Дисертації з теми "Structure des chromosomes"
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Sun, Lawrence (Lawrence J. ). "Inference of 3D structure of diploid chromosomes." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/119570.
Повний текст джерелаThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 61-62).
The spatial organization of DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome capture experiments (such as 3C, 4C, Hi-C) it is now possible to obtain the contact frequencies of the DNA at the whole-genome level. In this thesis, we study the problem of reconstructing the 3D organization of the genome from whole-genome contact frequencies. A standard approach is to transform the contact frequencies into noisy distance measurements and then apply semidefinite programming (SDP) formulations to obtain the 3D configurations. However, neglected in such reconstructions is the fact that most eukaryotes including humans are diploid and therefore contain two (from the available data) indistinguishable copies of each genomic locus. Due to this, the standard approach performs very poorly on diploid organisms. We prove that the 3D organization of the DNA is not identifiable from exclusively chromosome capture data for diploid organisms. In fact, there are infinitely many solutions even in the noise-free setting. We then discuss various additional biologically relevant constraints (including distances between neighboring genomic loci and to the nucleus center or higher-order interactions). Under these conditions we prove there are finitely many solutions and conjecture we in fact have identifiability. Finally, we provide SDP formulations for computing the 3D embedding of the DNA with these additional constraints and show that we can recover the true 3D embedding with high accuracy even under noise.
by Lawrence Sun.
M. Eng.
Stear, Jeffrey Hamilton. "Studies of chromosome structure and movement in C. elegans /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/5056.
Повний текст джерелаFrancki, Michael G. "The midget chromosome as a model to study cereal chromosome structure /." Title page, contents and summary only, 1995. http://web4.library.adelaide.edu.au/theses/09PH/09phf823.pdf.
Повний текст джерелаAlmagro, Sébastien. "Organisation structurale et fonctionnelle des chromosomes." Phd thesis, Université Joseph Fourier (Grenoble), 2003. http://tel.archives-ouvertes.fr/tel-00003099.
Повний текст джерелаNourse, Jamie. "The structure, organisation and function of dispensable chromosomes in the phytopathogenic fungus Colltotrichum Gloeosporioides /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16086.pdf.
Повний текст джерелаDi, Stefano Marco. "Structure and dynamics of entangled biopolymers: from knotted DNA to chromosomes." Doctoral thesis, SISSA, 2014. http://hdl.handle.net/20.500.11767/3886.
Повний текст джерелаBrinkman, Jacquelyn N. "Structure and evolution of supernumerary chromosomes in the Pacific Giant salamander Dicamptodon tenebrosus." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0028/MQ50727.pdf.
Повний текст джерелаWright, Matthew A. "Approaches to determining the three-dimensional structure and dynamics of bacterial chromosomes." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33653.
Повний текст джерелаVita.
Includes bibliographical references.
The information in genomes is only partially contained in the linear sequence of their nucleotides. Their folding into dynamic three-dimensional structures creates spatial relationships between loci that likely play important functional roles. Yet so far only the broad outlines of this spatial organization have been discerned. In chapter 2 of this thesis I describe a general constraint-based framework for defining the configuration space of chromosomes. Analogous to protein structure determination through NMR, such a framework allows the quantitative reduction of the conformation space down to the level of a single structure or an ensemble of structures. It is compatible with both experimentally determined and theoretical constraints, particularly those motivated by evolutionary optimality. In chapter 3., I describe the first method to search for signals of large-scale three- dimensional structure in genome sequences. The results suggest that there is strong selection for three-dimensional relationships within the chromosome, particularly those related to transcription. The signals generated recapitulate both known structural data from microscopy and functional data on genome-wide transcription levels.
(cont.) Moreover, a detailed analysis of these signals in E. coli suggests previously unknown structural features including chromosome-long periodic looping and an axis of high transcriptional activity. There are immediate applications to other bacteria and potentially to eukaryotes.
by Matthew A. Wright.
Ph.D.
Cinato, Elisa. "Structure et expression du gène IFNA R2 humain : identification de la deuxième chaîne du récepteur des interférons alpha/bêta." Montpellier 2, 1996. http://www.theses.fr/1996MON20042.
Повний текст джерелаJefferson, Andrew. "Chromosomes structure, nuclear architecture and the regulation of gene expression in ICF syndrome." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442821.
Повний текст джерелаHolland, Katalin Anna. "Analysis of the molecular structure of centromeres of Chinese hamster and human chromosomes." Thesis, University of Leicester, 1993. http://hdl.handle.net/2381/34425.
Повний текст джерелаOakey, Rebecca. "The structure of alphoid satellite DNA on normal and abnormal human Y chromosomes." Thesis, University of Oxford, 1989. http://ora.ox.ac.uk/objects/uuid:162cb1a7-3176-4b56-be8b-353b65fee236.
Повний текст джерелаRavel, Christophe. "Structure et dynamique du génome de Leishmania (protozoa, kinetoplastida)." Montpellier 1, 1996. http://www.theses.fr/1996MON1T004.
