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Morroll, Shaun Michael. "Mapping of yeast artificial chromosomes from Arabidopsis chromosome 5". Thesis, University of Nottingham, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308922.
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Bhuiyan, Hasanuzzaman. "Chromosome synapsis and recombination in yeast meiosis /". Stockholm : Institutionen för molekylärbiologi och funktionsgenomik, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-225.
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Almeida, Hugo Ricardo Noronha de. "Measuring chromosome-end fusions in fission yeast". Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2013. http://hdl.handle.net/10362/10629.
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Dissertation presented to obtain the Ph.D degree in Molecular BiologyThe ends of eukaryotic chromosomes are protected from illegitimate repair by structures called telomeres. These are comprised of specific DNA repeats bound by a specialized protein complex. When telomere function is compromised, chromosome ends fuse, generating chromosomal abnormalities and genomic instability.(...)
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Yang, Hui. "Chromosome dynamics and chromosomal proteins in relation to apoptotic cell death in yeast". Laramie, Wyo. : University of Wyoming, 2008. http://proquest.umi.com/pqdweb?did=1594496261&sid=1&Fmt=2&clientId=18949&RQT=309&VName=PQD.
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Smith, Victoria. "A molecular genetic analysis of yeast chromosome IX". Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239206.
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Priya, Vattem Padma. "Genomic distribution of histone H1 in budding yeast (Saccharomyces cerevisiae) : yeast chromosome III". Master's thesis, University of Cape Town, 2002. http://hdl.handle.net/11427/4324.
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Includes bibliographical references.The linker histone HI binds to the nucleosome and is essential for the organization of nucleosomes into the 30-nm filament of the chromatin. This compaction of DNA has a well-characterized effect on DNA function. In Saccharomyces cerevisiae, HHO 1 encodes a putative linker histone with very significant homology to histone HI. In vitro chromatin assembly experiments with recombinant Hho 1 p have shown that it is able to complex with the dinucleosomes in a similar manner to histone HI. It has also been reported that disruption of HHOl has little affect on RNA levels. A longstanding issue concerns the location of Hho 1 p in the chromatin and studies have shown using immunoprecipitation technique with anti-HA antibody, that Hho 1 p shows a preferential binding to rDNA sequences. In this project we have tried to confirm the above results in wild type cells, using immunopurifi ed anti rHho 1 p antibody.
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Brand, A. H. "Characterisation of a yeast silencer sequence". Thesis, University of Cambridge, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.377249.
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Lu, Wenqing. "Phenotypic impact of inversions in yeast genome". Electronic Thesis or Diss., Sorbonne université, 2021. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2021SORUS514.pdf.
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Les génomes sont des structures hautement dynamiques et les grandes variations structurelles (SVs) des chromosomes, telles que les inversions, contribuent à l'évolution des génomes et à l'adaptation des espèces. Il est essentiel de comprendre l'impact fonctionnel des inversions sur la diversité phénotypique, car il existe de plus en plus de preuves que les inversions joueraient un rôle important dans les variations phénotypiques. Afin d'expliquer l'impact phénotypique des inversions, nous avons choisi la levure de boulangerie comme modèle eucaryote unicellulaire dans notre travail. Sur la base d'un catalogue de 104 événements d'inversion caractérisés parmi un panel de 142 assemblages de génomes complets, nous nous sommes concentrés sur une inversion spéciale de 32kb localisée sur le chromosome XIV et qui est trouvée de manière récurrente dans diverses souches de Saccharomyces cerevisiae et S. paradoxus. Nous avons utilisé la méthodologie CRISPR/Cas9 d'édition du génome pour générer des bibliothèques de souches de S. cerevisiae contenant cette région dans les deux orientations par l'introduction de 2 cassures double-brin ((DSB pour Double-Strand Break) de l'ADN aux extrémités de cette région. Nous avons construit ce type d'inversions dans 3 souches hôtes présentant des fonds génétiques différents, S288C, YPS128 et Y12. Afin de tester les relations entre ce type de variation génétique et les traits phénotypiques, nous avons étudié l'impact fonctionnel des inversions pendant les cycles cellulaires sexuels et végétatifs, y compris le taux de croissance dans différentes conditions de culture, l'efficacité de la sporulation, l'efficacité des croisements et la viabilité des spores. Ce travail nous a permis de déterminer la contribution de cette inversion aux variations phénotypiques et son rôle adaptatif au cours de l'évolutionGenomes are highly dynamic structures and large-scale Structural Variations (SVs) of chromosomes such as inversions contribute to genome evolution and species adaptation. Understanding the functional impact of inversion on phenotypic diversity is essential because there are growing evidence that inversions play an important role in phenotypic variation. For the purpose of explaining the phenotypic impact of inversions, we choose yeast as single cell eukaryotic model in our work. Based on a catalogue of 104 inversion events characterized among a panel of 142 complete genome assemblies, we focused on a special 32kb inversion on chromosome XIV that is recurrently found in various strains of Saccharomyces cerevisiae and S. paradoxus. CRISPR/Cas9 methodology of genome editing is applied to generate strain libraries in S. cerevisiae containing this region in both orientations through the introduction of DNA double-strand breaks (DSBs) at the inversion boundaries. We constructed such inversion models in 3 different host strains with different genetic background, S288C, YPS128 and Y12. In order to test the relationships between this type of genetic variation and phenotypic traits, we investigated the functional impact of the inversions during both sexual and asexual cell cycles, including growth ratio in different culture conditions, sporulation efficiency, mating efficiency and spore viability. This work allows us to determine the contribution of inversions to phenotypic variations and their adaptive role during evolution
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Collins, Kimberly A. "Characterization of the budding yeast centromeric histone H3 variant, Cse4 /". Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/5011.
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Hassock, Sheila Ruth. "Physical and transcriptional mapping in the distal Xq28 region of the human X chromosome". Thesis, King's College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312021.
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Lee, Arianna. "Characterization of the Prp20 complex in yeast Saccharomyces cerevisiae". Thesis, McGill University, 1993. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=41654.
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Prp20, the Saccharomyces cerevisiae homolog to the mammalian regulator of chromosome condensation, RCC1, binds to double-stranded (ds) DNA in vitro through a multi-component complex. Three members of this complex bind GTP in vitro. The Prp20 complex specifically loses its ability to bind dsDNA during DNA replication as determined by an in vitro assay using cell extracts from arrested cdc mutants. This loss of dsDNA-binding activity does not affect the proper organization of the nucleoplasm as was the case for the prp20-1 and prp20-7 mutants, suggesting a segregation exists in the biochemical activities of the Prp20 protein. Detailed analysis of Prp20 demonstrates that specific and highly conserved amino acids coordinate these distinct activities of the Prp20 complex. These essential residues are mainly located in the second and the third repeats of the amino terminus and the last two repeats of the carboxyl terminus of Prp20. Furthermore, mutations in the last two repeats are suppressed by Gsp1, one of the GTP-binding components of the Prp20 complex, but not the mutations in the amino-terminus of Prp20.
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Chew, Joyce Siew Khim. "Isolation and characterization of Oreochromis niloticus DNA yeast artifical chromosome clones". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ36348.pdf.
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Brito, Ilana L. (Ilana Lauren). "Mechanisms for maintaining genomic integrity during chromosome segregation in budding yeast". Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/54633.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2009.Cataloged from PDF version of thesis.
Includes bibliographical references.
Maintaining genomic integrity is crucial for an organism's fitness and survival. Regulation of chromosome segregation requires complex surveillance mechanisms that vary for different loci within the genome. This thesis focuses on two complexes, monopolin (made up of Lrs4, Csml and Maml) and condensin, a protein complex required for chromosome condensation, and their roles in chromosome segregation during mitosis and meiosis. During mitosis, Lrs4-Csml and condensiin reside in the nucleolus where they regulate the maintenance and segregation of the budding yeast ribosomal DNA array, a highly repetitive and transcriptionally active locus. Here I show that Lrs4 and Csml bind the RENT complex at the non-transcribed space region 1 within the rDNA array and via cohesin or condensin inhibit unequal exchange between sister chromatids. This complex is released during anaphase, during which Lrs4 and Csml localize to kinetochores, where they play a role in mitotic chromosome segregation. Although their role in meiotic chromosome Here we show that Lrs4 and Csml collaborate with condensins at kinetochores to control mitotic and meiotic chromosome segregation. During meiosis, diploid cells must first segregate homologous chromosomes before sister chromatids can separate. Lrs4-Csml and condensin are required during the first meiotic division to bring about the co-segregation of sister chromatids towards one pole and for the binding of monopolin subunit Maml. In summary, I show here that condensins and Lrs4-Csml are required at various chromosomal locations to provide linkages between sister chromatids to promote high fidelity chromosome segregation.
by Ilana L. Brito.
Ph.D.
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Bähler, Jürg. "Meiotic chromosome structure, pairing and recombination in fission and budding yeast /". [S.l : s.n.], 1994. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.
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Gillett, Emily S. 1976. "The spindle checkpoint : Bubs, Mads, and chromosome-microtubule attachment in budding yeast". Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28934.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, February 2005.Includes bibliographical references.
(cont.) DNA damage response, we hypothesize that the perinuclear pool of Mad proteins may be required for spindle checkpoint-independent functions such as invoking metaphase arrest following DNA damage.
