Dissertations / Theses on the topic 'Genome damage'
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Banerjee, Ujjwal Kumar. "3-D Genome organization of DNA damage repair." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ121.
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Notre génome est constamment attaqué par des facteurs endogènes et exogènes qui menacent son intégrité et conduisent à différents types de dommages. Les cassures double brins (CDBs) font partie des dommages les plus nuisibles car elles peuvent entraîner la perte d'information génétique, des translocations chromosomiques et la mort cellulaire. Tous les processus de réparation se déroulent dans le cadre d'une chromatine hautement organisée et compartimentée. Cette chromatine peut être divisée en un compartiment ouvert transcriptionnellement actif (euchromatine) et un compartiment compacté transcriptionnellement inactif (hétérochromatine). Ces différents degrés de compaction jouent un rôle dans la régulation de la réponse aux dommages à l’ADN. L'objectif de mon premier projet était de comprendre l'influence de l'organisation 3D du génome sur la réparation de l'ADN. Pour cela, j’ai utilisé deux approches complémentaires dans le but d’induire et de cartographier les CDBs dans le génome de souris. Mes résultats ont mis en évidence un enrichissement de γH2AX, facteur de réparation des dommages à l’ADN, sur différentes régions du génome de cellules souches embryonnaires de souris, et ont également montré que les dommages persistent dans l’hétérochromatine, contrairement à l’euchromatine qui est protégée des dommages. Pour mon deuxième projet, j'ai cartographié l'empreinte génomique de 53BP1, facteur impliqué dans la réparation des CDBs, dans des cellules U2OS asynchrones et des cellules bloquées en G1 afin d’identifier de nouveaux sites de liaison de 53BP1. Mes résultats ont permis d’identifier de nouveaux domaines de liaison de 53BP1 couvrant de larges régions du génome, et ont montré que ces domaines de liaison apparaissent dans des régions de réplication moyenne et tardiveOur genome is constantly under attack by endogenous and exogenous factors which challenge its integrity and lead to different types of damages. Double strand breaks (DSBs) constitute the most deleterious type of damage since they maylead to loss of genetic information, translocations and cell death. All the repair processes happen in the context of a highly organized and compartmentalized chromatin. Chromatin can be divided into an open transcriptionally active compartment (euchromatin) and a compacted transcriptionally inactive compartment (heterochromatin). These different degrees of compaction play important roles in regulating the DNA damage response. The goal of my first project was to understand the influence of 3D genome organization on DNA repair. I used two complementary approaches to induce and map DSBs in the mouse genome. My results have shown that enrichment of the DNA damage repair factor γH2AX occurs at distinct loci in the mouse embryonic stem cell genome and that the damage persists in the heterochromatin compartment while the euchromatin compartment is protected from DNA damage. For my second project, I mapped the genomic footprint of 53BP1, a factor involved in DSBs repair, in asynchronous and G1 arrested U2OS cells to identify novel 53BP1 binding sites. My results have identified novel 53BP1 binding domains which cover broad regions of the genome and occur in mid to late replicating regions of the genome
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Alrumaihi, Faris Abdulrahman I. "Assessment of UVR-induced DNA damage and repair in nuclear genome versus mitochondrial genome." Thesis, University of Leicester, 2016. http://hdl.handle.net/2381/37614.
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DNA is a key molecular-target for the deleterious effects of ultraviolet radiation (UVR). Cells contain two types of DNA: nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) and UVR induces various types of damage in the both DNAs, notably CPDs and 8-oxodG. The aim of this thesis is to examine UVR induced DNA damage formation and repair in nDNA and mtDNA and to determine which is the most important genomic target with respect to cell killing in vitro using HaCaT calls as models of human skin. The cell viability data showed that UVB induces significant cell death, which increased over 48 h. SSR-exposure also showed significant levels of cell death after 24 h but with evidence of significant survival after 48 h. Alkaline modified comet assay data showed that CPDs and 8-oxodG were significantly produced in HaCaT cells exposed to UVB and SSR, with CPDs being formed in a greater yields and there being no significant repair of CPDs over 48 h post-exposure to UVB. However, HaCaT cells irradiated with SSR showed significant repair of both CPD and 8-oxodG over 48 h. QPCR data showed that UVB and SSR induced similar profiles of damage in both nDNA and mtDNA; despite the induced damage levels being higher with UVB. The data also showed that nDNA is the main target for UVR in HaCaT cells exposed to UVB and SSR. The UVB-induced QPCR-detectable DNA damage in nDNA and mtDNA was not fully repaired, with a significant level of DNA damage remaining at 48 h, however, there was significant repair of the induced-damage in nDNA post-exposure to SSR (correlating with survival/re-growth), whereas the damage to mtDNA was not fully repaired. The greater lethality of UVB is probably due to more the damage induced and poorer repair (notably of CPD) in nuclear DNA following UVB exposure. Whereas the proficient repair of SSR-induced CPD in nDNA probably dictates survival following SSR exposure – as there was still a notable level of residual damage in mtDNA post-SSR exposure. However, nDNA is the main target for UVR causing DNA damage and may lead to mutations, which increase the risk of skin cancer development.