Повний текст джерелаCosta, Lionel. "Etude de la régulation de la structure de la chromatine par la RiboNucléase Latente (RNase L) chez les mammifères." Thesis, Montpellier 2, 2011. http://www.theses.fr/2011MON20225/document.
Повний текст джерелаThe endoribonuclease Latente (RNase L) is mostly known as a critical factor in the innate immunity during the cell's defence against a viral infection. The antiviral activity of RNase L which is characterize by it capacity of cleavage of viral RNA, is regulated by several factors like it activator the oligoadénylates 2-5A and his inhibitor RLI. In this manuscript, we have studied the role of the activity of RNase L in the regulation of the structure of centromeric domains. Our results show a general destructuration of chromosomes observed in cells over-expressing RNase L or RLI. These major aberrations are demonstrated by a delocalization of essentials proteins for the structure of chromatin: HP1-alpha and CENP-C. The mislocalization of these proteins could be provoked by a default in the maturation of major transcripts due to a modulation of the activity of RNase L. moreover, in this study, we have identified a mechanism regulating the cyto-nuclear shuttling of RNase L. therefore, we propose that a new nuclear function of RNase L: it's implication in the regulation of pericentromeric transcripts needed to stabilize the integrity of the structure of chromatin
Tessé, Sophie. "Caractérisation de deux protéines, Spo11 et Ski8, impliquées dans la recombinaison, la ségrégation, le mouvement et la structure du chromosome en méiose chez Sordaria macrospora." Paris 11, 2003. http://www.theses.fr/2003PA112238.
Повний текст джерелаDuring meiotic prophase, chromosomes are organized into linear arrays of loops attached to the axial element of the synaptonemal complex (SC). Sister chromatids are linked by the cohesin complex and by Spo76/Pds5, isolated and characterized in the laboratory. Suppressor mutations which alleviate spo76-1 arrest were isolated and I characterized two of the corresponding genes: SPO11 and SKI8. Both are involved in the initiation of double-strand breaks (DSB), first step of the meiotic recombination. Chromosomal meiotic localization of Spo11p and Ski8p are mutually interdependent. Analyses of ski8 and spo11 mutants plus exogenous DSB showed that DSB promote recognition and presynaptic alignment of homologs. SC formation and normal segregation of chromosomes during bath meiotic divisions. DSB are not required for the formation of SC axial elements and for the bouquet formation but they are required for its resolution. We further found that Spo11p is a negative regulator of bouquet exit. SPO11 and SKI8 mutant phenotypes divide meiotic synapsis into three successive steps: DSB-independent recognition, DSB-dependent presynaptic coalignment of homologs at 400 nm and SC formation. We show that destabilization of chromosome cohesion and axis must be permitted locally at recombination sites and that Spo76p maintains the sister chromatids at supra-axial levels during this process. To understand the consequences of the spo76-1 mutation and of the DSB effects on meiotic progression, we studied the Spindle Checkpoint protein Mad2, implicated during the metaphase/anaphase transition. This work contributed to the understanding of the links between two important meiotic processes: recombination and pairing of homologous chromosomes
Flannery, A. V. "A study of loop retraction in the lampbrush chromosomes of Triturus cristatus carnifex (the Italian crested newt)." Thesis, University of Liverpool, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.377115.
Повний текст джерелаDuminil, Jérôme. "Etudes comparatives de la structure génétique des plantes." Nancy 1, 2006. http://www.theses.fr/2006NAN10009.
Повний текст джерелаThe level and the organisation of species genetic diversity are controlled for by mutation, selection, migration and drift. The respective role of these forces is influenced by ecological species traits, inheritance of their genome as well as by historical factors. Understanding the contribution of each of these factors on genetic structure necessitate a comparative framework that control for phylogenetic relatedness of the species. Dealing with phylogenetic controlled comparative method we had first study the evolution of organelle genomes, and its relationships with molecular and biological characteristics of the studied species. Many relationships were demonstrated and interpreted in the light of two different models of molecular evolution: (i) a nearly-neutral model, and (ii) a model of deletional bias. We had, in a second part, compiled plant genetic structure studies based on uniparental (chloroplast and mitochondria) and on biparental (nuclear) markers. The resulting database was then used to (i) study the influence of genome inheritance on the precision of the measure of the genetic structure, (ii) study the relationships between life history traits of the species and the way they partition genetic diversity. Finally, we had studied the repartition of genetic structure in a complex of tropical tree species: Carapa procera/guianensis. Difficulties in morphological recognition of these species were overlapped using genetic identification and a contrasted genetic structure between both species was demonstrated indicating differences in their seed migration abilities
Amadou, Claire. "Structure et évolution du bras court du chromosome 6 humain : la région de classe I du complexe majeur d'histocompatibilité et sa partie distale." Toulouse 3, 1996. http://www.theses.fr/1996TOU30039.
Повний текст джерелаWallace, Isha Kimisha. "The kinetochore protein Mif2p is targeted by Cdk1p and development of a selection for regulators of centromere/kinetochore structure/function." Diss., [Riverside, Calif.] : University of California, Riverside, 2010. http://proquest.umi.com/pqdweb?index=0&did=2019869861&SrchMode=2&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1274198666&clientId=48051.