The high fidelity of chromosome transmission in eukaryotes is achieved, in part, by the activity of the spindle checkpoint. This checkpoint monitors the status of chromosome-microtubule attachments and delays the onset of anaphase until all kinetochores have formed stable bipolar connections to the mitotic spindle. We have characterized the localization of the Bub and Mad spindle checkpoint proteins in Saccharomyces cerevisiae. In metazoan cells, all known spindle checkpoint proteins are recruited to kinetochores during normal mitoses. In contrast, we show that whereas S. cerevisiae Bublp and Bub3p are bound to kinetochores early in mitosis as part of the normal cell cycle, Madlp and Mad2p are kinetochore-bound only in the presence of spindle damage or kinetochore lesions that interfere with chromosome-microtubule attachment. We propose that differences in the behavior of spindle checkpoint proteins in metazoan cells and budding yeast are due primarily to evolutionary divergence in spindle assembly pathways. The spindle checkpoint proteins Madlp and Mad2p exhibit perinuclear localization in both budding yeast and metazoans. We find that the perinuclear localization of Madlp is dependent on Myosin-like proteins Mlplp and Mlp2p, two proteins that link nuclear pore complexes to the interior of the nucleus. Deletion of either MLPI or MLP2 releases Mad proteins from the nuclear periphery and allows them to associate with kinetochores during early mitosis. Ectopic binding of Madlp to kinetochores does not dramatically alter cell cycle progression, nor does loss of Madlp from the nuclear periphery appear to impair spindle checkpoint activation. However, as the Mlps have been implicated in several cellular processes, such as the
by Emily S. Gillett.
Ph.D.
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Botsios, Sotirios. "Identification and analysis of chromosome-organising-clamp sites in the budding yeast S. cerevisiae". Thesis, University of Aberdeen, 2010. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=165975.
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The three-dimensional spatial architecture of chromosomes is integrally connected to chromatin function. Budding yeast telomeres cluster at the nuclear periphery, the ribosomal genes are localised to the nucleolus, tRNA genes may also tend to localise to the nucleolus or centromeres, while the later cluster near the spindle pole body. Recently, in the fission yeast Schizosaccharomyces pombe, a novel role has been revealed for the RNA polymerase III transcriptional apparatus, and TFIIIC in particular, in chromosome spatial organisation and boundary function. In this project, I investigate whether Saccharomyces cerevisiae Extra TFIIIC (ETC) sites, which bind the TFIIIC transcription factor but do not recruit RNA polymerase III, act to position chromosomal domains. I show that six of the eight known S. cerevisiae ETC sites localise predominantly at the nuclear periphery. An ETC site retains its tethering function when moved to a new chromosomal location. TFIIIC binding is necessary for peripheral localisation, since deleting the TFIIIC binding consensus ablates ETC site peripheral positioning. I find that any of the six TFIIIC subunits can drive peripheral tethering, suggesting that the TFIIIC complex is central to the positioning mechanism. Interestingly, anchoring of ETC sites to the nuclear periphery also requires Mps3, a Sad1-UNC-84 domain protein that spans the inner nuclear membrane. Moreover, I show that the mechanism of ETC site peripheral tethering requires chromatin remodelling proteins, and in particular Histone 3 - Lysine 56 (H3K56) acetylation. Finally, I investigate the biological function of ETC sites and examine the connection between this biological function and their ability to anchor at the nuclear periphery. In summary, TFIIIC and Mps3 together position a new class of genomic loci crucial for correct spatial organisation of S. cerevisiae chromosomes.
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Clift, Dean. "Regulation of chromosome segregation by Shugoshin and protein phosphatase 2A in budding yeast". Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4672.
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The accurate distribution of genetic information (chromosomes) during cell division is essential for the growth and proliferation of all living organisms. Errors in chromosome segregation in humans have been linked to cancer progression, infertility and developmental diseases. In my PhD I study how chromosome segregation is regulated in the genetically amenable budding yeast Saccharomyces cerevisiae. Since the mechanisms of chromosome segregation are highly conserved amongst eukaryotes, studies in yeast will provide a fundamental understanding of this process. Sgo1 is the budding yeast member of a highly conserved family of shugoshin proteins, which play a key role in chromosome segregation. My work characterizes a previously unidentified role of Sgo1 in inhibiting separase; an enzyme that triggers chromosome segregation by cleaving the cohesin protein complex that holds replicated chromosomes together. I demonstrate that this novel function of Sgo1 requires a specific form of Protein Phosphatase 2A (PP2ACdc55), an enzyme that itself is highly conserved amongst eukaryotes. I propose that PP2ACdc55 is a separase inhibitor that is employed by Sgo1 when sister chromatids are not under tension. Finally, I go on to initiate preliminary studies into the mechanism whereby PP2ACdc55 inhibits separase. In sum, this study uncovers an additional layer of separase regulation mediated by Sgo1 and PP2ACdc55 and therefore makes a significant contribution to our understanding of the all-or-nothing nature of chromosome segregation.
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Huang, Wenwen. "Theoretical Study of Pulled Polymer Loops as a Model for Fission Yeast Chromosome". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-232516.
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In this thesis, we study the physics of the pulled polymer loops motivated by a biological problem of chromosome alignment during meiosis in fission yeast. During prophase I of meiotic fission yeast, the chromosomes form a loop structure by binding their telomeres to the Spindle Pole Body (SPB). SPB nucleates the growth of microtubules in the cytoplasm. Molecular motors attached to the cell membrane can exert the force on the microtubules and thus pull the whole nucleus. The nucleus performs oscillatory motion from one to the other end of the elongated zygote cell. Experimental evidence suggests that these oscillations facilitate homologous chromosome alignment which is required for the gene recombination. Our goal is to understand the physical mechanism of this alignment. We thus propose a model of pulled polymer loops to represent the chromosomal motion during oscillations.
Using a freely-jointed bead-rod model for the pulled polymer loop, we solve the equilibrium statistics of the polymer configurations both in 1D and 3D. In 1D, we find a peculiar mapping of the bead-rod system to a system of particles on a lattice. Utilizing the wealth of tools of the particle system, we solve exactly the 1D stationary measure and map it back to the polymer system. To address the looping geometry, the Brownian Bridge technique is employed. The mean and variance of beads position along the loop are discussed in detail both in 1D and 3D. We then can calculate the three-dimensional statistics of the distance between corresponding beads from a pair of loops in order to discuss the pairing problem of homologous chromosomes. The steady-state shape of a three-dimensional pulled polymer loop is quantified using the descriptors based on the gyration tensor.
Beyond the steady state statistics, the relaxation dynamics of the pinned polymer loop in a constant external force field is discussed. In 1D we show the mapping of polymer dynamics to the well-known Asymmetric Simple Exclusion Process (ASEP) model. Our pinned polymer loop is mapped to a half-filled ASEP with reflecting boundaries. We solve the ASEP model exactly by using the generalized Bethe ansatz method. Thus with the help of the ASEP theory, the relaxation time of the polymer problem can be calculated analytically. To test our theoretical predictions, extensive simulations are performed. We find that our theory of relaxation time fit very well to the relaxation time of a 3D polymer in the direction of the external force field.
Finally, we discuss the relevance of our findings to the problem of chromosome alignment in fission yeast.
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Mason, Jacqueline Ann. "Analysis of the centromere of chromosome two of the fission yeast Schizosaccharomyces pombe". Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244719.
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Hamza, Akil. "Deciphering the Role of Aft1p in Chromosome Stability". Thesis, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/20639.
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The Saccharomyces cerevisiae iron-responsive transcription factor, Aft1p, has a well established role in regulating iron homeostasis through the transcriptional induction of iron-regulon genes. However, recent studies have implicated Aft1p in other cellular processes independent of iron-regulation such as chromosome stability. In addition, chromosome spreads and two-hybrid data suggest that Aft1p interacts with and co-localizes with kinetochore proteins, however the cellular implications of this have not been established. Here, we demonstrate that Aft1p associates with the kinetochore complex through Iml3p. Furthermore, we show that Aft1p, like Iml3p, is required for the increased association of cohesin with the pericentromere and that aft1Δ cells display sister chromatid cohesion defects in both mitosis and meiosis. Our work defines a new role for Aft1p in the sister chromatid cohesion pathway.
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Tanaka, Karo. "Characterisation of the murine homologue of the CIC-5 gene : a voltage-gated chloride channel implicated in human X-linked hereditary nephrolithiasis". Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302335.
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Rojas, Julie [Verfasser], i Barbara [Akademischer Betreuer] Conradt. "Role of Spo13 in regulating meiotic chromosome segregation in yeast / Julie Rojas ; Betreuer: Barbara Conradt". München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1234911310/34.
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Galland, Lanie Maria. "Investigation of chromosome size effect on the rate of crossovers in the meiotic yeast Saccharomyces cerevisiae". DigitalCommons@CalPoly, 2014. https://digitalcommons.calpoly.edu/theses/1193.
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Meiosis is a specialized type of cell division characterized by a single round of DNA replication and two rounds of chromosome segregation, ultimately resulting in four haploid cells. During meiosis I, chromosomes align and reciprocal recombination results in the formation of a crossover, creating the tension required to properly segregate homologs during the first round of meiosis.