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Manning, Francis C. R. "The persistence of carcinogen damage in specific regions of the genome." Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.277377.
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Alpi, Arno. "DNA damage checkpoint pathways and the maintenance of genome stability in C. elegans." Diss., lmu, 2004. http://nbn-resolving.de/urn:nbn:de:bvb:19-24487.
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Kasparek, Torben Rudolf. "Identification and characterisation of determinants of genome stability in response to a double-strand break." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:78e0a145-22c8-4abd-a746-e18c1939f5c9.
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Chromosomal rearrangements can lead to loss of heterozygosity (LOH) and oncogene activation, both of which represent possible causative events in cancer development. Such outcomes can result from the misrepair of DNA damage arising from a variety of events including DNA double-strand breaks (DSBs), collapsed replication forks, and dysfunctional telomeres. In response to a DSB, chromosomal stability is principally maintained through the two major DNA repair pathways; non- homologous DNA end-joining (NHEJ) and homologous recombination (HR). The objective of this thesis was to identify novel factors functioning in prevention of chromosomal instability in response to a DSB in Schizosaccharomyces pombe. To achieve this, a central aim was to identify the genes mutated in a number of radiation-sensitive mutants in fission yeast, previously isolated by the laboratory. These include the ‘loh’ mutants loh-2, loh-5, loh-6 and loh-7, which were found to harbour mutations in known DNA repair genes rad3, rad17, and rad57. Further, a pan-genomic screen for novel HR repair factors was carried out. The Bioneer Version 2 deletion-library, consisting of 3308 haploid deletion strains, was screened for strains displaying hypersensitivity to the DNA damaging agents MMS, bleomycin and camptothecin. This screen yielded 209 hits which were further characterised, utilising a set of non-essential Ch16 minichromosomes . The minichromosome Ch16-LMYAU harbours an HO endonuclease recognition sequence and a centromere-distal ade6-M216 heteroallele. Following break-induction, failed repair of the DSB leads to loss of the ade6 allele, indicated by pink sectoring on low adenine plates. 39 sectoring hits were identified and further characterised to quantify levels of gene conversion via HR in response to a DSB, utilising Ch16-RMYAH. As a result of this study, a group of novel genes functioning in HR repair were identified. Finally, one of these hits, putative RNA metabolism protein Nrl1, was subjected to further characterisation, associating this protein with DNA damage repair for the first time. The work presented here, documents the approaches taken to successfully identify novel DNA repair factors in fission yeast.
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Durant, Stephen Thomas. "The role of DNA mismatch repair in cellular responses to DNA damage and drug resistance." Thesis, University of Glasgow, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312133.
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Frigola, Rissech Joan 1991. "Determinants of the local mutation rate variability along the genome." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/669530.