Повний текст джерелаIncludes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed May 18, 2010). Includes bibliographical references. Also issued in print.
Revaud, Déborah. "Etude des cassures de l'ADN et des mécanismes de réparation dans les séquences télomériques interstitielles : Influence de la structure chromatinienne." Paris 11, 2009. http://www.theses.fr/2009PA11T033.
Повний текст джерелаBuitrago, Ospina Diana Camila. "Understanding the link between chromatin structure, chromosome conformation and gene regulation." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668639.
Повний текст джерелаComprender la conexión entre la organización del ADN en el núcleo y el funcionamiento celular es uno de los problemas más interesantes en biología. Aunque se han desarrollado muchos esfuerzos interdisciplinarios para esto, los mecanismos de plegamiento del ADN son en gran medida desconocidos. Por lo tanto, la complejidad de la estructura del genoma requiere diferentes técnicas para abordar varios niveles de resolución. En esta tesis, se estudian varias escalas de plegamiento del genoma utilizando métodos teóricos. Primero, nos centramos en las propiedades dependientes de la secuencia de ADN que definen la propensión de regiones específicas a ser reconocidos por las proteínas, descubriendo que la flexibilidad de ciertas secuencias de ADN podría explicar su prevalencia en el genoma. Las propiedades físicas del ADN también son importantes para definir la primera capa de organización de la cromatina: el nucleosoma. Los descriptores físicos de la secuencia de ADN combinados con la propensión a la unión de factores de transcripción son muy informativos sobre la posición de las regiones no afines a la formación de nucleosomas, que guían la posición de los nucleosomas +1 y –último, y el resto de los nucleosomas en el cuerpo del gen se coloca por posicionamiento estadístico. Adicionalmente, encontramos que existe una clara correlación entre la actividad transcripcional y la fase de nucleosomas en el cuerpo del gen. En esta tesis también se desarrolló un paquete para el análisis comparativo de la organización de nucleosomas que permite identificar cuantitativamente los cambios en el posicionamiento de los nucleosomas que ocurren cuando se introducen perturbaciones en la célula. Finalmente, estudiamos tanto los cambios a nivel de nucleosomas como a mayor escala producidos por la inducción de metilación del ADN en un genoma que originalmente no tiene metilación, desarrollando un modelo 3D basado en Hi-C para estudiar la reorganización de la cromatina. Encontramos cambios muy significativos en la estructura de la cromatina inducidos por la metilación, que se reflejan en la expresión génica y el fenotipo celular, en un organismo modelo que no tiene proteínas que reconocen la metilación y, en consecuencia, pueden deberse a los efectos intrínsecos de la metilación.
Heurteau, Alexandre. "Etude bioinformatique intégrative : déterminants et dynamique des interactions chromosomiques à longue distance." Electronic Thesis or Diss., Toulouse 3, 2019. http://www.theses.fr/2019TOU30343.
Повний текст джерелаInsulator Binding Proteins (IBPs) could be involved in the three-dimensional folding of genomes into topological domains (or "TADs"). In particular, TADs would help to separate the inactive/heterochromatin and active/euchromatin compartments. IBPs are also able to block specific contacts between the activator or enhancer elements of one TAD and target gene promoters present in another TAD. Thus, insulators may influence gene expression according to several regulatory modes that have yet to be characterized at genome level. The results obtained in the first part of my thesis show how IBPs influence gene expression according to a new regulatory mechanism, as shown at the scale of the Drosophila genome. Our bioinformatics analyses show that IBPs regulate the spread of repressive heterochromatin (H3K27me3) both in cis and trans. Trans regulations involve chromatin loops between insulators positioned at the heterochromatin boundary and distant insulators positioned at the edges of euchromatic genes. Trans spreading leads to the formation of "micro-domains" of heterochromatin, thereby repressing distant genes. In particular, an insulator mutant that prevents loop formation significantly reduces the establishment of micro-domains. In addition, these micro-domains would be formed during development suggesting a new insulator-dependent mechanism for gene regulation. Furthermore, we could uncover a novel function of cohesion, a key regulator of 3D loops in humans, in regulating non-coding RNAs (ncRNAs), including "PROMoters uPstream Transcripts" (PROMPTs) and enhancers RNAs (eRNAs). The MTR4 helicase is essential to the control of coding and noncoding RNA stability by the human nuclear-exosome targeting (NEXT) complex and pA-tail exosome targeting (PAXT) complex. Remarkably, ncRNAs could be detected upon depletion of the Mtr4 helicase of the human NEXT complex. Moreover, depletion of additional NEXT subunits, ZFC3H1 and ZCCHC8 (or Z1 and Z8), also led to uncover ncRNAs often produced from the same loci as upon MTR4 depletion. Curiously however, mapping of Mtr4 binding sites highlighted that Mtr4 binds to sites that are distant from PROMPTs. Rather than acting in cis, our data suggest that regulation of PROMPTs could involve specific long-distance contacts between these distant MTR4 binding sites and promoters bound by Z1/Z8. As such, integration of Hi-C data together with the detection of PROMPTS upon MTR4-, Z1- or Z8- depletions highlight possible role of long-range interactions in regulating PROMPTs, from distant MTR4-bound sites. This work may establish a new relationship between the 3D structure of genomes and the regulation of ncRNAs
TIHY, FREDERIQUE. "Contribution a l'etude de la structure et de l'evolution des chromosomes humains par hybridation in situ en fluorescence." Paris 11, 1995. http://www.theses.fr/1995PA112303.