Two mechanisms involved in regulating the occurrence of crossing over are assurance and interference. Crossover assurance describes the phenomenon that at least one crossover will form between each pair of homologous chromosomes during prophase I. Crossover interference, on the other hand, describes the nonrandom placement of crossovers between homologs, increasing the probability that a second crossover will occur at a discrete distance away from the first one.
In addition to assurance and interference, chromosome size may play a role in the rate of meiotic recombination during prophase I. As a result of crossover assurance, small chromosomes receive a minimum of one crossover, the obligate crossover. Assuming chromosome size does not influence the rate of recombination, pairs of large chromosomes should experience the same number of crossovers per base pair as small chromosomes. Previous studies have been inconsistent: Kaback et al. (1999) saw decreased rates of crossing over between large chromosomes relative to small ones, suggesting that crossover interference acts across a larger distance on large chromosomes. Turney et al. (2004), however, saw no such effect, suggesting that these findings may be site- or sequence-specific.
The current study used the Cre-loxP system to create translocated chromosomes, decreasing the size of chromosome VIII from 562 kb to 125 kb. The rate of crossing over was evaluated using nutrient marker genes that were inserted on the left arm of chromosome VIII to facilitate phenotypic detection of crossing over between homologous translocated chromosomes in comparison to crossing over between homologous nontranslocated chromosomes.
Translocated strains were attempted, though further testing suggests that the translocation itself may be lethal. In the future, we plan to further investigate the potential lethal nature of the translocation.
We also experienced difficulty in curing yeast cells of the Cre expression plasmid: as pSH47 was removed, translocated chromosomes reverted to nontranslocated chromosomes. In addition, crossing over in nontranslocated yeast, along with subsequent molecular analysis, revealed that one of the marker genes presumed to be on the left arm of chromosome VIII is, in fact, located on a different chromosome, preventing analysis of crossing over in this region. As a result, we were unable to proceed with current experimentation.
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Nachimuthu, B. T. "The Mec1/ATR-induced checkpoint regulates the Rdh54DNA translocase in response to chromosome breaks in yeast". Doctoral thesis, Università degli Studi di Milano, 2010. http://hdl.handle.net/2434/158427.
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Saccharomyces cerevisiae cells with a single double-strand break (DSB) activate the ATR/Mec1-dependent checkpoint response as a consequence of extensive ssDNA accumulation. The recombination factor Rdh54, a member of the Swi/Sfn2 family of helicase-like proteins, has been implicated in chromatin remodeling and is required for adaptation from a G2/M arrest induced by an unrepaired DSB.
Here we show that both the ATR/Mec1 and Chk2/Rad53 kinases phosphorylate Rdh54 protein in the presence of DNA damage, suggesting that the protein is regulated during the DNA damage response. ATR/Mec1 activity is required for Rdh54 localization to a DSB. We will present additional genetic and biochemical evidences on the physiological role of the phosphorylation modification and the role of Rad51 in this.
Our results will be considered in the context of cellular regulatory networks that coordinate the checkpoint response and recombination process in the presence of DSB lesions.
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Coffey, Alison Jane. "Physical mapping on the human X chromosome and its application to the positional cloning of the XLP gene". Thesis, King's College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327181.
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Yuen, Wing Yee Karen. "Identification and characterization of chromosome instability mutants in the yeast Saccharomyces cerevisiae and implications to human cancer". Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/31189.
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Chromosome instability (CIN) is a hallmark of cancers and may contribute to tumorigenesis. Many genes involved in maintaining chromosome stability are conserved in eukaryotes, and some are mutated in cancers. The goal of this thesis is to use Saccharomyces cerevisiae as a model to identify and characterize genes important for chromosome maintenance, investigate the relevance of CIN to cancer, and develop a strategy to identify candidate therapeutic target genes for selective killing of cancer cells. To systematically identify genes important for chromosome stability, nonessential gene deletion yeast mutants were examined using 3 complementary CIN assays. The chromosome transmission fidelity assay monitors loss of an artificial chromosome. The bimater assay monitors loss of heterozygosity at the mating type locus in homozygous diploid deletion mutants. The a-like faker assay detects loss of the MATα mating type locus in haploid deletion mutants. 293 CIN mutants were identified, including genes functioning in the chromosome or cell cycle, and genes not clearly implicated in chromosome maintenance, such as MMS22, MMS1, RTT101 and RTT107. Phenotypic, genetic and biochemical analyses of these 4 gene products indicate that they function in double strand break repair. They may form a ubiquitin ligase complex that regulates the level of some proteins, including Mms22p itself, during DNA damage response. Human homologues of 10 yeast CIN genes identified were previously shown to be mutated in cancers, suggesting that other human homologues are candidate cancer genes. 101 human homologues of yeast CIN genes were sequenced in a panel of colorectal cancers, identifying 20 somatic mutations in 8 genes. In particular, 17 mutations were found in 5 genes involved in sister chromatid cohesion. Further functional studies should reveal whether mutations in cohesion genes contribute to CIN in cancers. While CIN mutations may contribute to cancer, CIN cancer cells may become inviable when combined with another non-essential mutation, providing the basis for cancer cell-specific therapy. Mutations in CTF4, CTF18, and DCC1 in yeast cause synthetic lethality when combined with mutations in various CIN genes whose human homologues are mutated in cancers. Such analyses in yeast can propose potential drug targets in human for cancer therapy.Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Bizzari, Farid Fouad Mahmoud. "Cdc55 controls the balance of phosphatases to coordinate spindle assembly and chromosome disjunction during budding yeast meiosis". Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/5876.
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Meiosis is the process by which haploid gametes are produced from a diploid cell. It is a specialised form of cell division which involves one round of DNA replication followed by two rounds of chromosome segregation. Errors in the segregation process can give rise to aneuploidy, which can result in miscarriages and birth defects. In the first meiotic division homologous chromosomes are segregated, and sister chromatids are segregated in the second division. This is coordinated with two rounds of spindle microtubule assembly and disassembly. How these two processes are coordinated is unknown. In my PhD, I study the role of the protein phosphatase 2A (PP2A) regulatory subunit, Cdc55, in budding yeast meiosis. PP2A is a conserved heterotrimeric enzyme that has important roles in mitosis and meiosis. These roles are dictated by binding to either of its two regulatory subunits, Rts1 and Cdc55, in budding yeast . I show that Cdc55 is required for the proper assembly of a meiotic spindle in meiosis I, through the maintenance of the Cdc14 phosphatase in the nucleolus early in meiosis. In addition, Cdc55 is also required to limit the formation of PP2A complexes with the Rts1 regulatory subunit, and this is essential for the timely dissolution of sister chromatid cohesion. Thus, Cdc55 couples spindle assembly with chromosome segregation through its interactions with Cdc14 and PP2ARts1. Finally, I show some preliminary studies looking at the possible downstream effectors of Cdc14 that are important in this mechanism.
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Sousa, Da Costa Maria Judite. "Csi2 modulates microtubule dynamics and helps organize the bipolar spindle for proper chromosome segregation in fission yeast". Paris 6, 2013. http://www.theses.fr/2013PA066626.
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Proper chromosome segregation is of paramount importance for proper genetic inheritance. Defects in chromosome segregation can lead to aneuploidy, which is a hallmark of cancer cells. Eukaryotic chromosome segregation is accomplished by the bipolar spindle. Additional mechanisms such as the spindle assembly checkpoint and centromere positioning further help to ensure complete segregation fidelity. We present here the fission yeast csi2+. Csi2p localizes to the spindle poles, where it regulates mitotic microtubule dynamics, bipolar spindle formation, and subsequent chromosome segregation. The bipolar mitotic spindle contains many short dynamic microtubules of ~1 micron scale, this represents a challenge for live cell imaging because the typical maximum resolution of the optical microscope is ~λ/2 or ~300 nm. We developed a novel method to image short fission yeast mitotic microtubules using the thermosensitive reversible kinesin-5 cut7. 24ts to create monopolar spindles. Csi2-deletion (csi2Δ) results in abnormally long mitotic microtubules, high rate of transient monopolar spindles, and a subsequent high rate of chromosome segregation defects. As csi2Δ has multiple phenotypes, it enables estimates of the relative contribution of the different mechanisms to the overall chromosome segregation process. Centromere positioning, microtubule dynamics, and bipolar spindle formation can all contribute to chromosome segregation. Our data suggests that the major determinant of chromosome segregation defects may be microtubule dynamic defectsLa ségrégation correcte des chromosomes est processus fondamental pour maintenir la stabilité génomique. Des défauts de ségrégation sont souvent à l’origine de l’apparition de cellules aneuploïdes, caractéristique fréquemment observée dans les cellules cancéreuses. Dans les cellules eucaryotes, la ségrégation correcte des chromosomes est assurée par le fuseau mitotique. Des mécanismes de contrôle, tels que le point de contrôle mitotique et le bon attachement des centromères, sont mis en œuvre pour assurer la bonne ségrégation des chromosomes. Dans cette étude, nous avons pu établir chez le levure fissipare, que la protéine csi2, localisée aux pôles du fuseau mitotique, joue un rôle sur la dynamique des MTs mitotiques, dans la formation d’un fuseau mitotique intègre et par conséquent dans la ségrégation correcte des chromosomes. Les MTs composants le fuseau mitotique bipolaire sont dynamiques et de petite taille ~1µm ce qui représente un défis technique pour les imager, en effet, la résolution optique d’un microscope ~λ/2 est en général de 300nm. Nous avons développé une nouvelle approche pour imager les MTs mitotiques basée sur l’utilisation du mutant réversible thermosensible kinesin-5 cut7. 24ts, pour obtenir des cellules ayant des fuseaux monopolaires. Ainsi, nous avons pu mettre en évidence que la délétion de la protéine csi2 chez la levure S. Pombe était à l’origine d’un allongement de la longueur des microtubules mitotiques, d’une augmentation du nombre de cellules présentant un fuseau monopolaire et d’une augmentation des défauts de ségrégation des chromosomes. L’étude de l’implication de la protéine csi2 dans ces différents mécanismes nous a permis de mettre en évidence la contribution de chacun de ces mécanismes dans la bonne ségrégation des chromosomes. Nous proposons dans cette étude que le facteur déterminant à l’origine d’une ségrégation incorrecte des chromosomes serait majoritairement imputable à des défauts de régulation de la dynamique des microtubules
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Fleiss, Aubin. "Impact phénotypique des réarrangements chromosomiques et évolution des génomes de levures". Electronic Thesis or Diss., Sorbonne université, 2018. http://www.theses.fr/2018SORUS491.