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The rate at which mutations accumulate along the genome is not uniform but influenced by
factors such as chromatin compactness, replication time or transcription. Most of these
factors create mutational biases that encompass large areas of the genomes, including
several megabases. In recent years, though, local mutational asymmetries spanning just a
few base pairs have also been identified. This thesis focuses on the study of two of these
local mutational asymmetries. First, we describe a reduction in the number of exonic
somatic mutations caused by DNA polymerase mismatches, which we attribute to a higher
efficacy of the mismatch repair mechanism in these locations. Second we study the UV
induced DNA damage formation and repair at transcription factor binding sites and assess
the relative contribution of these two factors to the unexpected number of mutations of
these areas across transcription factors families. The presence of these local mutation rate
variations illustrates the difficulty of properly modeling the mutation rate, an important
procedure in many cancer genomics and evolutionary studies.La velocitat a la que les mutacions s’acumulen al llarg del genoma no és uniforme sinó que depèn de diversos factors. Alguns dels més coneguts són l’empaquetament de la cromatina, el moment de replicació o la transcripció. La majoria d’aquests factors creen variacions mutacionals que abarquen grans àrees del genoma, incloent varies megabases. En els últims anys, però, també s’ha identificat variabilitat en el ritme en que s’acumulen les mutacions a escala molt més petita, en regions de poques bases. Aquesta tesi es centra en l’estudi de dos d’aquestes variacions locals en el ritme en que les mutacions tenen lloc. Primer, hem descrit una reducció en el número de mutacions somàtiques en els exons causades per errors de la AND polimerasa, que hem atribuït a una major eficàcia del mecanisme encarregat aquest tipus d’errors en els exons. En segon lloc, hem estudiat com les lesions en el DNA causades per la llum ultraviolada es generen i són reparades als llocs d’unió dels factors de transcripció i hem determinat fins a quin punt cada un d’aquests processos permeten explicar l’inesperat número de mutacions en aquestes regions. La presència d’aquestes variacions locals la velocitat a la que les mutacions s’acumulen al llarg del genoma posen de manifest la dificultat de modelar correctament aquest procés, un procediment central en molts estudis evolutius i de genòmica del càncer.
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Blance, Stephen J. "DNA repair and recombination in Streptomyces coelicolor." Thesis, University of Liverpool, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367139.
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Finneran, Bryan P. "Developing and Testing an ELISA Biosensor for Measuring UV-Induced Viral Genome and Protein Damage." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1593640837647181.
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Bhattacharjee, Sonali. "The role of Fml1 and its partner proteins Mhf1 and Mhf2 in promoting genome stability." Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.711640.
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Macpherson, Annie. "Metabolic dysfunction and impairments in the DNA Damage Response : dissecting a pathomechanistic link between Microcephalic Primordial Dwarfisms and cancer cachexia." Thesis, University of Sussex, 2017. http://sro.sussex.ac.uk/id/eprint/71421/.
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Yu, Wei [Verfasser], M. Cristina [Akademischer Betreuer] Cardoso, and Barbara [Akademischer Betreuer] Drossel. "Genome-wide analysis of DNA damage and repair / Wei Yu. Betreuer: M. Cristina Cardoso ; Barbara Drossel." Darmstadt : Universitäts- und Landesbibliothek Darmstadt, 2015. http://d-nb.info/1110980728/34.
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Walker, Sarah A. "Investigating the role of the ATR-dependent DNA damage response in the aetiology of microcephalic primordial dwarfism disorders." Thesis, University of Sussex, 2012. http://sro.sussex.ac.uk/id/eprint/43346/.
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Repair of damage to the DNA is essential for the maintenance of genomic stability, both during embryonic development and normal growth. The cell has therefore evolved a complex array of interconnected pathways to ensure the appropriate response to DNA damage is initiated, such as cell cycle checkpoint arrest, activation of DNA repair pathways or induction of apoptotic processes. These co-ordinated signal transduction pathways have been termed the DNA damage response (DDR). A previous study showed that ATR-dependent damage responses were frequently defective in cell lines from patients with Microcephalic Primordial Dwarfism (MPD) disorders. In this thesis I have further characterised ATR–dependent damage response signalling in several cell lines from patients with various MPD disorders. I have shown that novel mutations in PCNT, which encodes a structural centrosomal protein, result in an MPD disorder and have characterised the associated ATRdependent DNA damage responses. I also contributed to the identification of mutations in ORC1, encoding a component of the DNA replication Origin Recognition Complex, in further MPD patients and examined origin licensing and Sphase progression in the patient derived cell lines. As a novel finding, I observed defects in the ATR-dependent G2/M checkpoint response in these cells. Additionally, I have characterised novel mutations in ATRIP, a gene encoding the obligate partner of ATR, in Seckel Syndrome patients, denoting a novel genetic defect in this condition. Finally, I have explored the role of PLK1 and AurA kinase in ATRdependent G2/M checkpoint control and provided compelling evidence of misregulation of this pathway in various MPD-patient derived cell lines. Collectively these data provide important functional insights into the genetic defects that cause MPD disorders and further explore the link between defective ATR-dependent damage response signalling and microcephaly.
