Дисертації з теми "Chromosoms structure"
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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
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 джерелаStear, 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 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 джерелаMinnen, 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.
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 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 джерелаDadon, 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 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 джерелаSun, 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.
Horsley, 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.
Almagro, Sébastien. "Organisation structurale et fonctionnelle des chromosomes." Phd thesis, Université Joseph Fourier (Grenoble), 2003. http://tel.archives-ouvertes.fr/tel-00003099.
Повний текст джерелаMc, Elligott Richard. "Structures terminale des télomères chez les mammifères." Sherbrooke : Université de Sherbrooke, 1997.
Знайти повний текст джерелаAvelar, 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.
Riley, Anthony David. "Probing chromosome structure using multidimensional scaling of DNA contact matrices." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/7262/.
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 джерелаGunawardena, 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 джерелаHemming, D. J. "An immunological study of the role of histones in lampbrush chromosome structure." Thesis, University of Liverpool, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383516.
Повний текст джерелаJohansson, Anna-Mia. "Chromosome-wide gene regulatory mechanisms in Drosophila melanogaster." Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet), 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-33928.
Повний текст джерелаCaravaca, Guasch Juan Manuel. "Elementos estructurales de la cromatina en los cromosomas mitóticos." Doctoral thesis, Universitat Autònoma de Barcelona, 2004. http://hdl.handle.net/10803/3520.
Повний текст джерелаSe ha realizado un estudio exhaustivo de microscopía electrónica de transmisión sobre la estructura de los cromosomas metafásicos de células HeLa. Se han estudiado un total de 4410 micrografías de cromosomas metafásicos, que en su mayor parte han sido tratados con diversos medios parcialmente desnaturalizantes, para poder analizar su estructura interna.
Morfológicamente, los cromosomas estudiados en este trabajo pueden agruparse en tres tipos diferentes: compactos, granulados y fibrilados. La morfología más abundante es la compacta y se observa en presencia de cationes monovalentes y divalentes a concentración similar a la presente en la cromatina metafásica (Mg2+ 1.7-40 mM). Estos cromosomas tienen las cromátidas muy densas y en sus bordes se aprecian una serie de estructuras planas superpuestas. En condiciones de menor concentración de cationes (Mg2+£ 1.7 mM), la morfología dominante es la granular. Estos cromosomas están compuestos principalmente por gran cantidad de cuerpos circulares de 30-40 nm de diámetro. Únicamente en condiciones de fuerza iónica extremadamente baja podemos encontrar la morfología fibrilar, la cual se caracteriza por la abundancia de fibras de 30-40 nm.
Los resultados obtenidos con cromosomas parcialmente desnaturalizados nos permiten concluir que existen tres elementos estructurales en el interior de los cromosomas metafásicos: la fibra, el gránulo y la placa.
Las fibras gruesas con diámetros que oscilan entre los 100 y los 500 nm son el resultado de la deformación plástica de las cromátidas durante los diferentes procesos de preparación de las muestras. En función de las condiciones iónicas del medio las fibras gruesas muestran gránulos o placas en su interior. Las fibras delgadas están formadas por una sucesión de cuerpos de 30-40 nm de diámetro unidos irregularmente mediante interacciones cabeza-cola. Las fibras delgadas se observan dominantemente en condiciones de concentración salina extremadamente baja.
Los gránulos son unos cuerpos circulares compactos de unos 30-40 nm de diámetro. Estos cuerpos compactos descritos previamente por nuestro grupo y se interpretaron como una forma de plegamiento solenoidal de la fibra de 30 nm (Daban y Bermúdez, 1998). Se encuentran presentes en todas las condiciones estudiadas en este trabajo, siendo especialmente abundantes en presencia de iones divalentes a concentración baja y en muestras tratadas con nucleasa micrococal.
La placa es un elemento estructural característico de los cromosomas cuando éstos se encuentran en su forma más compacta, en presencia de concentraciones elevadas de cationes divalentes. Esta estructura no había sido descrita previamente por otros laboratorios. Es una estructura cromatínica de gran regularidad y con una superficie muy lisa. Hemos estimado la altura de estas placas a través de muestras sombreadas unidireccionalemente con platino. El promedio de los valores obtenidos es de 6.7 ± 1.4 nm.
