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Relevant bibliographies by topics / Genome conformation / Dissertations / Theses

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Dissertations / Theses on the topic 'Genome conformation'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Nicoletti, Chiara. "Genome conformation and transcription regulation: methods and applications." Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3424943.

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The 3D organization of chromatin within the nucleus is crucial for genome functionality. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories), at the level of individual chromatin fibers, organized in compartmentalized domains (as the Topologically Associating Domains, TADs), and down to the formation of short range chromatin interactions (as enhancer-promoter loops). The widespread adoption of high-throughput techniques derived from Chromosome Conformation Capture (3C) has been instrumental in advancing the know

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2

Boulos, Rasha. "Human genome segmentation into structural domains : from chromatin conformation data to nuclear functions." Thesis, Lyon, École normale supérieure, 2015. http://www.theses.fr/2015ENSL1024/document.

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Le programme de réplication d’environ la moitié du génome des mammifères est caractérisé par des U/N-domaines de réplication de l’ordre du méga-base en taille. Ces domaines sont bordés par des origines de réplication maitresses (MaOris) correspondantes à des régions (~200 kb) de chromatine ouverte favorables à l’initiation précoce de la réplication et de la transcription. Grâce au développement récent de technologies à haut débit de capture de conformations des chromosomes (Hi-C), des matrices de fréquences de co-localisation 3D entre toutes les paires de loci sont désormais déterminées expéri

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3

Marie-Nelly, Hervé. "A probabilistic approach for genome assembly from high-throughput chromosome conformation capture data." Paris 6, 2013. http://www.theses.fr/2013PA066714.

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Les approches modernes de séquençage d’adn ne permettent pas la lecture de fragments de plus de quelques kb. De ce fait, ont été développés des méthodes algorithmique permettant de former de plus grandes séquences ˆ partir de ces petits fragments. Nous avons développé une nouvelle méthodologie d’assemblage de génome basée sur le HiC. Le HiC est une procédure biochimique permettant l’inférence de la structure tridimensionelle d’un génome. Basée sur des probabilités bayesienne, notre méthode inverse le flux logique d’analyse de ces données. A partir des données 3D nous pouvons détecter et corrig

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4

Marti, Marimon Maria Eugenia. "3D genome conformation and gene expression in fetal pig muscle at late gestation." Thesis, Toulouse, INPT, 2018. http://www.theses.fr/2018INPT0099.

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Dans le secteur de l’élevage porcin, les truies ont été sélectionnées pendant des décennies pour leur prolificité afin de maximiser la production de viande. Cependant, cette sélection a été associée à une mortalité plus élevée des nouveau-nés. Dans ce contexte, le muscle foetal squelettique est essentiel à la survie du porcelet, car il est nécessaire pour les fonctions motrices et la thermorégulation. Par ailleurs, la structure tridimensionnelle du génome s'est avérée jouer un rôle important dans la régulation de l'expression génique. Ainsi, dans ce projet, nous nous sommes intéressés à la con

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5

Nilsson, Johan. "Membrane protein topology : prediction, experimental mapping and genome-wide analysis /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-963-3/.

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6

Jurneczko, Ewa. "Resolving intrinsically disordered proteins of the cancer genome with ion mobility mass spectrometry." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8844.

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For proteins the link between their structure and their function is a central tenet of biology. A common approach to understanding protein function is to ‘solve’ its structure and subsequently probe interactions between the protein and its binding partners. The first part of this approach is non-trivial for proteins where localised regions or even their entire structure fail to fold into a three-dimensional structure and yet they possess function. These so called intrinsically or inherently disordered proteins (IDP’s) or intrinsically disordered regions (IDR’s) constitute up to 40% of all expr

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7

Schröder, Wiebke [Verfasser]. "Athletic performance and conformation in Hanoverian warmblood horses - population genetic and genome-wide association analyses / Wiebke Schröder." Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2010. http://d-nb.info/1009653288/34.

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8

LUCINI, FEDERICA. "Unconventional nuclear architecture in CD4+ T lymphocytes uncouples chromatin solubility from function." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2020. http://hdl.handle.net/10281/262913.

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Nei nuclei delle cellule eucarioti, l'informazione genetica codificata nel DNA è concentrata nel microscopico volume nucleare in forma di cromatina, un complesso di DNA e proteine. I meccanismi molecolari che gestiscono la compattazione e il ripiegamento della cromatina e che consentono l'espressione mirata delle porzioni di genoma necessarie alle attività della cellula sono noti come ‘epigenoma’. L’azione dell’epigenoma determina un avvolgimento e un posizionamento nucleare della cromatina specifico per ogni tipo cellulare, con aree dense e trascrizionalmente inattive (eterocromatina) ed aree

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9

Lazar-Stefanita, Luciana. "Functional reorganization of the yeast genome during the cell cycle." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066400/document.