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Powell, James Rees. "Measuring DNA damage and associated epigenetic changes genome-wide in cells following exposure to platinum analogue chemotherapeutic drugs." Thesis, Cardiff University, 2014. http://orca.cf.ac.uk/65976/.
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Many chemotherapy drugs act by inducing DNA damage leading to cell death, and the platinum analogue class of anticancer drugs are the most commonly used DNA damaging chemotherapeutic drugs. Despite extensive analysis of platinum-DNA interactions, particularly characterising the individual adducts and their effects on DNA replication, transcription and cell survival, measurement of these adducts in cells with higher sensitivity and precision is necessary. Previous work studying platinum-DNA adduct formation has been performed using DNA damage assays such as immuno-slot-blots to detect whole genome DNA damage, or with combinations of chromatography and mass spectrometry to characterise each adduct individually. The ability to measure platinum-induced DNA damage genome-wide with high resolution in human cells could have profound implications for basic mechanistic research, as well as clinical translational research and treatment stratification, by providing a tool with the potential for predicting clinical response to these agents. The achievement of this PhD was developing an assay to measure platinuminduced DNA damage induction at high resolution, density and precision within the genome of human cells. This was achieved using DNA immunoprecipitation coupled with analysis using DNA microarrays, allowing measurements of platinum-induced DNA damage to be made at high resolution throughout the human genome for the first time. This assay was initially developed to measure cisplatin and oxaliplatin induced DNA damage in the genome of the yeast model organism Saccharomyces cerevisiae and experimental profiles of cisplatin and oxaliplatin-induced DNA damage were validated by demonstrating close correlation with mathematically generated predicted profiles for platinum-induced DNA damage. The assay was then applied and validated to measure cisplatin, oxaliplatin and ultraviolet-induced CPD formation in human fibroblast cells, and again, experimental profiles of cisplatin and oxaliplatin-induced DNA damage and UV-induced CPD formation were shown to correlate well with predicted profiles of DNA damage. Novel comparative analytical approaches for studying microarray data from these genome-wide DNA damage datasets are demonstrated and further validation of the assay is provided by demonstrating the contrast between platinum-induced DNA damage and UV-induced CPD formation genome-wide and in the context of repeat sequences of DNA. Finally, cisplatin and oxaliplatin-induced histone H3 acetylation changes are examined and histone H3 K14 acetylation is demonstrated to be a prominent histone modification following exposure to platinum analogues. Novel analysis is performed to investigate the influence of chromatin on platinum adduct formation, and greater platinum-induced DNA damage is demonstrated in DNA samples treated in vitro compared with DNA samples taken from cells treated in culture. Comparisons were also performed between histone H3 acetylation in yeast cells following exposure to cisplatin or UV irradiation and this comparison revealed very similar patterns of histone acetylation following exposure to these two different genotoxins.
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Duro, Eris. "Identification of MMS22 as a regulator of DNA repair." Thesis, University of Dundee, 2010. https://discovery.dundee.ac.uk/en/studentTheses/7b553aeb-8f92-492e-b16f-c4c96d36fb01.
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Obstacles such as DNA damage can block the progression of DNA replication forks. This is a major source of genome instability that can lead to cell transformation or death. The budding yeast MMS1 and MMS22 genes were identified in a screen for mutants that were hypersensitive to DNA alkylation that blocks replisome progression. I set out to investigate the cellular roles of these genes and found that cells lacking MMS1 or MMS22 are hypersensitive to a wide variety of genotoxins that stall or block replication forks, and are severely defective in their ability to recover from DNA alkylation damage. Homologous recombination (HR) is an important mechanism for the rescue of stalled or blocked replication forks and for the repair of double-strand breaks (DSBs). Strikingly, MMS1 and MMS22 are required for HR induced by replication stress but not by DSBs, and the underlying mechanisms were explored.I next identified the uncharacterized protein C6ORF167 (MMS22L) as a putative human Mms22 orthologue. MMS22L interacts with NF?BIL2/TONSL, the histone chaperone ASF1 and subunits of the MCM replicative helicase. MMS22L colocalizes with TONSL at perturbed replication forks and at sites of DNA damage. MMS22L and TONSL are important for the repair of collapsed replication forks as depletion of MMS22L or TONSL from human cells causes DNA damage during S–phase and hypersensitivity to agents that cause fork collapse. These defects are consistent with the observations that MMS22L and TONSL are required for the efficient loading of the RAD51 recombinase onto resected DNA ends and for efficient HR. These data indicate that MMS22L and TONSL are novel regulators of genome stability that enable efficient HR.