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Nous avons cherché à évaluer l’impact des réarrangements chromosomiques sur l’évolution des génomes de levures selon deux approches. La première approche a consisté à retracer les réarrangements chromosomiques au cours de l’évolution des Saccharomycotina. Nous avons construit un arbre phylogénétique à partir de 66 génomes issus de bases de données publiques et reconstruit la structure des génomes ancestraux des 66 espèces. La comparaison des génomes ancestraux a permi d’inférer 5150 réarrangements chromosomiques passés. Nous avons montré que selon les clades considérés, les génomes évoluent plutôt par inversion ou par translocation et que les réarrangements chromosomiques et les mutations non-synonymes s’accumulent à un rythme coordonné au cours de l’évolution. La seconde approche a consisté à quantifier l’impact phénotypique des variations structurelles (SV) du génome en termes de taux de croissance végétative et de viabilité méiotique chez Saccharomyces cerevisiae. Nous avons développé une technique pour induire à façon des SV ciblés dans le génome de S. cerevisiae, en induisant deux coupures simultanées dans le génome de S. cerevisiae avec CRISPR/Cas9 et à guider la réparation des cassures par recombinaison homologue avec des oligonucléotides chimériques. Nous avons alors adapté cette technique pour induire en une étape un grand nombre de SV aléatoires. L’impact phénotypique des SV obtenus a été quantifié en méiose et en croissance végétative. Ces travaux montrent que même des réarrangements chromosomiques balancés n’affectant aucune phase codante génèrent une grande diversité phénotypique qui participe à l’adaptation des organismes à leur environnementThe aim of this work was to assess the impact of chromosomal rearrangements on the evolution of yeast genomes with two approaches. The first approach consisted in retracing past rearrangements during the evolution of Saccharomycotina yeast genomes. We have built a phylogenetic tree of 66 genomes gathered from public databases, then reconstructed the structure of all ancestral genomes of these species. By comparing the structure of reconstructed ancestral genomes, we have inferred 5150 past rearrangements. We showed that depending on the clades, genomes tend to evolve mostly by inversion or by translocation. In addition, we showed that chromosomal rearrangements and non-synonymous mutations tend to accumulate at a coordinated pace during evolution. The second approach aimed at quantifying the phenotypic impact of structural variations of chromosomes (SVs) in terms of vegetative growth and meiotic viability in Saccharomyces cerevisiae. We developed a technique to induce easily targeted SVs in the genome of S. cerevisiae by inducing two chromosomal breaks with CRISPR/Cas9 and providing the cells with chimerical donor oligonucleotides to repair the split chromosomes by homologous recombination. We have then adapted this technique to induce multiple random SVs in a single step. The phenotypic impact of obtained variants on vegetative growth and on spore viability was quantified. These results show that even balanced chromosomal rearrangements that do not affect coding sequence generate a wide phenotypic diversity that contributes to the adaptation of organisms to their environment
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Wee, Boon Yu. "Analysis of mechanisms of chromosome restoration in response to a site-specific double-strand break in fission yeast". Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432262.
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Benzi, Giorgia. "Rôle de la kinase Mps1 dans la segregation chromosomique chez S. cerevisiae". Thesis, Montpellier, 2020. http://www.theses.fr/2020MONTT033.
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Mps1 est une protéine kinase conservée qui, pendant la mitose, corrige les attachements inappropriés entre kinétochores et microtubules, assurant ainsi la bi-orientation des chromosomes. Cependant, ses cibles critiques dans ce processus restent largement inconnues. Mps1 contrôle également le « spindle assembly checkpoint » (SAC), qui arrête la ségrégation des chromosomes en métaphase jusqu'à ce que la bi-orientation soit atteinte. Son rôle dans l'activation du SAC est antagonisé par la phosphatase PP1 et implique la phosphorylation de la protéine d’échafaudage au kinétochore KNL1/Spc105, qui à son tour recrute la kinase Bub1 pour favoriser l'assemblage des complexes effecteurs du SAC. Une question cruciale est si la correction des erreurs et l'activation du SAC font partie d'une seule et même voie ou des voies séparables.Au cours de ma thèse, j'ai caractérisé un nouveau mutant thermosensible, mps1-3, qui est défectueux dans la bi-orientation des chromosomes et la signalisation du SAC. La mutation mps1-3 change une sérine conservée dans le domaine kinase en phénylalanine et, de façon surprenante, la protéine Mps1-3 a une activité catalytique accrue par rapport à la protéine sauvage. Inversement, la protéine ne se localise pas aux kinétochores, ce qui suggère que les défauts mitotiques du mutant mps1-3 proviennent du manque de phosphorylation des cibles critiques aux kinétochores.Grâce à un crible génétique, j'ai identifié des mutations qui supprimaient la thermosensibilité du mutant mps1-3 en affectant l'interaction entre la protéine du kinétochore Spc105/KNL1 et la phosphatase PP1, et j’ai démontré que des niveaux réduits de PP1 aux kinétochores sous-tendent la suppression. Remarquablement, les suppresseurs restauraient à la fois la signalisation du SAC et la bi-orientation des chromosomes, ce qui suggère que Mps1 contrôle les deux processus par le même mécanisme moléculaire. Nous avons proposé que la phosphorylation de Spc105/KNL1, qui conduit au recrutement de Bub1 aux kinétochores et est antagonisée par la phosphatase PP1, est une fonction cruciale de Mps1 dans la correction des liaisons inappropriées kinétochores-microtubules comme pour l'activation du SAC. De façon cohérente, la phosphorylation de Spc105 et la localisation de Bub1au kinétochore étaient affectées dans les cellules mps1-3 et restaurées dans les suppresseurs susmentionnés. De plus, le recrutement artificiel de Bub1 à Spc105 supprimait les défauts de ségrégation des cellules mutantes mps1-3. Ainsi, une conclusion principale de mon travail de thèse est que le SAC et la correction d'erreurs sont déclenchés par un seul dispositif sensoriel impliquant Mps1 et antagonisé par PP1.Grâce au même crible génétique ci-dessus, j'ai également trouvé des suppresseurs portant des mutations dans la protéine F-box Grr1, qui fait partie du complexe ubiquitine-ligase SCF. Mes données préliminaires indiquent que Grr1 se localise aux kinétochores, suggérant que le complexe SCFGrr1 pourrait être un nouvel acteur dans le contrôle de la bi-orientation des chromosomes. Enfin, j'ai pu isoler des suppresseurs intragéniques, qui portent une seconde mutation dans MPS1 et restaurent les fonctions mitotiques de la protéine Mps1-3. Les données recueillies jusqu'à présent indiquent que cette classe de mutations, contrairement aux suppresseurs extragéniques ci-dessus, rétablit la localisation de Mps1 au kinétochore. Étant donné que Mps1 régule son propre turnover aux kinétochores par autophosphorylation, nous avions émis l’hypothèse que les suppresseurs puissent rétablir la localisation de Mps1-3 au kinétochore en diminuant son activité catalytique. Étonnamment, bien que la plupart des mutations suppressives réduisaient la capacité de Mps1-3 à phosphoryler une cible exogène, elles n'affectaient pas de façon significative l'autophosphorylation, ce qui suggère que la phosphorylation dépendante de Mps1 d'une protéine non identifiée au kinétochore pourrait influencer le turnover de Mps1Mps1 is a conserved protein kinase that during mitosis corrects improper kinetochore–microtubule attachments, thereby ensuring chromosome biorientation and balanced chromosome segregation. Yet, its critical phosphorylation targets in this process remain largely elusive. Mps1 also controls the spindle assembly checkpoint (SAC), which halts chromosome segregation in metaphase until biorientation is attained. Its role in SAC activation is antagonised by the PP1 phosphatase and involves phosphorylation of the kinetochore scaffold Knl1/Spc105, which in turn recruits the Bub1 kinase to promote assembly of SAC effector complexes. A crucial question is whether error correction and SAC activation are part of a single or separable pathways.During my PhD thesis, I characterized a novel temperature sensitive mutant, mps1-3, that is defective in chromosome biorientation and SAC signaling. The mps1-3 mutation changes a conserved serine in the kinase domain to phenylalanine, and, surprisingly, the Mps1-3 protein has enhanced catalytic activity compared to the wild type protein. Conversely, the protein does not localize at kinetochores, suggesting that the mps1-3 mitotic defects stem from the lack of phosphorylation of critical kinetochore substrates.Through an unbiased screen for spontaneous suppressors of the temperature-sensitivity of the mps1-3 mutant, I found suppressing mutations that affected the interaction between the kinetochore protein Spc105/KNL1 and the phosphatase PP1, suggesting that reduced levels of PP1 at kinetochores underlie the suppression of the temperature-sensitivity of mps1-3 cells. Importantly, the suppressors restored both SAC signaling and proper chromosome bi-orientation, suggesting that the same molecular mechanism underlies the role of Mps1 in both processes. We have proposed that phosphorylation of Spc105/KNL1, which leads to Bub1 kinetochore recruitment and is antagonized by the phosphatase PP1, is a crucial function of Mps1 in the correction of improper kinetochore-microtubule attachments as it is for SAC activation. Consistently, Spc105 phosphorylation and Bub1 kinetochore localization were affected in mps1-3 cells and restored in the aforementioned suppressors. Moreover, artificial recruitment of Bub1 to Spc105 suppressed the chromosome segregation defects of mps1-3 mutant cells.Thus, a main conclusion of my thesis work is that SAC and error correction are triggered by a single sensory device involving Mps1 and antagonized by PP1.Through the same genetic screen, I also found suppressors carrying mutations in the F-box protein Grr1 that is part of the SCF ubiquitin-ligase complex. My preliminary data indicate that Grr1 might localize at kinetochores, suggesting that the SCFGrr1 complex could be a novel player in the control of chromosome bi-orientation at kinetochores. Finally, I could isolate intragenic suppressors, carrying a second mutation in MPS1 that restored the mitotic functions of the Mps1-3 protein. The data gathered so far indicate that this class of suppressing mutations, unlike the extragenic suppressors above, re-establish Mps1 kinetochore localization. Since Mps1 regulates its own turnover at kinetochores by autophosphorylation, we postulated that the elevated kinase activity of the Mps1-3 mutant protein might be responsible for its displacement from kinetochores and the suppressors might re-establish kinetochore localization of Mps1-3 by decreasing its kinase activity. Surprisingly, although most of the suppressing mutations reduced the ability of Mps1-3 to phosphorylate an exogenous substrate, they did not significantly affect autophosphorylation, suggesting that Mps1-dependent phosphorylation of an unidentified kinetochore protein could influence Mps1 residence time
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Lazar-Stefanita, Luciana. "Functional reorganization of the yeast genome during the cell cycle". Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066400/document.
