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Dissertations / Theses on the topic 'Chromatin sequencing'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Cook, David. "SNF2H-Mediated Chromatin Remodelling and Its Regulation of the Pluripotent State." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35097.

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In embryonic stem cells (ESCs), the SWI/SNF, CHD, and INO80 families of ATP-dependent chromatin remodellers have been implicated in maintaining pluripotency-associated gene expression, however the involvement of ISWI family remodellers has yet to be defined. Here, we explore the importance of the mammalian ISWI homologue SNF2H (Smarca5) by deriving a conditional knockout mouse ESC line and observing the consequences of SNF2H depletion on the pluripotent state. Cre-mediated deletion of Snf2h disrupts hallmark characteristics of pluripotency, resulting in distinct morphological changes; reduced

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2

Josserand, Manon. "Exploring chromatin states in the Drosophila intestinal lineage." Electronic Thesis or Diss., Université Paris sciences et lettres, 2022. http://www.theses.fr/2022UPSLS056.

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Les cellules souches adultes s'auto-renouvellent et se différencient en un ou plusieurs types cellulaires, assurant ainsi l'homéostasie d’un tissu. Comprendre leur régulation est crucial pour mieux appréhender les mécanismes de prolifération incontrôlée et de défauts de différenciation observés lors de la tumorigenèse et du déclin fonctionnel des tissus pendant le vieillissement. Ma thèse avait pour but de mieux comprendre les états chromatiniens associés à l'activité des cellules souches adultes in vivo, dans un tissu homéostatique en utilisant l'intestin adulte de la drosophile comme modèle.

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3

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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Aitken, Sarah Jane. "The pathological and genomic impact of CTCF depletion in mammalian model systems." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284403.

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CCCTC-binding factor (CTCF) binds DNA, thereby helping to partition the mammalian genome into discrete structural and regulatory domains. In doing so, it insulates chromatin and fine-tunes gene activation, repression, and silencing. Complete removal of CTCF from mammalian cells causes catastrophic genomic dysregulation, most likely due to widespread collapse of 3D chromatin looping within the nucleus. In contrast, Ctcf hemizygous mice with lifelong reduction in CTCF expression are viable but have an increased incidence of spontaneous multi-lineage malignancies. In addition, CTCF is mutated in

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5

Deng, Chengyu. "Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience." Diss., Virginia Tech, 2021. http://hdl.handle.net/10919/101765.

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The epigenome carries dynamic information that controls gene expression and maintains cell identity during both disease and normal development. The inherent plasticity of the epigenome paves new avenues for developing diagnostic and therapeutic tools for human diseases. Microfluidic technology has improved the sensitivity and resolution of epigenomic analysis due to its outstanding ability to manipulate nanoliter-scale liquid volumes. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic platforms

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6

Hunt, Spencer Philip. "Whole-Genome Assembly of Atriplex hortensis L. Using OxfordNanopore Technology with Chromatin-Contact Mapping." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8580.

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Atriplex hortensis (2n = 2x = 18, 1C genome size ~1.1 gigabases), also known as garden orach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae family that has spread from its native Eurasia to other temperate and subtropical environments worldwide. Atriplex is a highly complex and polyphyletic genus of generally halophytic and/or xerophytic plants, some of which have been used as food sources for humans and animals alike. Although there is some literature describing the taxonomy and ecology of orach, there is a lack of genetic and genomic data that would otherwise h

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7

Kremsky, Isaac Jacob 1983. "Assessing the relationship between chromatin and splicing factors in alternative splicing." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/316790.

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Proteins that bind to DNA or RNA are both known to influence alternative splicing. However, there has not been so far a systematic experimental exploration of the relationship between these factors in their effect on splicing. In this thesis, we make use of the large amounts of publicly available high throughput sequencing data that now make it possible to explore this question on a genome-wide scale. We made exhaustive use of a method known as profiling to address this question. As most profiling methods in common use are merely qualitative, the first task of the thesis was to generate

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8

Sarma, Mimosa. "Microfluidic platforms for Transcriptomics and Epigenomics." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/90294.

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A cell, the building block of all life, stores a plethora of information in its genome, epigenome, and transcriptome which needs to be analyzed via various Omic studies. The heterogeneity in a seemingly similar group of cells is an important factor to consider and it could lead us to better understand processes such as cancer development and resistance to treatment, fetal development, and immune response. There is an ever growing demand to be able to develop more sensitive, accurate and robust ways to study Omic information and to analyze subtle biological variation between samples even with l

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9

Tavernari, Daniele. "Statistical and network-based methods for the analysis of chromatin accessibility maps in single cells." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/12297/.

