomères et c’est aussi un facteur de transcription ciblant des centaines de promoteurs. Il active ou réprime l’initiation de la transcription notamment en recrutant des complexes de remodelage de la chromatine sur les promoteurs ciblés. De façon surprenante, le motif de fixation de ce facteur a été identifié dans des séquences capables de terminer la transcription isolées au laboratoire. Mes travaux ont permis de caractériser le mécanisme de terminaison par Rap1 et de distinguer cette voie des voies de terminaison canoniques. Ce facteur, lié à l’ADN, agit comme une barrière en bloquant la progression de l’ARN polymérase II par un mécanisme de « road-block ». Les polymérases ainsi arrêtées sont ciblées par une voie qui permet leur élimination lorsqu’elles sont bloquées par des dégâts sur l’ADN, impliquant leur ubiquitination et vraisemblablement leur dégradation par le protéasome. Les ARN libérés sont polyadénylés par la poly(A)-polymérase Trf4 et dégradés par l’exosome nucléaire. Ce mécanisme de terminaison est utilisé dans un contexte naturel puisque j’ai identifié des transcrits endogènes de S. cerevisiae terminés par cette voie. Nous proposons que la terminaison par Rap1 contribue au contrôle de la transcription envahissante. Ce facteur assurerait ainsi au niveau des promoteurs qu’il lie une double fonction de facteur de transcription et de protection de ces promoteurs contre l’interférence transcriptionnelle. / Transcription termination is essential, both for the 3’ end formation of functional transcripts and to avoid transcriptional interference between adjacent transcription units. This is particularly important in a compact genome such as S. cerevisiae. Termination is also one of the main strategies used by the cell to control and limit the “pervasive” or “hidden” transcription. In S. cerevisiae, RNA pol II is responsible for the transcription of the mRNAs and numerous non-coding RNA families such as the sn(o)RNAs and the CUTs (Cryptic Unstable Transcripts). CUTs represent a large fraction of the “pervasive” or “hidden” transcription. There are two canonical transcription termination pathways for this RNA polymerase. They involve the cleavage and polyadenylation complex (CPF-CF), in particular for the mRNAs termination, or the NNS complex for sn(o)RNAs and CUTs termination. During my thesis I studied two aspects or the transcription termination: 1) the motifs involved in the NNS complex recruitment on RNA and 2) the identification and the characterization of a new termination pathway by Rap1. CPF-CF and NNS complex are both recruited on the nascent transcript and on the RNA pol II. The NNS complex binds the RNA through its subunits Nrd1 and Nab3 which recognize specific motifs. Nonetheless, even if these motif sequences are now known, their presence does not elicit the certain identification of NNS dependent terminators. To clarify the NNS dependent terminator structure and the organization of the motifs bound by Nrd1 and Nab3 I looked for the sequences involved in a specific CUT termination doing a random mutagenesis experiment and I identified by SELEX the Nrd1-Nab3 dimer optimal binding motifs. A second part of my thesis concerns the characterization of a new transcription termination pathway dependent on the Rap1 factor. Rap1 is important for the telomere structure and it is also a transcription factor that targets hundred of promoters. It activates or represses transcription initiation recruiting chromatin remodeling complexes on the targeted promoters. Surprisingly, the Rap1 binding motifs have been identified among sequences eliciting termination isolated in the laboratory. My work has led to the characterization of the termination mechanism by Rap1 and distinguished this pathway from the two canonical pathways. This factor, bound to DNA, acts as a barrier blocking the RNA pol II progression by a road-block mechanism. These arrested polymerases are targeted by a pathway responsible for the elimination of RNA pol II blocked by DNA damages, implying their ubiquitination and probably their degradation by the proteasome. The released RNAs are polyadenylated by the poly(A) polymerase Trf4 and degraded by the nuclear exosome. This termination mechanism is used in a natural context since I identified S. cerevisiae endogenous transcripts terminated by this pathway. We propose that the Rap1 termination contributes to the pervasive transcription control. This factor could elicit, on its bound promoters, a double function of both transcription factor and protection of these promoters against transcriptional interference.