En conjunto los resultados obtenidos en esta tesis permiten sugerir que el componente principal de la cromatina en los cromosomas metafásicos es el gránulo de 30-40 nm. Dependiendo de las condiciones iónicas, este elemento estructural fundamental se agrega a través de uniones cabeza-cola para formar fibras (fuerza iónica muy baja), o bien se agrega mediante interacciones laterales para formar placas (condiciones salinas próximas a las de la cromatina metafásica).
Our group has studied the chromatin structure in the chicken erythrocyte nuclei (Bartolome et al., 1994; Bartolomé et al., 1995; Bermúdez et al., 1998). The consequences of this studies has been the elaboration of a folding model of the chromatin fiber with a high local concentration of DNA. However, the maximum level of chromatin condensation, is found in the metaphase chromosomes. Although the bibliography has proposed different models to explain the chromatin folding inside the chromosomes, there is a low knowledge about the molecular structure of chromatin in the condensed chromosomes.
In this thesis, we have carried out an exhaustive electron microscopy study about the HeLa cells metaphase chromosomes. We have studied a large number of chromosome electron micrographs (4410). Chromosomes were partially denaturated under a wide variety of conditions in order to observe some chromatin structural element inside them.
Our studies indicate that chromosomes can adopt three global structural forms in function of the ionic conditions: compact, granular and fibrillar.
The compact form is the most frequent and we can observe it in the presence of monovalent and divalent cations in similar concentrations than the ones found in metaphase chromatin (Mg2+ 1.7-40 mM). These chromosomes have highly condensed chromatids and we can appreciate overlapped chromatin plates around the chromosomes edges. When the chromosomes are incubated with solutions containing lower cations concentration (Mg 2+£ 1.7 mM) they become granular. The granular structures seen inside these chromosomes show a diameter of about 35 nm. Fibrillar chromosomes are observed only at very low ionic strength. The fibers seen emanating from the chromatids have a diameter of 30-40 nm.
Our results obtained from partially denaturated chromosomes show that there are three structural elements inside the metaphase chromosomes: the fiber, the 30-40 nm chromatin granule and the plate.
The largest fibers with a diameter of 100-400 nm, presumably are produced by mechanical deformation of chromosomes during the preparation processes. Depending of the ionic conditions these fibrillar structures are composed by plates or granules. The thinnest fibers are formed by face to face association of the 30-40 nm chromatin granules. These kind of fibers are usually found only at very low ionic strength.
The chromatin granules are compact bodies with 35 nm of diameter. These compact bodies were previously described in our laboratory and were modeled as compact solenoids of nucleosomes forming (Daban and Bermúdez, 1998). They are usually seen at low divalent cation concentrations and in chromosome samples treated with micrococal nuclease.
The plate is the most frequent structural element when the chromosomes are in their compact form (high ionic strength, similar to physiological conditions). This element has not been described by any group. It is a chromatin element with a regular structure and very smooth surface. We have estimated the height of the steps between layers in unidirectional shadowing experiments. The value obtained is 6.7 ± 1.4 nm.
Our results suggest that the fundamental component inside the metaphase is the 30-40 nm chromatin granules. Depending of the ionic conditions, this basic structural element forms fibers through face to face interactions (very low ionic strength) or form plates through side to side interactions (high ionic strength similar to metaphase chromatin).
Buitrago, 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.
Wallace, Julie Ann 1977. "Mitotic regulators and their effects on Drosophila : chromosome structure during development." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/31187.
Повний текст джерелаIncludes bibliographical references.