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Humphryes, Neil. "Global genome nucleotide excision repair factors and the ubiquitin-proteasome system regulate the DNA damage response in Saccharomyces cerevisiae." Thesis, Cardiff University, 2010. http://orca.cf.ac.uk/55468/.
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Lashgari, Anahita. "Investigating the function of histone H2A.Z in the human genome and mechanisms of chromatin incorporation." Thèse, Université de Sherbrooke, 2017. http://hdl.handle.net/11143/9886.
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Abstract : Regulation of transcription is crucial for the appropriate development and function of eukaryotic cells. In eukaryotes, DNA is organized into a dynamic, complex, nucleoprotein structure called chromatin. Chromatin structure provides markedly restricted access of transcription factors to regulatory sites. Several mechanisms have evolved to modulate chromatin dynamics in order to regulate proper gene expression. One of the most intriguing mechanisms that modulate chromatin structure is the exchange of canonical histones with histone variants by chromatin remodeling complexes.
Among the histone variants, H2A.Z is an essential regulator of gene transcription. H2A.Z is enriched at regulatory regions but significant levels of the histone variant can also be found within gene bodies. However, the role of H2A.Z within the gene bodies is still not well understood. Recent evidence suggests that active recruitment of H2A.Z within gene bodies is required to induce gene repression. In contrast to this view, we show that global inhibition of transcription results in H2A.Z accumulation at gene transcription start sites, as well as within gene bodies. Our results indicate that accumulation of H2A.Z within repressed genes can also be a consequence of the absence of gene transcription rather than an active mechanism required to establish repression.
The second part of my Ph.D. project was to investigate the potential role of BRD8 - a subunit of the p400/Tip60 complex - in p53-mediated signaling. We find that knockdown of BRD8 leads to p21 induction and concomitant cell cycle arrest in G1/S. We further demonstrate that the p53 transcriptional pathway is activated in BRD8-depleted cells, and this accounts for upregulation of not only p21 but also proapoptotic genes, an event that leads to consequent apoptosis. Importantly, the DNA damage response is induced upon depletion of BRD8 and DNA damage foci are detectable in BRD8-depleted cells under normal growth conditions, as indicated by immunostaining for γ-H2AX. Notably, H4K16 acetylation is reduced in BRD8-depleted cells suggesting that BRD8 may have a role in recruiting and/or stabilizing the p400/Tip60 complex within chromatin, thus facilitating DNA repair. Consistent with the activated DNA damage response, we find that in BRD8-depleted cells, CHK2 is activated but, surprisingly, CHK1 protein levels are severely reduced. Taken together, our results suggest that BRD8 is involved not only in mediating p53-dependant gene suppression, but also in mediating the DNA damage response.
In the last part of my Ph.D. project, I investigated the possible mechanisms involved in recruitment of the p400 chromatin remodeler complex to chromatin. I showed that histone variant H2A.Z is essential for efficient recruitment of p53 and p400 to the distal p53 binding element of the p21 promoter. Furthermore, using double knockout (DKO) MEFs for p300/CBP I showed that the depletion of p300/CBP lead to a severe decrease in the recruitment of p400 at p21 promoter. Further studies are necessary to fully understand the role of p300/CBP in targeting p400 to chromatin.