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Des décennies d'études ont montré que la structure de la chromatine est étroitement liée aux processus métaboliques de l'ADN. Une bonne organisation des chromosomes tout au long du cycle cellulaire est particulièrement importante pour assurer le maintien de l'intégrité de l'ADN. Le but de mon projet de doctorat était de caractériser dans quelle mesure la réorganisation de la chromatine pendant le cycle cellulaire pourrait influencer la stabilité des chromosomes. Pour ce faire, nous avons d'abord effectué une étude complète de la réorganisation des chromosomes de la levure modèle Saccharomyces

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10

Lajoie, Bryan R. "Computational Approaches for the Analysis of Chromosome Conformation Capture Data and Their Application to Study Long-Range Gene Regulation: A Dissertation." eScholarship@UMMS, 2016. http://escholarship.umassmed.edu/gsbs_diss/833.

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Over the last decade, development and application of a set of molecular genomic approaches based on the chromosome conformation capture method (3C), combined with increasingly powerful imaging approaches have enabled high resolution and genome-wide analysis of the spatial organization of chromosomes. The aim of this thesis is two-fold; 1), to provide guidelines for analyzing and interpreting data obtained from genome-wide 3C methods such as Hi-C and 3C-seq and 2), to leverage the 3C technology to solve genome function, structure, assembly, development and dosage problems across a broad range o

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11

Lazar-Stefanita, Luciana. "Functional reorganization of the yeast genome during the cell cycle." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066400.pdf.

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Des décennies d'études ont montré que la structure de la chromatine est étroitement liée aux processus métaboliques de l'ADN. Une bonne organisation des chromosomes tout au long du cycle cellulaire est particulièrement importante pour assurer le maintien de l'intégrité de l'ADN. Le but de mon projet de doctorat était de caractériser dans quelle mesure la réorganisation de la chromatine pendant le cycle cellulaire pourrait influencer la stabilité des chromosomes. Pour ce faire, nous avons d'abord effectué une étude complète de la réorganisation des chromosomes de la levure modèle Saccharomyces

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12

Poterlowicz, Krzysztof. "An integrative bioinformatics approach for analyses of multi-level transcriptional regulation and three-dimensional organization in the epidermis and skin appendages : exploring genomic transcriptional profiles of the distinct stages of hair follicle and sweat gland development and analyses of mechanism integrating the transcriptional regulation, linear and high-order genome organization within epidermal differentiation complex in keratinocytes." Thesis, University of Bradford, 2013. http://hdl.handle.net/10454/5658.

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The transcription in the eukaryotic cells involves epigenetic regulatory mechanisms that control local and higher-order chromatin remodelling. In the skin, keratinocyte-specific genes are organized into distinct loci including Epidermal Differentiation Complex (EDC) and Keratin type I/II loci. This thesis introduces bioinformatics approaches to analyze multi-level regulatory mechanisms that control skin development and keratinocyte-specific differentiation. Firstly, integration of gene expression data with analyses of linear genome organization showed dramatic downregulation of the genes that

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13

Moindrot, Benoît. "Organisation de la chromatine et son lien avec la réplication de l'ADN." Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2012. http://tel.archives-ouvertes.fr/tel-00733254.

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L'organisation de la chromatine a une importance fonctionnelle pour contrôler le programme d'expression des gènes. Par contre, les liens qui l'unissent au déroulement de la réplication de l'ADN sont beaucoup moins connus. Grâce à des approches basées sur la capture d'interactions chromosomiques et sur l'imagerie cellulaire, nous avons étudié les liens entre le repliement à grande échelle de la chromatine et le timing de réplication. Cette analyse, effectuée dans des cellules humaines lymphoblastoïdes, des cellules mononucléées du sang (PBMC) et des cellules issues d'une leucémie myéloïde à car

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14

Smith, Emily M. "The Three-Dimensional Structure of the Cystic Fibrosis Locus: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/744.