Variants of the canonical cell cycle are frequently used in nature to accomplish specific developmental goals. In one such variant, the endocycle, synthesis phase alternates with a gap phase without an intervening mitosis, producing cells that have multiple copies of the genome. These cells show diversity in their chromosome structure; at one extreme, the sister chromatids are separate (polyploid) and at the other extreme, the sisters are held together (polytene). The endocycle itself can be modified and these variations are speculated to correlate with the observed differences in chromosome structure. In this thesis, we have analyzed the contribution of mitotic regulators to the endocycle and polytene chromosome structure in Drosophila. We show that morula, a gene required for the transition from polytene to polyploid chromosome structure in Drosophila nurse cells, is a subunit of the anaphase-promoting complex/cyclosome. Increasing levels of cyclin B, a known mitotic target of the APC/C, does not alter the timing of the transition, indicating that CYCLIN B is not the only APC/C target at the polyteny-polyploidy transition. In mitosis, activity of APC/C and POLO lead to the loss of sister-chromatid cohesion and we find that mutants in polo are unable to progress through the polyteny-polyploidy transition. Finally, we find that the cohesin complex, a complex required for the physical attachment of sister chromatids in mitosis, is required for proper polytene chromosome structure in the salivary gland. These results describe a requirement for the cohesin complex in a variant of the cell cycle lacking mitosis and indicate that sister-chromatid cohesion differentiates polytene and polyploid chromosome structures.
by Julie Ann Wallace.
Ph.D.
Cole-Showers, Curtis Lanre. "Population structure and demographics in Nigerian populations utilizing Y-chromosome markers." University of the Western Cape, 2014. http://hdl.handle.net/11394/5326.
Повний текст джерелаNigeria is peopled by ethnically and linguistically diverse populations of which little were known until the last few millennial. The absence of major natural geographical barrier increases the possibility of the populations being affected by the same demographic events. The aim of this thesis was to ascertain the genetic variations and demographics in five major Nigerian populations using Y-markers. This was done by determining the genetic structures of the Afro-asiatic speaking Hausa (n=78) of Northern Nigeria and the Niger Congo speaking populations of Igbo (n=119), Yoruba (n=238), Bini (n=13) and Ijaw (n=15) of Southern Nigeria all spread over 22 geographical origins and four (North, South east, south west and South south) geographical regions. They were compared with more than 2000 individuals from 46 populations of 20 other African and Middle Eastern countries, in published literature. The Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended Y-Short Tandem Repeats (STRs) and nine Y-Single Nucleotide Polymorphisms (SNPs) haplogroups were typed with multiplex Polymerase Chain Reaction (PCR), Restriction Fragment Length Polymorphisms (RFLP) and High Resolution Melting (HRM). Summary statistics and measures of diversity were determined. Population structure was assessed with Population Pairwise Differences, hierarchical Analysis of Molecular Variance, Multidimensional scaling and correspondence analysis plots. Mantel’s test was used to assess the correlation of genetic distances with geographic distances. Demographic inferences were assessed with lineage based Network reconstruction, Spatial autocorrelation plots, effective migrants per population and both Inter and Intra-lineages Times to the Most Recent Common Ancestor (TMRCA). The patterns of diversity of the Y-markers showed a North-South gradient and a notable sub-structure among the Hausa populations. The Niger-Congo speakers displayed rare presence of haplogroups R and E1b1b but a preponderance of E1b1a7. Overall, the Y markers showed high diversities and significant genetic sub-structure within the Hausa populations of Nigeria with stronger linguistic than geographical bias. The demographic evaluations gave credence for genetic validation of both historical records and archeological findings among these Nigerian populations. These populations showed stronger affiliations with other sub-Saharan African populations rather than with North African or Middle Eastern populations, lacking evidence for the Middle Eastern origins of the male founders of these populations. Finally, the contribution of these Nigerian dataset would greatly enhance the Africa meta-population on the YHRD with more than 274 new haplotypes of forensic estimation significance.
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.
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 джерелаNewman, Scott. "The structure and evolution of breast cancer genomes." Thesis, University of Cambridge, 2011. https://www.repository.cam.ac.uk/handle/1810/239397.
Повний текст джерелаBARRETO, L. M. "Estudos Citogenéticos em Dorstenia L. (Moraceae)." Universidade Federal do Espírito Santo, 2016. http://repositorio.ufes.br/handle/10/7838.