In conclusion, my studies provide insights into the molecular mechanisms involved in chromatin regulation by histone variant H2A.Z and chromatin remodeler complex p400.Résumé : La régulation de la transcription est un mécanisme crucial pour le bon développement et fonctionnement des cellules eucaryotes. Chez les eucaryotes, l'ADN est organisé dans une structure dynamique de nucléoprotéines appelée chromatine. La structure de la chromatine forme une barrière qui contrôle l'accès des facteurs de transcription à leurs sites de fixation sur l’ADN. Plusieurs mécanismes ont été acquis au cours de l'évolution pour moduler la dynamique de la chromatine afin de réguler de manière adéquate l'expression des gènes. Un des mécanismes les plus intriguant qui module la structure de la chromatine est le remplacement des histones canoniques par des variants d'histones. Il est effectué par des complex de remodelage de la chromatine. Parmi les variants d'histones, H2A.Z est un régulateur essentiel de la transcription des gènes. H2A.Z est enrichi aux régions régulatrices des gènes, mais des niveaux significatifs de ce variant d'histone peuvent aussi être observés au cœur des gènes. Le rôle de H2A.Z localisé a lèintérieur gènes n'est, pour l'instant, pas bien compris. Des résultats récents suggèrent que le recrutement actif de H2A.Z dans les gènes est requis pour induire leur répression. En opposition à ces résultats, nous montrons que l'inhibition globale de la transcription conduit à l'accumulation de H2A.Z aux sites d'initiation de la transcription, mais aussi au cœur des gènes. Nos résultats indiquent que l'accumulation de H2A.Z dans les gènes réprimés serait une conséquence de l'absence de transcription plutôt qu'un mécanisme actif requit pour établir la répression. La seconde partie de mon doctorat a été dédiée à l'étude du rôle de BRD8 (une sous-unité du complexe p400/Tip60) dans la signalisation contrôlée par p53. Nous avons trouvé que la déplétion de BRD8 conduit à l'induction de p21 et à l'arrêt concomitant du cycle cellulaire en phase G1/S. Nous montrons aussi que le circuit transcriptionnel de p53 est activé dans les cellules déplétées en BRD8. Cela résulte en l'induction de p21, mais aussi de gènes proapoptotiques, ce qui conduit la cellule en apoptose. De manière marquante, la voie de réponse aux dommages de l'ADN est induite suite à la déplétion de BRD8, ce qui est observée par l'apparition de foci de dommages à l'ADN révélés par immunocoloration de γ-H2AX. De plus, l'acétylation de H4K16 est réduite dans les cellules déplétées en BRD8, suggérant que BRD8 pourrait avoir un rôle dans le recrutement et/ou la stabilisation du complexe p400/Tip60 dans la chromatine, et pourrait donc faciliter la réparation de l'ADN. En accord avec le fait que la réponse aux dommages de l'ADN soit activée, nous trouvons que dans les cellules déplétées en BRD8, CHK2 est activé mais étonnamment le niveau de la protéine CHK1 était fortement diminué. Ensemble, nos résultats suggèrent que BRD8 est impliqué non seulement dans la répression des gènes régulés par p53, mais aussi dans la réponse aux dommages de l'ADN. Finalement, dans la dernière partie de mon doctorat j'ai étudié le mécanisme qui pouvait être responsable du recrutement du complexe p400 au niveau de la chromatine. Nous avons montré que le variant d'histone H2A.Z est essentiel pour le recrutement de p53 et de p400 au site distal de fixation de p53 sur le promoteur de p21. De plus, en utilisant des cellules MEF DKO pour p300/CBP, nous avons montré que la déplétion de p300/CBP conduit à une diminution sévère du recrutement de p400 au promoteur de p21. En conclusion, mes études permettent de mieux comprendre les mécanismes moléculaires impliqués dans la régulation de la chromatine par l'histone H2A.Z et le complexe de remodelage de la chromatine p400.
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Hiller, Björn. "The role of RNase H2 in genome maintenance and autoimmune disease." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-193520.
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Aicardi-Goutières syndrome (AGS) is an autosomal recessive encephalopathy with low incidence. The disease is caused by mutations in the genes encoding for TREX1, SAMHD1, ADAR, IFIH1 and the three genes encoding for the heterotrimeric RNase H2 enzyme. Biallelic mutations in any of the genes cause elevated type I interferon levels in the cerebrospinal fluid (CSF), the hallmark of AGS. In AGS patients, increased type I interferon levels cause massive inflammation in the brain that leads to mental and physical retardation that likely cause death in early childhood. AGS shows significant overlap with the prototypic autoimmune disease systemic lupus erythematosus (SLE). Like AGS patients, SLE patients are also characterized by increased type I interferon levels, anti-nuclear autoantibodies (ANAs) and arthritis. Moreover, heterozygous mutations in TREX1, SAMHD1 and RNase H2 are also found in a small fraction of SLE patients. Due to the genetic, molecular and clinical overlap, AGS is regarded as a monogenic variant of SLE. This overlap allows for the investigation of SLE pathomechanisms using genetically engineered mouse models with AGS-related mutations.