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The three dimensional structure of the human genome is known to play a critical role in gene function and expression. I used chromosome conformation capture (3C) and 3C-carbon copy (5C) techniques to investigate the three-dimensional structure of the cystic fibrosis transmembrane conductance regulator (CFTR) locus. This is an important disease gene that, when mutated, causes cystic fibrosis. 3C experiments identified four distinct looping elements that contact the CFTR gene promoter only in CFTR-expressing cells. Using 5C, I expanded the region of study to a 2.8 Mb region surrounding the CFTR

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15

Mugnier, Marie-Ange. "Rna 3 du virus de la mosaique de la luzerne (almv) : obtention d'une copie cdna complete et etude conformationnelle de la region 5' du rna 3 de differentes souches." Université Louis Pasteur (Strasbourg) (1971-2008), 1986. http://www.theses.fr/1986STR13160.

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Synthese d'une copie complete d'adn complementaire qui est ensuite clone dans un vecteur d'expression pgemi. La comparaison de la sequence des cdna avec celle de l'arn 3 met en evidence une duplication dans la region 5' non codante, d'une sequence de 56 nucleotides qui constitue la difference majeure entre ces 2 sequences. La structure primaire de la region 5' non codante a ete examinee dans l'arn 3 de 3 souches du virus. Cette etude est completee par une analyse conformationnelle, en utilisant des sondes chimiques (dms) et enzymatique (v1 et s1)

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Smith, Emily M. "The Three-Dimensional Structure of the Cystic Fibrosis Locus: A Dissertation." eScholarship@UMMS, 2011. http://escholarship.umassmed.edu/gsbs_diss/744.

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The three dimensional structure of the human genome is known to play a critical role in gene function and expression. I used chromosome conformation capture (3C) and 3C-carbon copy (5C) techniques to investigate the three-dimensional structure of the cystic fibrosis transmembrane conductance regulator (CFTR) locus. This is an important disease gene that, when mutated, causes cystic fibrosis. 3C experiments identified four distinct looping elements that contact the CFTR gene promoter only in CFTR-expressing cells. Using 5C, I expanded the region of study to a 2.8 Mb region surrounding the CFTR

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17

Xu, Meng. "Specialised transcription factories." Thesis, University of Oxford, 2008. http://ora.ox.ac.uk/objects/uuid:a41d3243-c233-491a-916b-4e329cace434.

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The intimate relationship between the higher-order chromatin organisation and the regulation of gene expression is increasingly attracting attention in the scientific community. Thanks to high-resolution microscopy, genome-wide molecular biology tools (3C, ChIP-on-chip), and bioinformatics, detailed structures of chromatin loops, territories, and nuclear domains are gradually emerging. However, to fully reveal a comprehensive map of nuclear organisation, some fundamental questions remain to be answered in order to fit all the pieces of the jigsaw together. The underlying mechanisms, precisely

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18

Tavoosidana, Gholamreza. "Epigenetic Regulation of Genomic Imprinting and Higher Order Chromatin Conformation." Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7435.

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The genetic information encoded by the DNA sequence, can be expressed in different ways. Genomic imprinting is an epigenetic phenomenon that results in monoallelic expression of imprinted genes in a parent of origin-dependent manner. Imprinted genes are frequently found in clusters and can share common regulatory elements. Most of the imprinted genes are regulated by Imprinting Control Regions (ICRs). H19/Igf2 region is a well known imprinted cluster, which is regulated by insulator function of ICR located upstream of the H19 gene. It has been proposed that the epigenetic control of the insula

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Tavoosidana, Gholamreza. "Epigenetics Regulation of Genomic Imprinting and Higher Order Chromatin Conformation /." Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7435.

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20

Perikala, Satish Kumar. "Evolution of Epitope regions in HIV genome: Delineating Selective Forces acting on Conformational and Linear Epitopes." [Kent, Ohio] : Kent State University, 2010. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=kent1270735952.

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Thesis (M.S.)--Kent State University, 2010.<br>Title from PDF t.p. (viewed Apr. 28, 2010). Advisor: Helen Piontkivska. Keywords: Conformational Epitopes; Linear Epitopes; HIV; Selective Forces; synonymous changes; nonsynonymous changes; Radical changes; Conservative changes. Includes bibliographical references (p. 81-96).

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21

Borrman, Tyler M. "Measuring Stability of 3D Chromatin Conformations and Identifying Neuron Specific Chromatin Loops Associated with Schizophrenia Risk." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1111.

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The 23 pairs of chromosomes comprising the human genome are intricately folded within the nucleus of each cell in a manner that promotes efficient gene regulation and cell function. Consequently, active gene rich regions are compartmentally segregated from inactive gene poor regions of the genome. To better understand the mechanisms driving compartmentalization we investigated what would occur if this system was disrupted. By digesting the genome to varying sizes and analyzing the fragmented 3D structure over time, our work revealed essential laws governing nuclear compartmentalization. At a f

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22

Göndör, Anita. "Epigenetic Regulation of Higher Order Chromatin Conformations and Gene Transcription." Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8296.