Повний текст джерелаBlanc, Guillaume. "Étude de la structure et de l'évolution du génome d'Arabidopsis : Identification et analyse de duplications segmentaires des chromosomes." Perpignan, 2000. http://www.theses.fr/2001PERP0440.
Повний текст джерелаMonfouilloux, Sylvaine. "Etude de la structure et de l'évolution d'une région de translocations sous télomériques chez l'homme." Rouen, 1997. http://www.theses.fr/1997ROUES065.
Повний текст джерелаBaudry, Lyam. "Investigating chromosome dynamics through Hi-C assembly." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS026.
Повний текст джерелаThe advent of high-throughput DNA sequencing technologies has set off an expanding trend in genome assembling and scaffolding. Such genome quality is an essential preliminary to understand interactions between and among chromosomes. We built upon a computational and technological framework that let us tackle genome assembly problems of increasing complexity. Our methods are mainly based on chromosome conformation capture technologies such as Hi-C. In a Hi-C experiment, DNA molecules are cross-linked with the surrounding proteins and form a large, static protein-DNA complex. This captures the spatial conformation by trapping together molecules that are physically close to each other. Therefore, Hi-C is very suitable for 3D genome structure analysis, which lets us infer a wealth of information about the genome. It was indeed shown that the tridimensional structure of the genome can be unambiguously linked to its 1D structure thanks to the physical properties of DNA polymers. Moreover, such 3D proximity also gives access to cell compartment information, thus opening the way for an additional approach for metagenomic binning, known as meta3C. In this work, we expand upon these methods and apply them to use cases with more and more complexity. We first improve on tools for genome assembly and demonstrate their validity with the scaffolding of Ectocarpus sp., then unveil rearrangements in joint scaffoldings of Trichoderma reesei and Cataglyphis hispanica. Lastly, we use the same approach with metagenomic binning on live mouse microbiome samples to reconstruct hundreds of genomes
Woodward, Jessica Christina. "Cell-lineage-specific chromosomal instability in condensin II mutant mice." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/22921.
Повний текст джерелаHeckmann, Stefan [Verfasser], Gunter [Akademischer Betreuer] Reuter, Andreas [Akademischer Betreuer] Houben, and Neil [Akademischer Betreuer] Jones. "Structure and regulation of centromeres in mono‐ and holocentric chromosomes : [kumulative Dissertation] / Stefan Heckmann. Betreuer: Gunter Reuter ; Andreas Houben ; Neil Jones." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2013. http://d-nb.info/103488137X/34.
Повний текст джерелаCarron, Léopold. "Analyse à haute résolution de la structure spatiale des chromosomes eucaryotes Boost-HiC : Computational enhancement of long-range contacts in chromosomal contact maps Genome supranucleosomal organization and genetic susceptibility to disease." Thesis, Sorbonne université, 2019. http://www.theses.fr/2019SORUS593.
Повний текст джерелаGenetic information is encoded in DNA, a huge-size nucleotidic polymer. In order to understand DNA folding mechanisms, an experimental technique is today available that quantifies distal genomic contacts. This high-throughput chromosome conformation capture technique, called Hi-C, reveals 3D chromosome folding in the nucleus. In the recent years, the Hi-C experimental protocol received many improvements through numerous studies for Human, mouse and drosophila genomes. Because most of these studies are performed at poor resolution, I propose bioinformatic methods to analyze these datasets at fine resolution. In order to do this, I present Boost-HiC, a tool that enhanced long-range contacts in Hi-C data. I will then used our extended knowledge to compare 3D folding in different species. This result provides the basis to determine the best method for obtaining genomic compartements from a chromosomal contact map. Finally, I present some other applications of our methodology to study the link between the borders of topologically associating domains and the genomic location of single-nucleotide mutations associated to cancer
Murat, Florent. "Etude de la plasticité évolutive et structurale des génomes de plantes." Thesis, Clermont-Ferrand 2, 2016. http://www.theses.fr/2016CLF22721.