In order to generate a mouse model that allows for the identification of pathomechanisms in AGS patients with mutations in the genes encoding for the RNase H2 enzyme, we generated mice with deficiency for the RNase H2 enzyme. Mice with complete deficiency for the RNase H2 enzyme (Rnaseh2c-/- or Rnaseh2bKOF/KOF) died perinatally or were stillborn. Mouse embryonic fibroblasts (MEFs) from E14.5 Rnaseh2bKOF/KOF embryos displayed impaired proliferation that was caused by the accumulation of MEF cells in G2/M of the cell cycle which increased with cultivation time or if MEF cells were isolated from E18.5 Rnaseh2bKOF/KOF embryos. Gene expression analysis of E14.5 fetal liver cells revealed a robust p53-mediated DNA damage response with the cell cycle inhibitor cyclin- dependent kinase inhibitor 1a (Cdkn1a, p21) being the most up-regulated gene. We found increased numbers of phosphorylated histone H2AX (γH2AX) in fetal liver and thymus cells from E18.5 Rnaseh2bKOF/KOF embryos, indicative of DNA double-strand breaks. Finally, we could show increased ribonucleotide loads in genomic DNA from embryos that were completely deficient for the RNase H2 enzyme.
Collectively, we have demonstrated that complete RNase H2 deficiency causes persistent genomic ribonucleotide loads that render the DNA instable and prone to DNA strand breaks. DNA damage leads to the activation of p53 that in turn activates the cell cycle inhibitor p21 that inhibits cell cycle progression and likely causes accumulation of RNase H2-deficient cells in G2/M.
To bypass early lethality we also generated bone marrow chimera and cell type-specific knockouts of the Rnaseh2b gene. While fetal liver cells of E14.5 Rnaseh2bKOF/KOF embryos could maintain hematopoiesis of irradiated recipient mice for almost one year, bone marrow cells from these primary recipients failed to reconstitute lethally irradiated mice in a secondary transfer. In line with this observation, VavCre-mediated deletion of the Rnaseh2b gene caused a more than hundred fold reduction of peripheral blood B cells, while B cell numbers remained unaltered upon CD19Cre-mediated deletion that occurs much later in B cell development. These data suggested that RNase H2 deficiency leads to the accumulation of genomic ribonucleotides that might cause the accumulation of a so far uncharacterized DNA damage species with increasing cell cycle passages. The data further supported our hypothesis that the impact of RNase H2 deficiency is determined by the number of cell proliferation.
Finally, an epidermis-specific knockout of the Rnaseh2b gene displayed the most dramatic phenotype. Knockout mice were characterized by hyperpigmentation, hair loss and spontaneous ulcerations of the skin. Microscopically, these mice displayed moderate thickening of the epidermis and dermal fibrosis as indicated by increased collagen deposition. Macroscopic skin phenotypes were completely dependent on p53 expression, since concomitant deletion of the p53 gene rescued mice from hyperpigmentation, hair loss and ulcerations. This data demonstrated that Rnaseh2b deficiency in the epidermis may also lead to DNA damage and subsequent p53 activation as shown for fetal liver from E14.5 RNase H2-deficient embryos. Preliminary data also indicate an increased incidence of cancer formation in RNase H2/p53 double knockouts, identifying the RNase H2 enzyme as an important tumor suppressor.
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Adamson, Brittany Susan. "A Genome-Wide Study of Homologous Recombination in Mammalian Cells Identifies RBMX, a Novel Component of the DNA Damage Response." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10723.