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Epigenetic states constitute heritable features of the chromatin to regulate when, where and how genes are expressed in the developing conceptus. A special case of epigenetic regulation, genomic imprinting, is defined as parent of origin-dependent monoallelic expression. The Igf2-H19 locus is considered as paradigm of genomic imprinting with a growth-promoting gene, Igf2, expressed paternally and a growth antagonist, H19 encoding a non-coding transcript, expressed only from the maternal allele. The monoallelic expression patterns are regulated by the epigenetic status at an imprinting control

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23

Powers, Kyle Thomas. "Structure and function of the disordered regions within translesion synthesis DNA polymerases." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6625.

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Normal DNA replication is blocked by DNA damage in the template strand. Translesion synthesis is a major pathway for overcoming these replication blocks. In this process, multiple non-classical DNA polymerases form a complex at the stalled replication fork called the mutasome. This complex is structurally organized by the replication accessory factor PCNA and the non-classical DNA polymerase Rev1. One of the non-classical DNA polymerases within the mutasome then catalyzes replication through the damage. Each non-classical DNA polymerase has one or more cognate lesions, which the enzyme bypasse

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24

Prakash, Ashwin. "Evolution and Function of Compositional Patterns in Mammalian Genomes." University of Toledo Health Science Campus / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=mco1321301839.

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25

Ben, Zouari Yousra. "The functional and spatial organization of chromatin during Thymocyte development." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAJ025.

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Malgré les vastes études démontrant le rôle de la conformation génomique dans le contrôle transcriptionnel, de nombreuses questions restent en suspens, et en particulier, comment ces structures chromatiniennes sont formées et maintenues. Pour mieux comprendre les liens entre l’état de la chromatine au niveau des éléments régulateurs, la topologie de la chromatine et la régulation de la transcription, nous utilisons la technique CHi-C basée sur la technologie de capture de la conformation chromosomique (3C). En utilisant deux stratégies de capture ciblant deux différentes structure chromatinien

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26

Matala, Ilunga Benjamin. "Une correction à l’échelle et progressive des données Hi-C révèlent des principes fondamentaux de l’organisation tridimensionnelle et fonctionnelle du génome." Thèse, 2016. http://hdl.handle.net/1866/18662.

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Au cours des dernières années, de nouvelles évidences semblent indiquer que, tout autant que sa séquence, l’organisation d’un génome dans l’espace et le temps est importante pour comprendre la fonction de celui-ci. Une des avancées fonda- mentales sur le sujet a été de présenter à l’échelle du génome la carte des inter- actions ADN-ADN. Ces interactions sont essentiellement de 2 types, soit entre chromosomes ou entre régions du même chromosome. Par la suite, la modélisa- tion a permis de visualiser et appréhender la structure tridimensionnelle (3D) du génome à partir des donn

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27

"Protein Conformational Dynamics In Genomic Analysis." Doctoral diss., 2016. http://hdl.handle.net/2286/R.I.41277.

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abstract: Proteins are essential for most biological processes that constitute life. The function of a protein is encoded within its 3D folded structure, which is determined by its sequence of amino acids. A variation of a single nucleotide in the DNA during transcription (nSNV) can alter the amino acid sequence (i.e., a mutation in the protein sequence), which can adversely impact protein function and sometimes cause disease. These mutations are the most prevalent form of variations in humans, and each individual genome harbors tens of thousands of nSNVs that can be benign (neutral) or lead t

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Codina-Fauteux, Valérie-Anne. "Investigation des variants génétiques dans la dysfonction endothéliale et le risque de maladies cardiovasculaires." Thèse, 2018. http://hdl.handle.net/1866/22272.

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29

Držmíšek, Jakub. "Produkce a sekrece faktorů virulence Bordetella pertussis." Master's thesis, 2015. http://www.nusl.cz/ntk/nusl-353805.

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Bordetella pertussis is a strictly human pathogen and causative agent of infectious respiratory disease called whooping cough. In order to establish successful infection and colonization of the host, B. pertussis uses a broad spectrum of virulence factors such as adhesins (filamentous hemagglutinin, pertactin, and fimbriae) and toxins (adenylate cyclase and pertussis toxins). In addition, the type 3 secretion system (T3SS) was also found in the genus Bordetella. In connection to our previous characterisation of B. pertussis strain lacking the gene encoding RNA chaperone Hfq (Δhfq), which prove

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