Повний текст джерелаPrevious cytogenetic studies in Dorstenia mention that the species may have 24 to 72 chromosomes, and suggested a conserved chromosome number 2n = 32 for the Neotropic species. However, some information reported in the literature are dubious or insufficient to assess the potential of cytogenetic data to the better understand of systematics and evolution issues within this genus. Here, eight species of Neotropical Dorstenia had their karyotypes characterized, and the nuclear DNA content measured. Dorstenia bahiensis, D. cayapia, D. grazielae, D. hirta and D. turnerifolia had their karyotypes characterized and the DNA nuclear content measured for the first time. Morphological plant characters and morphometric data were submitted to cluster analysis, followed by a test of group sharpness, and ordination analysis, aiming to support the discussion about the potential of cytogenetic data to infrageneric systematic of Dorstenia. The species showed chromosome number of 2n = 32, varying in chromosomes morphology. The karyotypes least asymmetric were observed in Dorstenia elata, and the more asymmetric were registered in D. bahiensis and D. bonijesu. The 2C value ranged from 3.21 picograms (pg) D. bahiensis to 5.47 pg in D. arifolia. Morphologically similar species, like D. hirta and D. turnerifolia, grouped together based on morphometric data. The sharp groups based on morphometric data correspond to species circumscribed under the sections Dorstenia, Lecania and Emygodia, previously established based on the plant morphology. Our results supports that the chromosome number 2n = 32 is possible conserved in the Neotropical species of Dorstenia, and indicate the potential of cytogenetic data to the systematics of this genus.
Goward, Melanie Elizabeth Anne. "Structural, functional and comparative studies of human chromosome 22q13.31." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620370.
Повний текст джерелаCapela, Delphine. "Analyse structurale du chromosome de Sinorhizobium meliloti souche 1021." Toulouse 3, 2000. http://www.theses.fr/2000TOU30111.
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 джерелаBenoist, Camille. "Intégration fonctionnelle du complexe SMC chez bacillus subtilis : étude de suppresseurs." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA112268.
Повний текст джерелаSMC proteins (for "Structural Maintenance of Chromosomes") are involved in different aspects of chromosome dynamic such as condensation, segregation and DNA repair. Indeed, a Bacillus subtilis mutant lacking the SMC complex shows severe phenotypes such as defects in condensation and chromosome partitioning, an increase in sensitivity DNA damaging drugs or gyrase inhibitors. The viability of such strain is limited to conditions of slow growth. To understand the range of phenotypes associated with loss of this gene, a genetic identification of new partners was undertaken: spontaneous suppressors of smc deletion were isolated in rapid growth conditions. Different classes of suppressors have been identified, suggesting that different mutations could restore the viability of a strain lacking SMC complex. Characterization of suppressors revealed they can restore some of the defects shown in Δsmc mutant, particularly resistance to gyrase inhibitors, and seemed to limit the formation of DNA breaks. By sequencing the complete genome of suppressors, some of these mutations have been identified and cause an alteration of the biosynthetic pathway of transfer RNA. This disruption can restore the growth defect more efficiently than inhibition of translation by drugs such as chloramphenicol, or by reducing the pool of nucleotides by hydroxyurea. Taken together, these results suggest that the stringent response could be partly responsible for the suppressor phenotype. It is proposed that apart from the compaction of the chromosome, the SMC complex is directly involved in maintaining the integrity of replication forks
Dossin, François. "Mechanistic dissection of SPEN functionduring X chromosome inactivation." Thesis, Université Paris sciences et lettres, 2021. http://www.theses.fr/2021UPSLS042.