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Des décennies d'études ont montré que la structure de la chromatine est étroitement liée aux processus métaboliques de l'ADN. Une bonne organisation des chromosomes tout au long du cycle cellulaire est particulièrement importante pour assurer le maintien de l'intégrité de l'ADN. Le but de mon projet de doctorat était de caractériser dans quelle mesure la réorganisation de la chromatine pendant le cycle cellulaire pourrait influencer la stabilité des chromosomes. Pour ce faire, nous avons d'abord effectué une étude complète de la réorganisation des chromosomes de la levure modèle Saccharomyces cerevisiae pendant tout un cycle cellulaire. Ce travail, en plus de récapituler les caractéristiques chromosomiques attendues, a conduit à la caractérisation de structures chromosomiques particulières, telle qu'une boucle d'ADN reliant l'ADNr et les centromères. Le rôle des complexes SMC et des microtubules a été étudié en profondeur. Une deuxième partie de mon travail a porté sur la description de l'organisation de la chromatine de cellules qui ont quitté le cycle cellulaire prolifératif et sont entrées en quiescence. Nous avons ainsi caractérisé le statut dense de l'hétérochromatine silencieuse dans des loci spécifiques tels que les télomères. Enfin, nous avons essayé de mieux comprendre l'interaction fonctionnelle entre la stabilité chromosomique et l'architecture 3D du génome durant la réplication en étudiant la stabilité génomique à des sites de pause de réplication. Nos résultats indiquent une adaptabilité frappante des structures de réplication sous différentes contraintes. Le travail futur vise à cartographier les réarrangements chromosomiques dépendants de la réplicationDecades of studies showed that chromatin structure is tightly linked to DNA related metabolic processes, through the dynamic regulation of a myriad of molecular factors. The proper organization of chromosomes is notably important to ensure the maintenance of DNA integrity during cell cycle progression. Using the model S. cerevisiae, the aim of my PhD project was to characterize to which extent chromatin reorganization during the cell cycle may influence chromosome stability. To do so, we first generated a comprehensive genome-wide study of the reorganization of yeast’s chromosomes during an entire cell cycle. This work, besides recapitulating expected chromosomal features of the replication and mitotic stages, led to the characterization of peculiar chromosome structures such as a DNA loop bridging the rDNA and the centromeres. The role of structural maintenance of chromosomes (SMC) complexes and of microtubules were thoroughly investigated. A second part of my work focused on describing features of the chromatin organization of cells that exited the proliferative cell cycle and entered into quiescence. We characterized the dense status of silenced heterochromatin at specific loci, such as telomeres, in relation to the silent information regulators (SIRs). Finally, we tried to achieve a better understanding of the functional interplay between chromosome stability and the 3D genome architecture during replication, by investigating the genomic stability at replication pausing sites. Overall, our results point at a striking plasticity of replication structures to different stresses. Future work aims to map replication-dependent chromosomal rearrangements on the genomic maps
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Kaochar, Salma. "Fusion of Inverted Repeats Leads to Formation of Dicentric Chromosomes that Cause Genome Instability in Budding Yeast". Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/204271.
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Large-scale changes are common in genomes, and are often associated with pathological disorders. In the work presented in this dissertation, I provide insights into how inverted repeat sequences in budding yeast fuse during replication. Fusion leads to the formation of dicentric chromosomes, a translocation, and other chromosomal rearrangements.Using extensive genetics and some molecular analyses, I demonstrate that dicentric chromosomes are key intermediates in genome instability of a specific chromosome in budding yeast. I provide three pieces of evidence that is consistent with this conclusion. First, I detect a recombination fusion junction that is diagnostic of a dicentric chromosome (using a PCR technique). Second, I show a strong correlation between the amount of the dicentric fragment and the frequency of instability of the entire chromosome. Third, I demonstrate that a mutant known to stabilize dicentric chromosomes suppress instability. Based on these observations, I conclude that dicentric chromosomes are intermediates in causing genome instability in this system.Next, we demonstrate that fusion of inverted repeats is general. Both endogenous and synthetic nearby inverted repeats can fuse. Using genetics, I also show that many DNA repair and checkpoint pathways suppress fusion of nearby inverted repeats and genome instability. Based on our analysis, we propose a novel mechanism for fusion of inverted repeats that we term `faulty template switching.'Lastly, I discuss two genes that are necessary for fusion of nearby inverted repeats. I identified a mutant of the Exonuclease 1 (Exo1) and a mutant of anaphase inhibitor securin (Pds1) that suppress nearby inverted repeat fusion and genome instability. Studies of Exo1 and Pds1 provide us with insights into the molecular mechanisms of fusion.Our finding that nearby inverted repeats can fuse to form dicentric chromosomes that lead to genome instability may have great implications. The generality of this fusion reaction raises the possibility that dicentric chromosomes formed by inverted repeats can lead to genome instability in mammalian cells, and thereby contribute to a cancer phenotype.
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Lazar-Stefanita, Luciana. "Functional reorganization of the yeast genome during the cell cycle". Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066400.pdf.
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Des décennies d'études ont montré que la structure de la chromatine est étroitement liée aux processus métaboliques de l'ADN. Une bonne organisation des chromosomes tout au long du cycle cellulaire est particulièrement importante pour assurer le maintien de l'intégrité de l'ADN. Le but de mon projet de doctorat était de caractériser dans quelle mesure la réorganisation de la chromatine pendant le cycle cellulaire pourrait influencer la stabilité des chromosomes. Pour ce faire, nous avons d'abord effectué une étude complète de la réorganisation des chromosomes de la levure modèle Saccharomyces cerevisiae pendant tout un cycle cellulaire. Ce travail, en plus de récapituler les caractéristiques chromosomiques attendues, a conduit à la caractérisation de structures chromosomiques particulières, telle qu'une boucle d'ADN reliant l'ADNr et les centromères. Le rôle des complexes SMC et des microtubules a été étudié en profondeur. Une deuxième partie de mon travail a porté sur la description de l'organisation de la chromatine de cellules qui ont quitté le cycle cellulaire prolifératif et sont entrées en quiescence. Nous avons ainsi caractérisé le statut dense de l'hétérochromatine silencieuse dans des loci spécifiques tels que les télomères. Enfin, nous avons essayé de mieux comprendre l'interaction fonctionnelle entre la stabilité chromosomique et l'architecture 3D du génome durant la réplication en étudiant la stabilité génomique à des sites de pause de réplication. Nos résultats indiquent une adaptabilité frappante des structures de réplication sous différentes contraintes. Le travail futur vise à cartographier les réarrangements chromosomiques dépendants de la réplicationDecades of studies showed that chromatin structure is tightly linked to DNA related metabolic processes, through the dynamic regulation of a myriad of molecular factors. The proper organization of chromosomes is notably important to ensure the maintenance of DNA integrity during cell cycle progression. Using the model S. cerevisiae, the aim of my PhD project was to characterize to which extent chromatin reorganization during the cell cycle may influence chromosome stability. To do so, we first generated a comprehensive genome-wide study of the reorganization of yeast’s chromosomes during an entire cell cycle. This work, besides recapitulating expected chromosomal features of the replication and mitotic stages, led to the characterization of peculiar chromosome structures such as a DNA loop bridging the rDNA and the centromeres. The role of structural maintenance of chromosomes (SMC) complexes and of microtubules were thoroughly investigated. A second part of my work focused on describing features of the chromatin organization of cells that exited the proliferative cell cycle and entered into quiescence. We characterized the dense status of silenced heterochromatin at specific loci, such as telomeres, in relation to the silent information regulators (SIRs). Finally, we tried to achieve a better understanding of the functional interplay between chromosome stability and the 3D genome architecture during replication, by investigating the genomic stability at replication pausing sites. Overall, our results point at a striking plasticity of replication structures to different stresses. Future work aims to map replication-dependent chromosomal rearrangements on the genomic maps
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Barbosa, Anne Caroline. "Using chromosome engineering on a natural isolate of the fission yeast, Schizosaccharomyces pombe, to investigate the epigenetic inheritance of the kinetochore". Thesis, University of Nottingham, 2018. http://eprints.nottingham.ac.uk/49006/.