Повний текст джерелаAngiosperms (or flowering plants) consist in approximatively 350 000 species that have diverged 150 to 200 million years ago in two main families, monocots (orchids, palm trees, banana, bulrushes, grasses...) and dicots (Brassicaceae, Rosaceae, legumes...) representing respectively 20% and 75% of flowering plants. Angiosperms are the subject of intense researches, in particular in genomics since 2000 with the sequence release of the first plant genome (Arabidopsis thaliana) preceding a large number of genomes of plant models and/or species of agronomical interest (around 100 today). Increasing access to plant genome sequences has allowed the identification of their structural diversity, in terms of genome size, number of chromosomes and genes as well as transposable element content. The evolutionary forces that have shaped such structural genomic divergence are at the center of this thesis. Our paleogenomics approach will investigate, through ancestral genome reconstructions, how modern species have diverged from common ancestors and which mechanisms have contributed to such present-day genome plasticity. In this thesis, we have developed methods based on comparative genomics to study plant genome evolution and reconstruct ancestral genomes, extinct progenitors of the modern angiosperm species. An ancestral angiosperm genome has been reconstructed made of 5 chromosomes and 6707 ordered genes allowing the integration in the same model of monocots and eudicots and finally elucidating evolutionary trajectories for species of major agricultural interest such as cereals, rosids and Brassicaceae. The reconstructed paleohistory of modern flowering plants enabled the identification as well as the investigation of the impact of polyploidy events (WGD, whole genome duplications), ubiquitous in plants, as a major driver of the observed structural plasticity of angiosperms. We established that genomes tend to return to a diploid status following a polyploidy event. This structural diploidization is performed at the karyotypic level through chromosomal rearrangements (involving ancestral centromeres and telomeres losses) as well as the gene level (through ancestral duplicates loss). It has been shown that this diploidization is preferentially done on one of the post-polyploidy subgenome, leading to the "sub-genome dominance" phenomenon. This structural plasticity bias (also referenced as plasticity partitioning) is acting differentially between species, chromosomes, chromosomal compartments, gene types, resulting in the structural diversity observed between the present-day plant genomes. This thesis is clearly within the scope of fundamental researches but also has a strong applied objective through translational research in creating bridges between species of major relevance for agriculture. The comparison of one species to another through the reconstructed ancestral genomes allows transferring knowledge gained on genes or any region of interest from model species to crops. Paleogenomics, in reconstructing ancestral genome and unveiling the forces driving modern plant genome plasticity, is therefore of fundamental (toward understanding species evolution) but also applied (toward improving orphan species from knowledge gained in models) objectives
Pingault, Lise. "Analyses structurales et fonctionnelles de l'espace génique du chromosome 3B du blé tendre (Triticum aestivum L.)." Thesis, Clermont-Ferrand 2, 2014. http://www.theses.fr/2014CLF22504/document.
Повний текст джерелаGenome-wide studies of the bread wheat are a complicated task due to its large size (17 Gb), its allohexaploidy and its high content in repeat sequences (>80%). Using a chromosome-specific approach, the chromosome 3B (995 Mb) was successfully isolated and sequenced leading to the assembly of one pseudomolecule. The work presented in this thesis investigated the impact of the 3B chromosome size on the gene space organization. Production of transcriptomic data was achieved using RNA-Seq approach. The chromosome 3B was annotated and we predicted 7 264 features, including 5 326 full genes and 1 938 pseudogenes. We constructed RNA-Seq libraries for 15 developmental wheat conditions. Using this data we detected expression of 71.4% of the predictions, and 3 692 novel transcribed regions (NTR). We also detected alternative transcripts for 61% of the expressed genes, with 5.8 isoforms on average for one gene. Using these transcriptional data, we highlighted a partitioning of the chromosome 3B gene space. Indeed, transcription was found all along the chromosome, but genes were organized according to an increasing density gradient along the centromere-telomere axis. Based on recombination profile, we segmented the chromosome in 3 major regions: R1, R2 and R3. The region R2 was identified with low or no recombination rate corresponding to the centromeric and peri-centromeric regions (647 Mb). The regions R1 and R3 were associated with a higher recombination rate, both localized on the distal part of the short arm (58 Mb) and the long arm (69 Mb) respectively, where the recombination rate is higher. All three regions showed distinct level and specificity of gene expression as well as unique gene structure (variation size, exon number, intron size). Indeed, genes expressed in a specific condition and with a small number of alternatives transcripts were localized on regions R1 and R3. We showed that two evolutionary model could explain the link between gene structure and the level/specificity of expression : “selection for economy” and “genome design”. In conclusion, a transcriptomic studies was achieved along the 3B chromosome for the first time. This study demonstrated a relationship between gene characteristics (structure, expression level, expression specificity and evolution) and the chromosome 3B organization. Future pseudomolecule assemblies will help us to assess the structural organization of these chromosomes. In order to better understand the cellular mechanisms of gene expression, an epigenomic study of the 3B chromosome was started
Oldfield, Andrew. "Etude du réseau transcriptionnel du gène Xist, acteur principal de l'inactivation du chromosome X." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2010. http://tel.archives-ouvertes.fr/tel-00815096.
Повний текст джерелаMascarenhas, Judita. "Chromosome dynamics in Bacillus subtilis characterization of the structural maintenance of chromosomes (SMC) complex /." [S.l. : s.n.], 2004. http://archiv.ub.uni-marburg.de/diss/z2004/0125/.
Повний текст джерелаDoco-Fenzy, Martine. "De l'adn satellite aux satellites chromosomiques : etude du polymorphisme de la structure des bras courts des chromosomes acrocentriques humains par hybridation in situ revelee en fluorescence (doctorat : genie biologique)." Reims, 1998. http://www.theses.fr/1998REIMM205.