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In questo lavoro, metodi provenienti dalla Fisica, dalla Statistica e dalla Teoria dei Grafi sono stati impiegati per caratterizzare ed analizzare profili di apertura e accessibilità della cromatina ottenuti con la tecnica ATAC-seq in singole cellule, nella fattispecie linfociti B provenienti da tre pazienti affetti da Leucemia Linfocitica Cronica. Una pipeline bioinformatica è stata sviluppata per processare i dati di sequencing ed ottenere le posizioni accessibili del genoma per ciascuna cellula. La quantità di regioni aperte e la loro distribuzione spaziale lungo il DNA sono state caratter

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10

Ma, Sai. "Microfluidics for Genetic and Epigenetic Analysis." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/78187.

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Microfluidics has revolutionized how molecular biology studies are conducted. It permits profiling of genomic and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this thesis, we focus on three projects (diffusion-based PCR, MID-RRBS, and SurfaceChIP-seq), which improved the sensitivities of conventional assays by coupling with microfluidic technology. MID-RRBS and SurfaceChI

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11

Herzel, Lydia. "Co-transcriptional splicing in two yeasts." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-179274.

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Cellular function and physiology are largely established through regulated gene expression. The first step in gene expression, transcription of the genomic DNA into RNA, is a process that is highly aligned at the levels of initiation, elongation and termination. In eukaryotes, protein-coding genes are exclusively transcribed by RNA polymerase II (Pol II). Upon transcription of the first 15-20 nucleotides (nt), the emerging nascent RNA 5’ end is modified with a 7-methylguanosyl cap. This is one of several RNA modifications and processing steps that take place during transcription, i.e. co-trans

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12

Andersson, Robin. "Decoding the Structural Layer of Transcriptional Regulation : Computational Analyses of Chromatin and Chromosomal Aberrations." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-130999.

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Gene activity is regulated at two separate layers. Through structural and chemical properties of DNA – the primary layer of encoding – local signatures may enable, or disable, the binding of proteins or complexes of them with regulatory potential to the DNA. At a higher level – the structural layer of encoding – gene activity is regulated through the properties of higher order DNA structure, chromatin, and chromosome organization. Cells with abnormal chromosome compaction or organization, e.g. cancer cells, may thus have perturbed regulatory activities resulting in abnormal gene activity. Henc

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13

Murphy, Travis Wilson. "Microfluidic tools for molecular analysis and engineering." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/90793.

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The shift of medical technology from a doctor's application of individualized medicine toward precision medicine has been accelerated by the advent of Next Generation Sequencing. Individualized medicine is where a doctor tries to understand the intricacies of a patient's medical state, where precision medicine uses a wealth of data to understand the individuality of a patient on a biological level to determine treatment course. Next Generation Sequencing allows for the collection of genome wide analyses such as genomic, transcriptomic, and epigenomic sequencing, which provides the backbone of

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14

Cao, Zhenning. "Microfluidic Engineering for Ultrasensitive Molecular Analysis of cells." Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/76721.

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The main focus of this research was the development of microfluidic technology for ultrasensitive and fast molecular analysis of cells. Chromatin immunoprecipitation (ChIP) assay followed by next generation sequencing serves as the primary technique to characterize the genomic locations associated with histone modifications. However, conventional ChIP-seq assay requires large numbers of cells. We demonstrate a novel microfluidics-based ChIP-seq assay which dramatically reduced the required cell number. Coupled with next generation sequencing, the assay permitted the analysis of histone modi

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15

Marchioretto, Lisa. "Development and validation of methods for genome-wide epigenetic analyses of human myogenic cells." Doctoral thesis, Università degli studi di Padova, 2014. http://hdl.handle.net/11577/3423853.

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Epigenetics is subjected to a pressing attention from the scientific community, because of its potential to explain the mechanisms of gene activation or repression. In this thesis I present a discovery-driven project aimed to the investigation of the epigenetic role in human myogenesis (and in particular the differentiation of myoblasts in myotubes). Studying epigenetics still presents significant hurdles, both experimental and computational. Therefore my first task was the establishment of robust protocols for investigating the role of epigenetics players during skeletal muscle differentiati

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16

Naler, Lynette Brigitte. "Epigenomic and Transcriptomic Changes in the Onset of Disease." Diss., Virginia Tech, 2021. http://hdl.handle.net/10919/103388.

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Current sequencing technologies allows researchers unprecedented insight into our biology, and how these biological mechanisms can become distorted and lead to disease. These aberrant mechanisms can be brought about by many causes, but some occur as a result of genetic mutations or external factors through the epigenome. Here, we used our microfluidic technology to profile the epigenome and transcriptome to study such aberrant mechanisms in three different diseases and illnesses: breast cancer, chronic inflammation, and mental illness. We profiled the epigenome of breast tissue from healthy wo

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17

Zhu, Yan. "Microfluidic Technology for Low-Input Epigenomic Analysis." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/83402.