Повний текст джерелаIn female placental mammals, dosage compensation of X-linked gene expression is achieved early during development through transcriptional inactivation of one of the two X chromosomes (XCI). This process is dependent on Xist, a long non-coding RNA which coats and silences the X chromosome from which it is transcribed. The mechanisms through which Xist initiates transcriptional silencing during XCI remain however completely unknown. In 2015, several studies identified that the SPEN protein binds Xist RNA directly, and its implication in mediating gene silencing was reported. However, its precise function and mechanism(s) of action during XCI are unclear.During my PhD, I made use of a conditional loss of function approach, the auxin inducible degron, to acutely deplete SPEN in mouse embryonic stem cells (mESCs) undergoing XCI. Using this approach, I demonstrate that SPEN is absolutely necessary for chromosome-wide Xist-mediated gene silencing during initiation of XCI. Furthermore, using conditional Spen KO mouse embryos, I show that SPEN is also required for the transcriptional inactivation of the paternal X chromosome during imprinted X inactivation. Depleting SPEN in differentiated cells, in which XCI has been established, reveals that SPEN is neither required to maintain gene silencing nor to preserve the spatial organization of the inactive X chromosome.By combining fixed and live cell imaging of Xist and SPEN, I show that SPEN colocalizes with Xist RNA, and accumulates on the X chromosome, immediately upon Xist upregulation, suggesting that SPEN can initiate gene silencing very early on during XCI. Profiling SPEN chromatin binding sites reveals that SPEN is recruited to promoters and enhancers of active genes specifically. The magnitude of SPEN recruitment to X-linked promoters dictates the efficiency with which these genes will be silenced. Remarkably, SPEN disengages from chromatin after gene silencing, indicating that active transcription required for SPEN’s association with chromatin.Using a functional complementation approach, I identify the SPOC domain as the effector of SPEN’s gene silencing activity during XCI. Artificial tethering of SPOC to Xist RNA results in transcriptional repression along the entire X chromosome, demonstrating that SPOC contains all the sufficient potential to instruct gene silencing during XCI. I further characterize the protein interactors of SPOC using mass spectrometry and reveal that SPOC interacts with several protein complexes involved in repressing transcription, including the NCoR/SMRT (histone deacetylation), the NuRD (nucleosome remodeling/histone deacetylation) and the m6A writing (governing mRNA fate) complexes. Finally, several transcription initiation and elongation factors are found to interact with SPOC, as well as the RNA polymerase II (RNAPII) transcription machinery.I identify that SPOC interacts directly and specifically with the C-terminal domain (CTD) of RNAPII only when the latter is phosphorylated on Ser5, and determine the 3D structure of the SPOC/RNAPII-CTD Ser5-P complex at 1.8Å resolution. These results suggest that SPEN could directly repress transcription during XCI by interfering with RNAPII-CTD Ser5-P templated processes.Altogether, my PhD work reveals that SPEN is essential for chromosome-wide transcriptional silencing during XCI, both in mESCs and in vivo. Following Xist upregulation, SPEN is immediately recruited to active gene promoters and enhancers, silences transcription, and subsequently disengages from chromatin. Through its RRMs and SPOC domains, SPEN acts as a molecular integrator, bridging Xist with histone deacetylases, nucleosome remodelers, RNA methyltransferases and most importantly, the transcription machinery
Bland, Michael Jason. "Study of the constraints sustaining the two chromosome genome structure of vibrio cholerae." Paris 6, 2013. http://www.theses.fr/2013PA066794.
Повний текст джерелаLa majorité des bactéries ont leur génome organisé en un seul chromosome circulaire. Ces chromosomes sont organisés en régions spatialement confinés, qui sont caractérisés par des fréquences de contact faible entre les loci dans les régions différentes. Ces régions sont formées à la suite de processus liés à la transcription des gènes, la réplication et à la ségrégation des chromosomes, et la terminaison de la réplication et la division cellulaire. La bactérie Vibrio cholerae est parmi les 10 % des bactéries connues pour avoir leur génome divisé entre plusieurs chromosomes. Les deux chromosomes diffèrent en termes de mécanismes de réplication et de ségrégation, car le deuxième chromosome, comme tous les chromosomes bactériens secondaires, est dérivé d'un plasmide acquis par l'ancêtre commun des vibrions. La structure des chromosomes dans cet organisme est actuellement inconnue. Cette thèse détaille la construction d'un système basé sur la recombinaison conçu pour explorer la structure génomique de deux chromosomes de V. Cholerae. Cet outil prend appui sur un système de recombinaison utilisé pour décrire la structure du chromosome d'Escherichia coli, et son utilisation peut être élargie aux bactéries avec de multiples chromosomes, en travaillant d'une manière similaire aux systèmes de « Recombinase-mediated cassette exchange » (RMCE). En utilisant cet outil, nous démontrons que les régions terminales des chromosomes de V. Cholerae entrent en contact physique avec l'autre. Ce travail ouvre la voie à une étude à grande échelle du génome de V. Cholerae
Wright, 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.