Повний текст джерелаBouverot, Romain. "Etudes structurales de la protéine ACAD9 et des facteurs d'assemblage du complexe 1 de la chaîne respiratoire mitochondriale pour établir leur implication dans les processus neurodégénératifs." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV005.
Повний текст джерелаMitochondria are responsible for bioenergetics, particularly critical in the human brain, where neurons are extremely energy demanding and highly dependent on the oxidative phosphorylation (OXPHOS) system. They generate energetic potential through the electron transport chain (ETC), also named the respiratory chain, which is composed of four protein complexes embedded into the mitochondrial inner membrane (MIM) to enable the phosphorylation of ADP into ATP by the ATP synthase in the mitochondrial matrix. Together these complexes form the OXPHOS system. Complex I (CI), the first enzyme of the respiratory chain, is composed of 45 protein subunits (of which 44 are different) and initiates the OXPHOS system, being essential in cellular energy production. Defects in CI assembly severally impair ATP production, increase the production of reactive oxygen species (ROS) and are implicated in several mitochondrial disorders, including neurodegenerative diseases. The integration of the 45 subunits and the insertion of cofactors into the nascent complex requires the help of assembly factors. Assembly factors may act as chaperones that stabilize the intermediate complexes or subunits and help to attach them to other intermediate assemblies to build the complete enzyme. However, they may also have additional functions besides their requirement for CI assembly, in line with the emerging evidence that mitochondria are involved with various (sub)cellular processes that regulate cell metabolic activity.How CI assembly factors function at the molecular level is currently unclear, with very little structural information available. Nevertheless, it is thought that most identified assembly factors are involved in early assembly, more specifically in the incorporation of hydrophobic membrane subunits. Recently, the CI assembly factors NDUFAF1 (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 1), ACAD9 (Acyl-CoA dehydrogenase 9), ECSIT (Evolutionarily conserved signaling intermediate in Toll pathway), and potentially TMEM126B (Transmembrane protein 126B) and TIMMDC1 (Translocase of inner mitochondrial membrane domain-containing 1) were proposed to form the so-called mitochondrial complex I assembly (MCIA) complex. However, the composition and stoichiometry of the MCIA complex are unknown, which precludes a proper understanding of the structural and mechanistic bases for building-up assembly intermediates and how the MCIA complex achieves specificity.This thesis pursues the characterisation of the MCIA core components ACAD9, ECSIT and NDUFAF1, mapping their interactions and characterising their structures using a combination of biophysical and biochemical approaches in order to elucidate the molecular mechanisms underlying the MCIA complex formation
Minnen, Anita [Verfasser], and Thorsten [Akademischer Betreuer] Mascher. "Structural Maintenance of Chromosomes (SMC) localization on the Bacillus subtilis chromosome / Anita Minnen. Betreuer: Thorsten Mascher." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1101344172/34.
Повний текст джерелаLindow, Janet C. (Janet Christine) 1974. "A role for the Bacillus subtilis Structural Maintenance of Chromosomes (BsSMC) protein in chromosome organization and compaction." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/8385.
Повний текст джерелаIncludes bibliographical references.
All cells must compact their chromosomes in order for the DNA to fit inside the cell or nucleus. In Bacillus subtilis, and other bacteria, replication occurs simultaneously with the organization, compaction and segregation of newly duplicated chromosomal regions. My work indicates that the B. subtilis Structural Maintenance of Chromosomes (BsSMC) protein is involved in compacting and organizing the chromosome. Increasing the amount of supercoiling of DNA is a means to compact the chromosome. This thesis describes a role for BsSMC in supercoiling. I determined that BsSMC can alter the DNA topology of plasmids in vivo. There is also genetic evidence that BsSMC is involved in supercoiling. An smc null mutant is hypersensitive to inhibitors of DNA gyrase, which reduce the level of negative supercoiling in the cell. Conversely, depletion of Topoisomerase I, which increases the amount of negative supercoiling of the chromosome, partially suppresses the phenotype of an smc null mutant. These data are consistent with the model that BsSMC affects chromosome compaction by constraining positive supercoils. Interestingly, SMC-containing complexes in eukaryotes are able to constrain positive supercoils in vitro and affect chromosome architecture suggesting that there is a conserved function for SMC proteins in chromosome structure. I also determined the subcellular localization of BsSMC. I found that BsSMC is a moderately abundant protein that can bind to many regions of the chromosome. A portion of BsSMC localizes in a pattern similar to the replication machinery.
(cont.) Simultaneous localization of BsSMC and a component of the replisome revealed that they are usually in the same region of the cell but are not always colocalized. Finally, the formation of BsSMC foci is dependent on the presence of the nucleoid but not ongoing replication. I propose that BsSMC is acting to compact newly replicated DNA by affecting DNA topology and is thereby facilitating the partitioning of sister chromosomes to opposite halves of the cell.
by Janet C. Lindow.
Ph.D.
Rustenholz, Camille. "Impact de la structure du génome sur l'organisation, la régulation et la fonction des gènes sur le chromosome 3B du blé hexaploïde (Triticum aestivum L.)." Thesis, Clermont-Ferrand 2, 2010. http://www.theses.fr/2010CLF22091.