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Epigenetic modifications, such as DNA methylation and histone modifications, play important roles in gene expression and regulation, and are highly involved in cellular processes such as stem cell pluripotency/differentiation and tumorigenesis. Chromatin immunoprecipitation (ChIP) is the technique of choice for examining in vivo DNA-protein interactions and has been a great tool for studying epigenetic mechanisms. However, conventional ChIP assays require millions of cells for tests and are not practical for examination of samples from lab animals and patients. Automated microfluidic chips off

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18

Müller, Lydia, Daniel Gerighausen, Mariam Farman, and Dirk Zeckzer. "Sierra platinum." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-216471.

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Background: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results: We propose a new peak-caller called \"Sierra Platinum\" that allows peak-calling of

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19

CROCI, OTTAVIO. "GENOMIC LANDSCAPE AND TRANSCRIPTIONAL REGULATION BY YAP AND MYC IN THE LIVER." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/556194.

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This thesis is divided in three sections; the main project is described in the first part, while additional projects are developed in two appendixes. In the main project we studied YAP, the downstream effector of the Hippo pathway, a transcriptional co-factor that plays a fundamental role in de-differentiation, cell proliferation and transformation. While its upstream regulation has been extensively studied, its role as transcriptional co-factor is still poorly understood. We show that YAP co-adjuvates the transcriptional responses of Myc oncogene to promote cell proliferation and transfor

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20

Chapus, Fleur. "Role of the DEAD-box Helicases DDX5 and DDX17 in Hepatitis B Virus RNA processing." Thesis, Lyon, 2020. http://www.theses.fr/2020LYSE1098.

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Rôle des hélicases DDX5 et DDX17 dans la régulation transcriptionnelle et la maturation des ARN du Virus de l'hépatite B. La chronicité du virus de l'hépatite B (VHB) repose sur la persistance de l'ADN circulaire et clos de manière covalente (ADNccc) dans le noyau des hépatocytes infectés. Le génome viral présente une structure chromatinisée sujette à des régulations épigénétiques impactant son activité biologique à différents niveaux. Une meilleure connaissance des facteurs cellulaires orchestrant la régulation transcriptionnelle et post-transcriptionnelle de l'ADNccc est fondamentale dans la

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21

Picard, Marion. "Etude des bases moléculaires du déterminisme sexuel et de la différenciation chez une espèce hétérogamétique femelle ZZ-ZW : Schistosoma mansoni." Thesis, Perpignan, 2015. http://www.theses.fr/2015PERP0032/document.

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Parmi plus de 20000 espèces de trématodes hermaphrodites, les Schistosomatidae ont un statut particulier car ils sont gonochoriques (i.e. deux sexes séparés). Le gonochorisme chez ces espèces, et leur dimorphisme sexuel, seraient en fait une stratégie d’adaptation à leur habitat : le système veineux des vertébrés à sang chaud, dont l’Homme. Malgré un mode chromosomique de déterminisme du sexe (i.e. hétérogamétie femelle ZW), les individus mâles et femelles demeurent phénotypiquement identiques durant tous les stades larvaires de leur cycle de vie hétéroxène. La différenciation sexuelle n’a lie

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22

Zapata, Ortiz Luis 1985. "On the evolution of cancer genomes : Signatures of selection reveal cancer genes across multiple tumor types." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/456685.

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Tumors are composed of fast-growing cells that become malignant under selection of biological functions needed for cancer development. In this thesis, I intend to uncover the basic evolutionary principles underlying cancer etiology. The first part constitutes a longitudinal analysis of a single CLL case, which tumor heterogeneity and clonal evolution were revealed by sequencing. The second explores the signatures of positive selection of somatic mutations allowing the identification of driver genes. The last part is an attempt to uncover the essential functions of the cancer cell using signals

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23

David, Sarah-Anne. "Impact de l'acclimatation embryonnaire à la chaleur sur des modifications post-traductionnelles des histones chez le poulet." Thesis, Tours, 2017. http://www.theses.fr/2017TOUR4036.

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L’altération de l’environnement périnatal peut impacter à long terme l’expression des gènes notamment par le biais de modifications épigénétiques. Une stratégie pour accroitre la thermotolérance des poulets de chair, sensibles à la chaleur en fin d’élevage (J35) est la thermo-manipulation embryonnaire (TM). Lors d’un coup de chaleur à J35, les modifications d’expression de gènes observées chez les poulets TM pourraient être liées à une altération de l’épigénome induite lors de l’embryogenèse et persistante au cours du développement. Cette thèse s’intéresse à deux modifications post-traductionn

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24

"Studies on Human Chromatin Using High-Throughput DNaseI Sequencing." Diss., 2009. http://hdl.handle.net/10161/1634.

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Boyle, Alan P. "Studies on Human Chromatin Using High-Throughput DNaseI Sequencing." Diss., 2009. http://hdl.handle.net/10161/1634.