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In many eukaryotes, kinetochores may form over a variety of unrelated centromeric sequences. This fact has led to the idea that an epigenetic process determines kinetochore location. To investigate the nature of this epigenetic process, I have established a system that allows the manipulation of the chromosomal centromeric DNA in a genetically tractable model organism, Schizosaccharomyces pombe. The system enables the definition of the relationship between centromeric DNA size, sequence, chromosome position and function. I have used this system to measure how binding of the conserved kinetochore protein Cnp1 (CENP-A homolog) varies as a function of the amount, sequence and position of the centromeric DNA. In humans, cytogenetic data suggests that the number of centromere-specific CENP-A nucleosomes at each centromere is approximately uniform regardless of the sequence and length of the centromeric DNA. These observations suggest that the number of these centromere-specific nucleosomes is tightly regulated. I set out to test whether such mechanism is evolutionarily conserved in the fission yeast S. pombe. I did this by manipulating the amount of the centromeric DNA at one centromere and then measuring the amount of Cnp1 bound to it. The results showed that in S. pombe, the amount of bound Cnp1 is proportional to the amount of centromeric DNA and thus the relationship between centromeric DNA size and CENP-A binding differs from humans. During these measurements, I observed that the size and sequence of the centromeric DNA do have a role in determining Cnp1 binding to centromeric DNA but, as described by others, it is not sufficient and sometimes not necessary for functional centromere formation. The requirement of the kinetochore protein Swi6 for neo-centromere formation but not for the maintenance of a pre-established centromere was also confirmed.
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Mercy, Guillaume. "L'organisation 3D des chromosomes synthétiques de levure". Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS034/document.
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Le projet international de synthèse des chromosomes de S. cerevisiae (projet Sc2.0) a débuté il y a une dizaine d'années en suivant des principes établis par le Pr. Jef Boeke. Les chromosomes synthétiques ont été conçus pour augmenter la stabilité du génome en supprimant toutes les séquences répétées (ARNt, éléments transposables...), tout en y ajoutant un système d'évolution inductible dépendant du système Cré/LoxP (système SCRaMbLE), permettant de générer rapidement des réarrangements chromosomiques. Bien que le design du projet Sc2.0 soit très conservateur en ce qui concerne le contenu des gènes, la suppression de plusieurs classes de séquences répétées peut affecter l'organisation du génome et potentiellement altérer les fonctions cellulaires. En utilisant la méthode de capture de conformation de chromosome couplée au séquençage de seconde génération (Hi-C), mon objectif a été de caractériser l'organisation 3D des génomes des souches synthétiques et évoluées. À ce jour, huit chromosomes (syn I, II, III, V, VI, IX-R, X et XII) ont été entièrement assemblés séparément. En utilisant les souches contenant un ou plusieurs de ces chromosomes, nous avons pu montrer que leur organisation génomique n'est globalement pas affectée par leur présence. Quelques exceptions subsistent, avec synIII dont les cassettes HML et HMR ont été retirées, et synXII d'où l'ADNr a été déplacé sur un autre chromosome. À ce stade, nous concluons que l'ADN répétitif dispersé ne conduit pas la conformation moyenne globale du génome de S. cerevisiae. Nous avons aussi exploité les cartes de contacts pour identifier les réarrangements dans les souches SCRaMbLEThe international project Sc2.0 started 10 years ago by the Pr. Jef Boeke aims to build a fully synthetic genome of S. cerevisiae which increases the genome stability by removing all repeated sequences (tRNA, transposable elements, etc.), and implements SCRaMbLE (for Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution), an inducible, high-throughput chromosome rearrangement system. This design is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes. However, it may affect genome organization and potentially alter cellular functions. To determine wether those modifications affected the three-dimensional conformation of synthetic chromosmes, we investigated it using chromosomes conformation capture coupled to second generation sequencing method (Hi-C). Currently, eight synthetic chromosomes (synI, synII, synIII, synV, synVI, synIX-R, synX et synXII) have been fully assembled. Using these strains we observed that the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploited the contact maps to detect rearrangements induced in these SCRaMbLE strains
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Fauque, Lydia. "Mécanismes Moléculaires de la Condensation Mitotique des Chromosomes chez la levure Schizosaccharomyces pombe". Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10179/document.
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La condensation mitotique des chromosomes est l'un des mécanismes assurant la transmission fidèle de l'information génétique. Les complexes condensines et leur association à la chromatine sont nécessaires à cette condensation. Cependant, les mécanismes par lesquels ces complexes s'associent aux chromosomes et contribuent à leur condensation sont mal compris. L'objectif de ma thèse était d'identifier et de caractériser des facteurs de condensation encore inconnus collaborant avec le complexe condensine présent chez S. pombe. Par un crible génétique, nous avons recherché des mutants viables lorsque le complexe condensine est complètement fonctionnel mais morts lorsque ce complexe est partiellement défectif. Nous avons ainsi identifié 7 protéines jusqu'alors jamais impliquées dans la condensation mitotique. Parmi ces dernières, nous avons identifié des protéines impliquées dans le remodelage de la chromatine et des facteurs de transcription comme Gcn5, une HAT très conservée, connue pour son rôle de coactivateur de la transcription ; suggérant un lien entre la condensation et la machinerie transcriptionnelle. Gcn5 s'associe à la chromatine au niveau des promoteurs des gènes où elle acétyle principalement H3K9, H3K14 et H3K18. Sa présence au niveau des promoteurs est directement corrélée avec le niveau de transcription des gènes correspondants. Bien que la majorité de la chromatine soit dé-acétylée et que la présence de Gcn5 soit réduite au niveau des chromosomes en mitose, des traces de H3K9 acétylée persistent au niveau de certains promoteurs. Nos résultats suggèrent que cette acétylation persistante pourrait être liée au recrutement du complexe condensine à la chromatineFrom yeasts to human, Condensin is essential for mitotic chromosome condensation. However, how Condensin binds to chromatin and, in this context, shapes mitotic chromosome remain poorly understood. Mappings performed from yeasts to mouse have revealed that condensin is enriched near highly expressed genes along chromosome arms, suggesting that as yet identified features associated with transcription take part in condensin binding to chromatin. To identify factors that collaborate with Condensin we performed a synthetically lethal genetic screen in fission yeast. We searched for mutants that are alive when Condensin is fully functional but dead when Condensin is partly defective. We identified 7 proteins never known for their roles in the mitotic condensation, such as some chromatin remodelling and some transcription factors. All these results were consistent with a link between condensation and transcription. Among theses 7 proteins, we found Gcn5, which encodes a conserved HAT, well known for the role it plays as a transcriptional co-activator. Gcn5 binds to gene promoters where it acetylates mainly H3K9, K14 and K18, and its occupancy correlates with transcription rates. Remarkably, although the bulk of chromatin is de-acetylated and Gcn5 reduced from chromatin upon mitosis entry, traces of Gcn5 dependant H3K9 acetylated persist at condensin binding sites. Here, we provide evidence that Gcn5-mediated histone H3 K9 acetylation could assist the binding of Condensin to chromatin
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Mercy, Guillaume. "L'organisation 3D des chromosomes synthétiques de levure". Electronic Thesis or Diss., Sorbonne université, 2018. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2018SORUS034.pdf.