Kabir, Sadia. "Molecular analysis of structure of chromosome 6R of triticale T701-4-6 /." Title page, summary and contents only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phk108.pdf.
Повний текст джерелаSabir, Kenneth Spencer. "Visual Analytics Of 3D Macro Molecular Structure." Thesis, The University of Sydney, 2018. http://hdl.handle.net/2123/18860.
Повний текст джерелаFielder, Anne. "A structural role for the H-NS protein in bacterial chromatin." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308709.
Повний текст джерелаPulicani, Sylvain. "Lien entre les réarrangements chromosomiques et la structure de la chromatine chez la Drosophile." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTS105/document.
Повний текст джерелаDifferent species have different genome organization. Whether it be the karyotype or gene order, these differences are seen even with relatively close species like Human and Mouse. This is caused by the chromosomal rearrangement. Infererence of rearrangement scenarios that transform one present-day species into another can give insight into evolutionary states, the ancestral genome being one of the intermediates of the true scenario.The chromosomal rearrangements are violent biological events for the cell. Indeed, numerous mechanisms are present to stop the cell cycle when the genome sequence is altered. Moreover, rearrangements can be the source of aberrant phenotypes, which are probably unfavorable for the carrier. With all that, it seams reasonable to assume the rearrangement scenarios are parsimonious.However, it is accepted that this criterion alone is not sufficient to efficiently build the evolutionary history of the genomes. Indeed, for whatever model we choose, the number of scenario is exponential in the number of rearrangements. Another biological constraint is needed. The spatial structure of the chromatin could be an essential missing criterion. It has been shown in vitro that when a double-stranded break of the DNA is non-homologously repaired, the strand used for repairing is close in space to the breakpoint. Our hypothesis is that the closer the breakpoints are in space, the more probable they are to participate in a rearrangement. This hold on genomics analysis of somatic cells, and between species. Let's name that hypothesis the locality hypothesis.We proposed a method to use the structural information in order to prioritize the rearrangements scenarios. The Hi-C data were the structural information that allowed us to apply our method to scenarios between D. melanogaster and D. yakuba.This results led us to ask whether the chromatin structure could evolve by itself. Then, it could be used as a phylogenetic mark. This idea is related to previous results showing the conservation of topological domains between species.This question seams to be new, and could open a new line of investigation. If the chromatin structure holds a phylogenetical signal, it becomes possible to ask ourselves about the mechanisms that occur during the selection, or if it is possible for the ancestral state to be inferred. Then, it could even be possible to compare the evolution of the sequence with the one of the chromatin structure.Thus, we defined a distance between genome structures, based on the comparison of contacts between orthologous loci. We applied this distance to a set of six species, including the Human, the Mouse and four Drosophila. This result confirms the presence of a phylogenetic signal in the spatial structure of the genomes. They also showed that we're in need for efficient methods to compare contacts data between species
Ravel, Christophe. "Structure et dynamique du génome de Leishmania (protozoa, kinetoplastida)." Montpellier 1, 1996. http://www.theses.fr/1996MON1T004.
Повний текст джерелаGarmendia, Eva. "A Unified Multitude : Experimental Studies of Bacterial Chromosome Organization." Doctoral thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-332471.
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 джерелаCrolla, John Anthony Cesidio. "Molecular investigations of structural and numerical chromosome abnormalities in man." Thesis, University of Southampton, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241901.
Повний текст джерелаStavrides, George Stavros. "Human chromosome 20q12-13.2 : structural, comparative and sequence variation studies." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619575.
Повний текст джерелаMansouri, Mahmoud R. "Molecular Characterisation of Structural Chromosomal Abnormalities Associated with Congenital Disorders." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6887.
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