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<p>Cis-elements govern the key step of transcription to regulate gene expression within a cell. Identification of utilized elements within a particular cell line will help further our understanding of individual and cumulative effects of trans-acting factors. These elements can be identified through an assay leveraging the ability of DNaseI to cut DNA that is in an open and accessible state making it hypersensitive to cleavage. Here we develop and explore computational techniques to measure open chromatin from sequencing and microarray data. We are able to identify 94,925 DNaseI hypersensitive

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26

Liang, Xiaoshan. "Studies of rainbow trout Ki-ras gene : sequencing, aflatoxin B1 binding, and chromatin structure." Thesis, 1993. http://hdl.handle.net/1957/36253.

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Characterization of the 5' flanking region of rainbow trout ki-ras gene was begun with the cloning and sequencing of this region by the inverse PCR technique and dideoxynucleotide chain termination method. In total, a nucleotide sequence of 1080 bp upstream from the first coding ATG was sequenced. Although this region showed certain promoter elements, it does not share common features with other mammalian ras promoters, which lack the TATA and contain multiple GC boxes with Spl binding activities. In contrast, this region in trout ras contains typical TATA and CCAAT boxes. This structural diff

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27

Belsky, Jason Alan. "Genome-wide Footprinting Uncovers Epigenetic Regulatory Paradigms by Revealing the Chromatin Occupancy Landscape." Diss., 2015. http://hdl.handle.net/10161/11371.

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<p><p>Eukaryotic genomes have extensive flexibility and plasticity to modify transcription and replication programs, yielding a myriad of differentiated cell types and survival mechanisms to adverse environmental conditions. As these genomic processes require precise localization of DNA-binding factors, their dynamic temporal and spatial distributions provide dramatically different interpretations of a static genome sequence. DNA-binding factors must compete with nucleosomes, the basic subunit of chromatin, for access to the underlying DNA sequence. Even though the spatial preferences of th

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28

Yu-ChengHung and 洪彧丞. "Construction of a database for transcription factor binding sites identified by plant chromatin immunoprecipitation sequencing (ChIP-seq) experiments." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/ss24mj.

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29

Ilic, Aleksandar. "Role of UCHL1 in regulating gene expression in prostate cancer cells." 2014. http://hdl.handle.net/1993/23912.

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Ubiquitin C-terminal hydrolase L1 (UCHL1) is a multifunctional protein primarily expressed in neuronal cells and involved in numerous cellular processes. UCHL1 has been linked with neurodegenerative diseases and a wide range of cancers but its specific role remains unknown. Previous UCHL1 knockdown studies have shown that UCHL1 controls the expression of pro- and anti-apoptotic genes as well as genes involved in cell cycle regulation but it is unknown how UCHL1 regulates these genes. We have shown that UCHL1 is cross-linked to DNA in DU145 but not in LNCaP or PC3 prostate cancer cells. There

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30

Lee, Bum Kyu. "Genome-wide target identification of sequence-specific transcription factors through ChIP sequencing." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-05-3038.

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The regulation of gene expression at the right time, place, and degree is crucial for many cellular processes such as proliferation and development. In addition, in order to maintain cellular life, cells must rapidly and appropriately respond to various environmental stimuli. Sequence-specific transcription factors (TFs) can recognize functional regulatory DNA elements in a sequence-specific manner so that they can regulate only a specific group of genes, a process which enables cells to cope with diverse internal and external stimuli. Human has approximately 1,400 sequence-specific TFs whose

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31

Paço, Susana Maria Santos do. "Data Science Methods Applied to the Study of The Signature of Regulatory CD4 T Cells in the Human Thymus and its Modulation by the Chromatin Landscape." Master's thesis, 2022. http://hdl.handle.net/10362/134919.

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Dissertation presented as the partial requirement for obtaining a Master's degree in Data Science and Advanced Analytics, specialization in Data Science.<br>This work was supported by: GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Por tugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Opera tional Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agree ment, through the European Regional Development Fund (ERDF), and by Fundação para a Ciênci

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32

"Genome sequencing of Leptolyngbya Heron Island, 2Å crystal structure of phycoerythrin and spectroscopic investigation of chromatic acclimation." Doctoral diss., 2014. http://hdl.handle.net/2286/R.I.25015.

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abstract: Photosynthesis is the primary source of energy for most living organisms. Light harvesting complexes (LHC) play a vital role in harvesting sunlight and passing it on to the protein complexes of the electron transfer chain which create the electrochemical potential across the membrane which drives ATP synthesis. phycobilisomes (PBS) are the most important LHCs in cyanobacteria. PBS is a complex of three light harvesting proteins: phycoerythrin (PE), phycocyanin (PC) and allophycocyanin (APC). This work has been done on a newly discovered cyanobacterium called Leptolyngbya Heron Island

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