Cytoplasmic dynein is a microtubule-dependent motor protein which participates in numerous cellular processes. The motor complex consists of two heavy chains, intermediate, light intermediate and 3 families of light chains. Dynein is able to bind to these accessory chains as well as to regulatory proteins which enables the motor protein to fulfil such a variety of cellular processes. The associated light chains participate in long-distance organelle and vesicle transport in interphase and in chromosome segregation during mitosis. However, how these light chains control the activity of the motor protein is still unknown. In this study, I combine molecular genetics and live cell imaging to elucidate the role of the associated dynein light intermediate and light chains in dynein behaviour and early endosome (EE) motility in hyphal interphase cells as well as the anchorage of dynein to the microtubule (MT) plus-end in interphase and mitotic cells. I show that the dynein light intermediate chain (DLIC) as well as the light chain 2 (DLC2, Roadblock) are involved in dynein processivity and EE movement in interphase. The downregulation of either protein results in short hyphal growth which could be caused by a decreased runlength of EE and dynein. In addition, both proteins participate in dynein anchorage to the microtubule plus-end in interphase and mitosis as well as in spindle elongation during mitosis. Each protein causes a decrease of the motor protein dynein at MT plus-ends. Surprisingly, I found only minor or no defects in LC8 or Tctex mutants in the observed functions of dynein. LC8 seems to affect the dynein but not the EE runlength. In this case, dynein is still able to move into the bipolar MT array from where kinesin3 is able to take over EEs and move them towards the cell center. In contrast, Tctex has no effect on dynein or EE runlength or any other observed dynein function in hyphal cells. However, it causes a reduction in spindle elongation. Taken together, DLIC and DLC2 are important for dynein behaviour in long distance transport as well as in spindle positioning and elongation during mitosis. Furthermore, I studied the involvement of the dynein regulators Lis1 and NudE as well as the plus-end binding protein Clip1 (Clip-170 homologue) in the anchorage of dynein to the astral microtubule plus-ends during mitosis. The disruption of the anchorage complex at the astral MT plus-end causes a decrease in dynein number at this site and therefore slower spindle elongation in Anaphase B. Taken together, all three proteins are involved in anchorage of dynein to the astral microtubule tip and the subsequent spindle elongation. Furthermore, these findings also show that Ustilago maydis evolved two different mechanisms to anchor the motor protein to MT plus-ends in hyphal and mitotic cells. The plus-end binding protein Peb1 (EB1 homologue) and the dynein regulator dynactin mediate the dynein anchorage in hyphal cells whereas in mitotic cells the plus-ends binding protein Clip1 and the dynein regulators Lis1 and NudE anchor dynein to astral MT plus-ends.

Movement of motor proteins along cytoskeletal filaments is fundamental for various cellular processes ranging from muscle contraction over cell division and flagellar movement to intracellular transport. Not surprisingly, the impairment of motility was shown to cause severe diseases. For example, a link between impaired intracellular transport and neurodegenerative diseases, such as Alzheimer’s, has been established. There, the movement of kinesin-1, a neuronal motor protein transporting vesicles along microtubules toward the axonal terminal, is thought to be strongly affected by roadblocks leading to malfunction and death of the nerve cell. Detailed information on how the motility of kinesin-1 deteriorates in the presence of roadblocks and whether the motor has a mechanism to circumvent such obstructions is scarce. In this thesis, kinesin-1 motility was studied in vitro in the presence of rigor kinesin-1 mutants, which served as permanent roadblocks, under controlled single-molecule conditions. The 25 nm wide microtubule track, consisting of 13 individual protofilaments, resembles a multi-lane environment for transport by processive kinesin-1 motors. The existence of multiple traffic-lanes, allows kinesin-1 to utilize different paths for cargo transport and potentially also for the circumvention of roadblocks. However, direct observation of motor encounters with roadblocks has been intricate in the past, mainly due to limitations in both, spatial and temporal resolution. These limitations, intrinsic to fluorescent probes commonly utilized to report on the motor positions, originate from a low rate of photon generation (low brightness) and a limited photostability (short observation time). Thus, studying kinesin-1 encounters with microtubule-associated roadblocks requires alternative labels, which explicitly avoid the shortcomings of fluorescence and consequently allow for a higher localization precision. Promising candidates for replacing fluorescent dyes are gold nanoparticles (AuNPs), which offer an enormous scattering cross-section due to plasmon resonance in the visible part of the optical spectrum. Problematic, however, is their incorporation into conventionally used (fluorescence) microscopes, because illumination and scattered light have the same wavelength and cannot be separated spectrally. Therefore, an approach based on total internal reflection (TIR) utilizing a novel parabolically shaped quartz prism for illumination was developed within this thesis. This approach provided homogenous and spatially invariant illumination profiles in combination with a convenient control over a wide range of illumination angles. Moreover, single-molecule fluorescence as well as single-particle scattering were detectable with high signal-to-noise ratios. Importantly, AuNPs with a diameter of 40 nm provided sub-nanometer localization accuracies within millisecond integration times and reliably reported on the characteristic 8 nm stepping of individual kinesin-1 motors moving along microtubules. These results highlight the potential of AuNPs to replace fluorescent probes in future single-molecule experiments. The newly developed parabolic prism-type TIR microscope is expected to strongly facilitate such approaches in the future. To study how the motility of kinesin-1 is affected by permanent roadblocks on the microtubule lattice, first, conventional objective-type TIRF microscopy was applied to GFP-labeled motors. An increasing density of roadblocks caused the mean velocity, run length, and dwell time to decrease exponentially. This is explained by (i) the kinesin-1 motors showing extended pausing phases when confronted with a roadblock and (ii) the roadblocks causing a reduction in the free path of the motors. Furthermore, kinesin-1 was found to be highly sensitive to the crowdedness of microtubules as a roadblock decoration as low as 1 % sufficed to significantly reduce the landing rate. To study events, where kinesin-1 molecules continued their runs after having paused in front of a roadblock, AuNPs were loaded onto the tails of the motors. When observing the kinesin-1 motors with nanometer-precision, it was interestingly found that about 60 % of the runs continued by movements to the side, with the left and right direction being equally likely. This finding suggests that kinesin-1 is able to reach to a neighboring protofilament in order to ensure ongoing transportation. In the absence of roadblocks, individual kinesin-1 motors stepped sideward with a much lower, but non-vanishing probability (0.2 % per step). These findings suggest that processive motor proteins may possess an intrinsic side stepping mechanism, potentially optimized by evolution for their specific intracellular tasks.