Повний текст джерелаBecause of its size (17 Gb), allohexaploid nature and high repeat content (>80%), the bread wheat genome has always been perceived as too complex for efficient molecular studies. As a consequence, our knowledge of the wheat genome structure is still limited. Following a chromosome-specific approach, the physical map of wheat chromosome 3B has recently been constructed and allowed the development of unique genomic resources. During my PhD the use of transcriptomic approaches based on these resources allowed me analysing the relationships between the structure of the genome, the evolution, the function and the regulation of the genes along wheat chromosome 3B. First macroarrays carrying the BACs of the chromosome 3B “Minimal Tiling Path” (MTP) were hybridised with 15 mRNA samples to identify the BACs carrying genes. Then barley Agilent 15K expression microarrays were hybridised with the MTP of chromosome 3B pooled in three-dimension (3D) to precisely locate the genes on the physical map. To build the first transcription map of a wheat chromosome, the 3D pools as well as the 15 mRNA samples were hybridised onto wheat NimbleGen 40K expression microarrays. The results from these experiments allowed drawing some conclusions about gene space organisation on chromosome 3B. Thus the genes are spread all along chromosome 3B with a gradient of the gene density from the centromere to the telomeres with a higher proportion of genes organised in islands at the telomeres. An evolutionary analysis demonstrated that the islands would essentially be composed of genes that have undergone rearrangements in the wheat genome. Furthermore the transcription map also showed that a significant fraction of the genes organised in islands display similar expression profiles and / or share the same function and / or play a role in the same biological process. Moreover, at the scale of the whole chromosome 3B, mechanisms of long distance regulation between gene islands were suspected. In conclusion this study allowed for the first time to find relationships between the genome structure, the evolution, the function and the regulation of the genes at a wheat chromosome scale. The sequencing and the annotation of chromosome 3B as well as the use of technologies like RNAseq will enable to analyse these relationships in an even more precise and exhaustive way
Labbé, Jessy. "Contribution à l'étude de la structure et du polymorphisme du génome du basidiomycète ectomycorhizien "Laccaria bicolor" (Maire) Orton et identification de QTLs de mycorhization chez les peupliers, "Populus trichocarpa Torr. & A. Gray ex Hook. et "Populus deltoides (Bartr.) Marsh." Thesis, Nancy 1, 2009. http://www.theses.fr/2009NAN10079/document.
Повний текст джерелаThe mycorrhizal symbioses between fungi and roots concern 95 % of the plant species. Social trees of boreal and temperate forests form a particular type of root association with fungi: the ectomycorrhizal symbiosis. Ectomycorrhizas play a major role in tree hydromineral nutrition, nutrient cycles and primary production. However, their complexity have so far prevented from deciphering their precise function and role. The recent availability of the genome of the ectomycorrhizal fungus Laccaria bicolor and that of the host-tree Populus trichocarpa provides an unprecedented opportunity to decipher the key components of development and functioning of this symbiosis. The aims of this study were to participate to the characterization and deciphering of the genome of L. bicolor, and to determine the genes involved in the formation of ectomycorrhizas in both partners. Firstly, in order to facilitate the assembly of the genomic sequence of L. bicolor, we have identified the repeated sequences and generated a genetic map. On the 60 Mb of this genome, 8 % are microsatellite sequences and 24 % transposable elements. A genetic map was built from 111 monokaryons issued from L. bicolor S238N. This map includes 326 markers (8 RAPD, 243 AFLP, 59 SSR and 14 SNP) distributed on 10 linkage groups anchored onto the genomic sequence of L. bicolor. Secondly, we have identified the genes involved in the establishment of ectomycorrhizas in poplar by combining QTL detection and DNA microarrays. We targeted 81 genes which can be involved in the establishment and/or the functioning of the symbiosis
Rezende, Karina Fernandes Oliveira. "Alterações morfológicas de Tilápias do Nilo (Oreochromis niloticus) (Linnaeus, 1758) expostas às águas da represa Billings." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/42/42134/tde-26012012-105551/.
Повний текст джерелаThe Billings dam shows eutrophic waters due to the large amount of sewage from urban occupation neaby, and consequently, the fish can be a public health problem. The gills and liver become target organs for the action of pollutants in the aquatic environment and may present several levels of biological organization. These biological responses to stress caused by pollutants can be used to identify early signs of damage to fish and can be called biomarkers. Thus, this project aimed to analyze the histological gills and liver of Nile Tilapia, by means of measurements, Histological Alterations Index and Assessment Medium Value; the frequency of micronuclei was done. We observed histological alterations in gills and livers of Nile Tilapia classified as mild to severe, and the presence of micronucleus. The results enable better environmental monitoring and quality control of this species.
Dadon, Daniel Benjamin. "3D chromosome structure and chromatin proteomics." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104174.
Повний текст джерелаCataloged from PDF version of thesis. "May 2016."
Includes bibliographical references.