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Le projet international de synthèse des chromosomes de S. cerevisiae (projet Sc2.0) a débuté il y a une dizaine d'années en suivant des principes établis par le Pr. Jef Boeke. Les chromosomes synthétiques ont été conçus pour augmenter la stabilité du génome en supprimant toutes les séquences répétées (ARNt, éléments transposables...), tout en y ajoutant un système d'évolution inductible dépendant du système Cré/LoxP (système SCRaMbLE), permettant de générer rapidement des réarrangements chromosomiques. Bien que le design du projet Sc2.0 soit très conservateur en ce qui concerne le contenu des gènes, la suppression de plusieurs classes de séquences répétées peut affecter l'organisation du génome et potentiellement altérer les fonctions cellulaires. En utilisant la méthode de capture de conformation de chromosome couplée au séquençage de seconde génération (Hi-C), mon objectif a été de caractériser l'organisation 3D des génomes des souches synthétiques et évoluées. À ce jour, huit chromosomes (syn I, II, III, V, VI, IX-R, X et XII) ont été entièrement assemblés séparément. En utilisant les souches contenant un ou plusieurs de ces chromosomes, nous avons pu montrer que leur organisation génomique n'est globalement pas affectée par leur présence. Quelques exceptions subsistent, avec synIII dont les cassettes HML et HMR ont été retirées, et synXII d'où l'ADNr a été déplacé sur un autre chromosome. À ce stade, nous concluons que l'ADN répétitif dispersé ne conduit pas la conformation moyenne globale du génome de S. cerevisiae. Nous avons aussi exploité les cartes de contacts pour identifier les réarrangements dans les souches SCRaMbLEThe international project Sc2.0 started 10 years ago by the Pr. Jef Boeke aims to build a fully synthetic genome of S. cerevisiae which increases the genome stability by removing all repeated sequences (tRNA, transposable elements, etc.), and implements SCRaMbLE (for Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution), an inducible, high-throughput chromosome rearrangement system. This design is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes. However, it may affect genome organization and potentially alter cellular functions. To determine wether those modifications affected the three-dimensional conformation of synthetic chromosmes, we investigated it using chromosomes conformation capture coupled to second generation sequencing method (Hi-C). Currently, eight synthetic chromosomes (synI, synII, synIII, synV, synVI, synIX-R, synX et synXII) have been fully assembled. Using these strains we observed that the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploited the contact maps to detect rearrangements induced in these SCRaMbLE strains
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FINARDI, ALICE. "THE POLO-LIKE KINASE CDC5 AND THE CDK-COUNTERACTING PHOSPHATASE CDC14 PLAY DISTINCT ROLES IN THE RESOLUTION OF DNA LINKAGES IN MITOSIS". Doctoral thesis, Università degli Studi di Milano, 2022. http://hdl.handle.net/2434/906786.
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During mitosis, the newly duplicated genetic material, organized in pairs of sister chromatids, is distributed between the daughter cells by the spindle machinery, in a process called chromosome segregation. Errors in this process can compromise genome integrity. Faithful chromosome segregation requires the removal of all sorts of cohesion between sister chromatids. Although the main contributors of sister chromatid cohesion are cohesin complexes, which are cleaved at anaphase onset, another source of cohesion is represented by DNA linkages, also called Sister Chromatid Intertwines (SCIs). These linkages comprise unreplicated segments, recombination intermediates, and double-stranded catenanes. If not properly removed, SCIs can break during cell division causing DNA damage and jeopardizing genome stability. Although most DNA linkages are removed before mitosis, their complete resolution only occurs concomitantly with chromosome segregation, in a process whose regulation is still poorly understood.
In this thesis, to investigate the mechanisms of SCI resolution during mitosis, we exploited the unique phenotype of S. cerevisiae cells lacking the activities of the polo-like kinase Cdc5 and the Cdk-counteracting phosphatase Cdc14. These cells arrest after cohesin cleavage, with short bipolar spindles and undivided nuclei, because impaired in spindle elongation. Evidence suggests that cdc5 cdc14 cells are also impaired in sister chromatid separation, due to the presence of unresolved SCIs, and previous work in our laboratory revealed that these linkages mainly consist of DNA catenanes. Here, we found that both Cdc14 and Cdc5 contribute to the resolution of DNA linkages, with different functions. Cdc14 is mainly involved in nucleolar segregation and processing of recombination intermediates, while Cdc5 seems to act through a more generalized mechanism and promote the removal of DNA catenanes. At the molecular level, Cdc14 acts through its known substrate Yen1. On the other hand, we found that Cdc5 controls post-translational modification of the decatenating enzyme Top2 during mitosis, particularly conjugation with small ubiquitin-like modifier (SUMO) and, possibly, also phosphorylation. The polo-like kinase is known to inactivate the SUMO protease Ulp2 in metaphase, thus increasing SUMOylation of Ulp2 substrates, like Top2. Since the decatenation defect of cdc5 cells correlates with a dysregulation of the SUMO pathway and this pathway is known to regulate sister chromatid cohesion, we speculate that the hyperactivation of Ulp2 may be the reason behind the sister chromatid separation defect of cdc5 cells. Taken together, our findings integrate the current knowledge of the mechanisms of sister chromatid separation and allow us to propose a model that foresees Cdc5 and Cdc14 coordinating cohesin cleavage and spindle elongation with the removal of DNA intertwines.
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MASSARI, LUCIA FRANCESCA. "Complete resolution of sister chromatid intertwines requires the Polo-like kinase Cdc5 and the phosphatase Cdc14 in budding yeast". Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/556680.
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During mitosis the newly replicated genetic material, organized in sister chromatids, is equally subdivided into the daughter cells through a fine-regulated process called chromosome segregation. Sister chromatids are held together and identified as sisters by cohesin. At the metaphase-to-anaphase transition, when all chromatids are correctly attached to the spindle, cohesin is cleaved and chromosome segregation initiates. Beside cohesin, all linkages between sister chromatids need to be removed to allow for their complete separation. Additional linkages include DNA linkages (or sister chromatid intertwines, SCIs), such as recombination intermediates and DNA catenanes.
In Saccharomyces cerevisiae a mutant that lacks the activities of the Polo-like kinase Cdc5 and the phosphatase Cdc14, two major mitotic regulators, has been identified that proved to be particularly suitable for studying SCIs that persist in mitosis. The cdc5 cdc14 double mutant arrests with short and stable mitotic spindles and unseparated nuclei, despite having cleaved cohesin. In addition to having a spindle elongation defect, these cells are also impaired in the resolution of cohesin-independent linkages between chromatids.
We found that these linkages mostly consist of DNA catenanes, that persist in cdc5 cdc14 cells at their terminal arrest and that are sufficient to counteract spindle elongation. Our results suggest that Cdc5 is required for their resolution.
This finding, together with the knowledge that Cdc5 promotes Cdc14 activation and that both proteins are essential for spindle elongation and mitotic exit, allows us to speculate that they coordinate different aspects of chromosome segregation to guarantee genome integrity throughout mitosis.
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Huang, Wenwen Verfasser], Frank [Akademischer Betreuer] [Jülicher, Frank [Gutachter] Jülicher, Stephan [Gutachter] Grill i Nenad [Gutachter] Pavin. "Theoretical Study of Pulled Polymer Loops as a Model for Fission Yeast Chromosome / Wenwen Huang ; Gutachter: Frank Jülicher, Stephan Grill, Nenad Pavin ; Betreuer: Frank Jülicher". Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://d-nb.info/1151816914/34.
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Huang, Wenwen [Verfasser], Frank [Akademischer Betreuer] Jülicher, Frank [Gutachter] Jülicher, Stephan [Gutachter] Grill i Nenad [Gutachter] Pavin. "Theoretical Study of Pulled Polymer Loops as a Model for Fission Yeast Chromosome / Wenwen Huang ; Gutachter: Frank Jülicher, Stephan Grill, Nenad Pavin ; Betreuer: Frank Jülicher". Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://d-nb.info/1151816914/34.
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Li, Tong. "Analyse quantitative et multi-paramétrique de la mitose afin de comprendre la ségrégation des chromosomes". Thesis, Toulouse 3, 2019. http://www.theses.fr/2019TOU30265.