Movement of motor proteins along cytoskeletal filaments is fundamental for various cellular processes ranging from muscle contraction over cell division and flagellar movement to intracellular transport. Not surprisingly, the impairment of motility was shown to cause severe diseases. For example, a link between impaired intracellular transport and neurodegenerative diseases, such as Alzheimer’s, has been established. There, the movement of kinesin-1, a neuronal motor protein transporting vesicles along microtubules toward the axonal terminal, is thought to be strongly affected by roadblocks leading to malfunction and death of the nerve cell. Detailed information on how the motility of kinesin-1 deteriorates in the presence of roadblocks and whether the motor has a mechanism to circumvent such obstructions is scarce. In this thesis, kinesin-1 motility was studied in vitro in the presence of rigor kinesin-1 mutants, which served as permanent roadblocks, under controlled single-molecule conditions. The 25 nm wide microtubule track, consisting of 13 individual protofilaments, resembles a multi-lane environment for transport by processive kinesin-1 motors. The existence of multiple traffic-lanes, allows kinesin-1 to utilize different paths for cargo transport and potentially also for the circumvention of roadblocks. However, direct observation of motor encounters with roadblocks has been intricate in the past, mainly due to limitations in both, spatial and temporal resolution. These limitations, intrinsic to fluorescent probes commonly utilized to report on the motor positions, originate from a low rate of photon generation (low brightness) and a limited photostability (short observation time). Thus, studying kinesin-1 encounters with microtubule-associated roadblocks requires alternative labels, which explicitly avoid the shortcomings of fluorescence and consequently allow for a higher localization precision. Promising candidates for replacing fluorescent dyes are gold nanoparticles (AuNPs), which offer an enormous scattering cross-section due to plasmon resonance in the visible part of the optical spectrum. Problematic, however, is their incorporation into conventionally used (fluorescence) microscopes, because illumination and scattered light have the same wavelength and cannot be separated spectrally. Therefore, an approach based on total internal reflection (TIR) utilizing a novel parabolically shaped quartz prism for illumination was developed within this thesis. This approach provided homogenous and spatially invariant illumination profiles in combination with a convenient control over a wide range of illumination angles. Moreover, single-molecule fluorescence as well as single-particle scattering were detectable with high signal-to-noise ratios. Importantly, AuNPs with a diameter of 40 nm provided sub-nanometer localization accuracies within millisecond integration times and reliably reported on the characteristic 8 nm stepping of individual kinesin-1 motors moving along microtubules. These results highlight the potential of AuNPs to replace fluorescent probes in future single-molecule experiments. The newly developed parabolic prism-type TIR microscope is expected to strongly facilitate such approaches in the future. To study how the motility of kinesin-1 is affected by permanent roadblocks on the microtubule lattice, first, conventional objective-type TIRF microscopy was applied to GFP-labeled motors. An increasing density of roadblocks caused the mean velocity, run length, and dwell time to decrease exponentially. This is explained by (i) the kinesin-1 motors showing extended pausing phases when confronted with a roadblock and (ii) the roadblocks causing a reduction in the free path of the motors. Furthermore, kinesin-1 was found to be highly sensitive to the crowdedness of microtubules as a roadblock decoration as low as 1 % sufficed to significantly reduce the landing rate. To study events, where kinesin-1 molecules continued their runs after having paused in front of a roadblock, AuNPs were loaded onto the tails of the motors. When observing the kinesin-1 motors with nanometer-precision, it was interestingly found that about 60 % of the runs continued by movements to the side, with the left and right direction being equally likely. This finding suggests that kinesin-1 is able to reach to a neighboring protofilament in order to ensure ongoing transportation. In the absence of roadblocks, individual kinesin-1 motors stepped sideward with a much lower, but non-vanishing probability (0.2 % per step). These findings suggest that processive motor proteins may possess an intrinsic side stepping mechanism, potentially optimized by evolution for their specific intracellular tasks.