The selective interpretation of the genome through transcription enables the production of every cell type's distinct gene expression program from a common genome. Transcription takes place within, and is controlled by, highly organized three-dimensional (3D) chromosome structures. The first part of the work presented here describes the generation of 3D chromosome regulatory landscape maps of human naive and primed embryonic stem cells. To create these 3D chromosome regulatory landscape maps, genome-wide enhancer and insulator locations were mapped and then placed into a 3D interaction framework formed by cohesin-mediated 3D chromosome structures. Enhancer (H3K27ac) and insulator (CTCF) locations were mapped using ChIP-sequencing, whereas 3D chromosome structures were detected by cohesin-ChIA-PET. 3D chromosome structures connecting insulators (CTCF-CTCF loops) were shown to form topologically associating domains (TADs) and insulated neighborhoods, which were mostly preserved in the transition between naive and primed states. Insulated neighborhoods are critical for proper gene expression, and their disruption leads to the improper regulation of local gene expression. Changes in enhancer-promoter loops occurred within preserved insulated neighborhoods during cell state transition. The CTCF anchors of CTCF-CTCF loops are conserved across species and are frequently mutated in cancer cells. These 3D chromosome regulatory landscapes provide a foundation for the future investigation of the relationship between chromosome structure and gene control in human development and disease. The work presented in the second part focuses on developing an approach called "chromatin proteomic profiling" to identify protein factors associated with various active and repressed portions of the genome marked by specific histone modifications. The histone modifications assayed by chromatin proteomic profiling are associated with genomic regions where specific transcriptional activities occur, thus implicating the identified proteins in these activities. This chromatin proteomic profiling study revealed a catalog of known, implicated, and novel proteins associated with these functionally characterized genomic regions.
by Daniel Benjamin Dadon.
Ph. D.
Croft, Jenny Anne. "Correlating mammalian chromosome structure and function." Thesis, University of Edinburgh, 1998. http://hdl.handle.net/1842/13491.
Повний текст джерелаMc, Elligott Richard. "Structures terminale des télomères chez les mammifères." Sherbrooke : Université de Sherbrooke, 1997.
Знайти повний текст джерелаAlmuhur, Rana Ahmad Suleiman. "Integrating chromatin structure and global chromosome dynamics." Thesis, University of Birmingham, 2015. http://etheses.bham.ac.uk//id/eprint/5573/.
Повний текст джерелаGilbert, Sandra L. (Sandra Leigh) 1968. "Chromatin structure of the inactive X chromosome." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/85344.
Повний текст джерелаHorsley, Sharon Wendy. "Characterisation of chromosome 16 rearrangements in patients with alpha thalassaemia." Thesis, Oxford Brookes University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325201.
Повний текст джерелаSmith, Helen. "Condensin II Regulation and Function in Polyploid and Female Meiotic Cells in Drosophila melanogaster." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/194783.
Повний текст джерелаRoss, Brian Christopher. "Computational tools for modeling and measuring chromosome structure." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/79262.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references (p. 99-112).
DNA conformation within cells has many important biological implications, but there are challenges both in modeling DNA due to the need for specialized techniques, and experimentally since tracing out in vivo conformations is currently impossible. This thesis contributes two computational projects to these efforts. The first project is a set of online and offline calculators of conformational statistics using a variety of published and unpublished methods, addressing the current lack of DNA model-building tools intended for general use. The second project is a reconstructive analysis that could enable in vivo mapping of DNA conformation at high resolution with current experimental technology.
by Brian Christopher Ross.
Ph.D.
Avelar, Ana Teresa. "Chromosomal structure: a selectable trait for evolution." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2012. http://hdl.handle.net/10362/8576.
Повний текст джерелаEvolution is driven by biological diversity, which is displayed by different phenotypes. These phenotypes arise as a coordinated response to the genetic composition of each organism. Chromosomal rearrangements (CRs), such as inversions and translocations, are a type of mutation contributing both to be-tween and within species phenotypic variation. Additionally, they are a promi-nent feature of several types of cancer, in particular lymphomas. However, unlike other types of mutations, the effects of inversions and translocations have not yet been directly quantified. The objective of this thesis is to quantify the mitotic and meiotic effects of CRs and to understand if chromosomal di-versity is an important macromutation for the generation of biological diversity. Initially, we asked whether chromosomal rearrangements are a poly-morphic mutation in the fission yeast Schizosaccharomyces pombe. We found, like others, that karyotype differences are very common in S. pombe isolates in spite of nucleotide diversity of the order observed within species diversity. This fact led us to test the genetic isolation between the natural iso-lates by scoring hybrid viabilities in pairwise crosses. We found that in some cases hybrid viability was severely impaired. These results prompted us to measure the meiotic and mitotic effects of single CRs in an otherwise isogenic background.(...)
This dissertation was sponsored by Fundação para a Ciência e Tecnologia. Apoio financeiro da FCT e do FSE no âmbito do Quadro Comunitário de apoio, BD nº SFRH/BD/33214/2007.
Gunawardena, Shermali Dione Shiranthini Harina, and Shermali Dione Shiranthini Harina Gunawardena. "A 3-dimensional structural analysis of diploid chromosomes." Thesis, The University of Arizona, 1994. http://hdl.handle.net/10150/626984.
Повний текст джерела