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La mitose est un processus cellulaire robuste, mais les mécanismes qui contrôlent la fidélité de la mitose restent une question importante en Biologie. La compréhension des processus conduisant à des défauts mitotiques sont essentiels pour déchiffrer les mécanismes moléculaires conduisant à la tumorigenèse, à la trisomie ou encore aux maladies génétiques. Une ségrégation chromosomique fidèle repose sur la coopération de nombreuses protéines tout au long du cycle cellulaire. De ce fait, l'utilisation d'approches quantitatives sophistiquées s'est avérée nécessaire pour l'étude de la robustesse de la mitose. Au cours de ce travail, j'ai donc développé un outil informatique puissant, appelé "système expert pour l'analyse quantitative de la mitose" ou MAARS. Cet outil permet une quantification multiparamétrique de la mitose en ciblant principalement la dynamique de l'appareil mitotique, le mouvement des chromosomes et l'apparition des défauts d'attachement des chromosomes. En développant une version avancée de MAARS (MAARS 2.0), basée sur une méthode d'apprentissage par ordinateur, j'ai filmé et analysé avec plus de 70 paramètres caractéristiques, des centaines de cellules mitotiques issues de 14 souches de levure à fission dont les fonctions mitotiques étaient connues pour être altérées. Pour la première fois, des données temporelles de la mitose en haut-débit sont maintenant disponibles. Ces données ont dors et déjà soulevé de nombreuses questions intéressantes, en suggérant par exemple de nouvelles fonctions pour la protéine Mad2p, normalement cruciale pour le fonctionnement du point de contrôle de l'attachement des chromosomes au fuseau mitotique. En conclusion, MAARS 2.0 est un système expert modulaire, axé sur l'étude de la mitose, qui relie la biologie cellulaire et l'informatique pour effectuer une analyse reproductible, impartiale et de haut débit. Compte tenu de la capacité de MAARS à identifier et analyser les phénotypes rares sur des milliers de cellules, ce sera un outil de choix pour la compréhension et le développement futurs de la biologie des systèmes dans la levure à fissionMitosis is a robust cellular process, yet, the mechanisms controlling mitotic fidelity remain an interesting question in Biology. The precise understanding of mitotic processes will undoubtedly highlight the molecular mechanisms leading to tumorigenesis, Down's syndrome or other genetic diseases. How chromosome segregation remains so faithful is poorly understood but it seems to rely on the cooperation of a large number of proteins throughout the cell cycle. Therefore, the use of state-of-the-art quantitative approaches appears necessary to decipher the processes controlling mitotic robustness. In this thesis, I developed an expert system, called mitosis analysis and recording system (MAARS), to perform an unbiased and multiparametric analysis of mitosis, focusing on the mitotic apparatus dynamics, the movement of the chromosomes and the presence of attachment defects. By using an improved version of MAARS, MAARS 2.0, based on machine learning, hundreds of mitotic cells in 14 different fission yeast strains previously described to be involved in mitosis, were acquired and analyzed. More than 70 mitotic features were extracted from each of them making high-content temporal data of mitosis available for the first time. The data I obtained led to several interesting observations, including potential new functions for the spindle assembly checkpoint protein Mad2p. MAARS 2.0 is a modular, mitosis-focused expert system that bridges cell biology with computer science to perform reproducible, unbiased, high-content analysis. Considering MAARS's capacity to tackle rare phenotypes out of thousand of cells, it will become a tool of choice for the future understanding and development of system biology in fission yeast
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Khuzwayo, Sabelo Lethukuthula. "Functional analysis of subtelomeric breakage motifs using yeast as a model organism". Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41119.
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Genome wide studies have uncovered the existence of large-scale copy number variation (CNV) in the human genome. The human genome of different individuals was initially estimated to be 99.9% similar, but population studies on CNV have revealed that it is 12-16% copy number variable. Abnormal genomic CNVs are frequently found in subtelomeres of patients with mental retardation (MR) and other neurological disorders. Rearrangements of chromosome subtelomeric regions represent a high proportion of cytogenetic abnormalities and account for approximately 30% of pathogenic CNVs. Although DNA double strand breaks (DSBs) are implicated as a major factor in chromosomal rearrangements, the causes of chromosome breakage in subtelomeric regions have not been elucidated. But due to the presence of repetitive sequences in subtelomeres, we hypothesized that chromosomal rearrangements in these regions are not stochastic but driven by specific sequence motifs. In a collaborative effort with Dr. Rudd (Department of human genetics at Emory University), we characterized subtelomeric breakpoints on different chromosome ends in search of common motifs that cause double-strand breaks. Using a yeast-based gross chromosomal rearrangement (GCR) system, we have identified a subtelomeric breakage motif from chromosome 2 (2q SBM) with a GCR rate that is 340 fold higher than background levels. To determine if the fragility of 2q SBM was driven by the formation of secondary structures, the helicase activities of Sgs1 and Pif1 were disrupted. These helicases have been shown to destabilize DNA secondary structures such as G-quadruplex structures. Disruption of these helicases augmented chromosomal rearrangements induced by 2q SBM, indicating that these helicases are required for maintenance of this sequence. We also donwregulated replication fork components to determine if 2q SBM was imposing any problems to the replication fork machinery. Downregulation of replication fork components increased chromosomal rearrangements, indicating that intact replication fork was a critical determinant of 2q SBM fragility. Using a yeast-based functional assay, these experiments have linked human subtelomeric repetitive sequences to chromosomal breakage that could give rise to human CNV in subtelomeric regions.
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Meaney, Paul James. "Mapping the Plasmodium falciparum genome with yeast artificial chromosomes". Thesis, University of Edinburgh, 1995. http://hdl.handle.net/1842/12640.
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Yeast Artificial Chromosome cloning vectors, with their capacity to maintain up to 1 Mb of cloned DNA in a stable form, have proved extremely useful in mapping the genomes of higher eukaryotes. These vectors possess features which can circumvent some of the problems associated with classical molecular manipulation in Plasmodium falciparum. The research presented in this thesis is aimed at contributing to genome mapping in P. falciparum. The primary objective is the construction of a complete, detailed YAC- based physical map of chromosome 6, with a resolution of 10 Kb. To accomplish this, an 1100 YAC library of the P. falciparum isolate HB3 was constructed. The library contains clones with an average insert size of 100 Kb. Insert DNA is stable when cultured over 100 generations and the library is predicted to have a 4/5 fold genome redundancy, corresponding to 90% of the genome. Chromosome 6 specific YAC's have been isolated and three contigs initiated. Overlapping YAC's have been identified by using Sequence Tagged Site markers obtained from the 5 and 3 ends of each YAC by Inverse PCR. A total of 700 Kb of P. falciparum DNA has been cloned and this has been extensively mapped with seven restriction enzyme. Maps for all available YAC's will be presented. In addition, an attempt has been made to evaluate the degree of stage specific gene expression of cloned DNA within each YAC. The implications of these findings for genome mapping in P. falciparum will be discussed in the thesis.
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Chakraverty, Ronjon. "A yeast model of Bloom's syndrome". Thesis, Open University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264397.
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Muller, Carolin Anne. "Comparative genomics of chromosome replication in sensu stricto yeasts". Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603592.
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Precise, complete and timely replication of eukaryotic genomes is a prerequisite to cell division. Each chromosome replicates in a defined temporal order that is dictated by the variable activation timings and efficiencies of replication origins. However, so far the mechanisms regulating origin activity have remained elusive. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae. Powerful comparative genomic approaches are possible in budding yeasts due to the evolutionary range of sequenced genomes available and their tractability to genetic approaches. Previously, functional sequence elements at replication origins have been identified based upon their phylogenetic sequence conservation amongst closely related species of the sensu stricto group. To gain insight into the selective pressures contributing to this phylogenetic conservation, mutant strains with chromosomally inactivated origins were grown in competition with wild-type strains. Origin mutant strains did not have a growth defect compared to the wild-type, suggesting that the selective advantage conferred by evolutionary conserved origins is not the requirement for a rapid cell cycle time. To improve the reference sequence annotation, the S. cerevisiae genome was systematically screened for origin function, confirming more than 200 additional replication origins. The resulting comprehensive map of origin locations in S. cerevisiae was used to assess the accuracy of origin predictions from published studies and two newly developed techniques. These two approaches use high-throughput sequencing to either identify replication origin locations or measure replication dynamics genome-wide. Using the latter method on haploid and diploid S. cerevisiae strains showed that replication dynamics are independent of cell ploidy. Genome replication in divergent budding yeasts was investigated using a combination of replication timing profiles acquired with deep sequencing and plasmid-based assays. These analyses formed the basis for a comparative genomics approach, which revealed that the relative order of genome replication is conserved. A minority of replication origins with identical genomic locations show differences in activity between the analyzed species. To gain insight into the mechanisms underlying origin regulation, the replication dynamics of a hybrid between S. cerevisiae and its most distant relative in the sensu stricto group - S. bayanus - were measured. Replication origin function was found to be controlled by both local and global regulators .
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Francis, Michael J. "Physical mapping around the SMA gene using yeast artificial chromosomes (YACs)". Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259879.
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Beyer, Tracey, i Ted Weinert. "Ontogeny of Unstable Chromosomes Generated by Telomere Error in Budding Yeast". PUBLIC LIBRARY SCIENCE, 2016. http://hdl.handle.net/10150/622117.
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DNA replication errors at certain sites in the genome initiate chromosome instability that ultimately leads to stable genomic rearrangements. Where instability begins is often unclear. And, early instability may form unstable chromosome intermediates whose transient nature also hinders mechanistic understanding. We report here a budding yeast model that reveals the genetic ontogeny of genome rearrangements, from initial replication error to unstable chromosome formation to their resolution. Remarkably, the initial error often arises in or near the telomere, and frequently forms unstable chromosomes. Early unstable chromosomes may then resolve to an internal "collection site" where a dicentric forms and resolves to an isochromosome (other outcomes are possible at each step). The initial telomere-proximal unstable chromosome is increased in mutants in telomerase subunits, Tel1, and even Rad9, with no known telomere-specific function. Defects in Tel1 and in Rrm3, a checkpoint protein kinase with a role in telomere maintenance and a DNA helicase, respectively, synergize dramatically to generate unstable chromosomes, further illustrating the consequence of replication error in the telomere. Collectively, our results suggest telomeric replication errors may be a common cause of seemingly unrelated genomic rearrangements located hundreds of kilobases away.
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Potier, Serge. "Translocation reciproque entre sites chromosomiques choisis : remplacement du locus ura2 sauvage par des alleles deletes in vitro chez saccharomyces cerevisiae". Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13121.
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Etude fine du gene ura2 grace aux techniques d'integration chromosomique ou loeus ou remplacement genique et analyse de l'expression, la regulation du gene et du fonctionnement de l'enzyme bifonctionnel codee pae ce gene. Mise au point d'une methode permettant de faire des translocations reciproques stables entre 2 sites choisis