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Repair of DNA double-strand breaks is critical to the maintenance of genomic stability, and failure to repair these DNA lesions can cause loss of chromosome telomeric regions, complex translocations, or cell death. In humans this can lead to severe developmental abnormalities and cancer. A central pathway for double-strand break repair is homologous recombination (HR), a mechanism that operates during the S and G2 phases of the cell cycle and primarily utilizes the replicated sister chromatid as a template for repair. Most knowledge of HR is derived from work carried out in prokaryotic and eukaryotic model organisms. To probe the HR pathway in human cells, we performed a genome-wide siRNA-based screen; and through this screen, we uncovered cellular functions required for HR and identified proteins that localize to sites of DNA damage. Among positive regulators of HR, we identified networks of pre-mRNA-processing factors and canonical DNA damage response effectors. Within the former, we found RBMX, a heterogeneous nuclear ribonucleoprotein (hnRNP) that associates with the spliceosome, binds RNA, and influences alternative splicing. We found that RBMX is required for cellular resistance to genotoxic stress, accumulates at sites of DNA damage in a poly(ADP-ribose) polymerase 1-dependent manner and through multiple domains, and promotes HR by facilitating proper BRCA2 expression. Screen data also revealed that the mammalian recombinase RAD51 is commonly off-targeted by siRNAs, presenting a cautionary note to those studying HR with RNAi and highlighting the vulnerability of RNAi screens to off-target effects in general. Candidate validation through secondary screening with independent reagents successfully circumvented the effects of off-targeting and set a new standard for reagent redundancy in RNAi screens.
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Guillemette, Shawna S. "Investigating Tumor Suppressors in the DNA Damage Response: Caretakers of the Genome and Biomarkers to Predict Therapeutic Response: A Dissertation." eScholarship@UMMS, 2004. http://escholarship.umassmed.edu/gsbs_diss/712.
Full textAbstract:
Our genome is constantly challenged by sources that cause DNA damage. To repair DNA damage and maintain genomic stability eukaryotes have evolved a complex network of pathways termed the DNA damage response (DDR). The DDR consists of signal transduction pathways that sense DNA damage and mediate tightly coordinated reactions to halt the cell cycle and repair DNA with a collection of different enzymes. In this manner, the DDR protects the genome by preventing the accumulation of mutations and DNA aberrations that promote cellular transformation and cancer development. Loss of function mutations in DDR genes and genomic instability occur frequently in many tumor types and underlie numerous cancer-prone hereditary syndromes such as Fanconi Anemia (FA).
My thesis research applies candidate-based and unbiased experimental approaches to investigate the role of several tumor suppressor genes (TSGs) in the DDR. My dissertation will first describe a novel function for the breast and ovarian cancer tumor suppressor and FA-associated gene FANCJ in the DDR to ultraviolet (UV) irradiation. In response to UV irradiation FANCJ supports checkpoint induction, the arrest of DNA synthesis, and suppresses UV induced point mutations. Suggesting that FANCJ could suppress UV induced cancers, in sequenced melanomas from multiple databases I found somatic mutations in FANCJ previously associated with breast/ovarian cancer and FA syndrome.
The second part of my dissertation will describe an RNA interference screen to identify genes modulating cellular sensitivity to the chemotherapeutic drug cisplatin. The hereditary breast/ovarian cancer tumor suppressor BRCA2 is essential for DNA repair, thus BRCA2 mutant ovarian cancer cells are initially sensitive to cisplatin chemotherapy that induces DNA damage. However, drug resistance develops and remains a major problem in the clinic. My screen identified the chromatin remodeling factor CHD4 as a potent modulator of cisplatin sensitivity and predictor of response to chemotherapy in BRCA2 mutant cancers. Taken together, my investigations highlight the important contribution of the DDR and the role they play in tumorigenesis and predicting therapeutic response.
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Lawson, Jonathan Luke Done. "Genome-wide microscopy screening identifies links across processes including a conserved connection between DNA damage control and the microtubule cytoskeleton." Thesis, University of Cambridge, 2015. https://www.repository.cam.ac.uk/handle/1810/253007.
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Previous PhD students in the lab created a method for large-scale, high-content microscopy screening of a cell library consisting of over 3000 single mutant strains of the fission yeast, Schizosaccharomyces pombe. Each strain has one nonessential gene knocked-out, allowing investigation of the resulting phenotypes. I report the implementation and completion of this screen; developing methods to ensure reliable and accurate results through inclusion of many controls across multiple screening repeats. In total, over 4.5 million images from approximately 19 000 biologically independent cell populations were imaged and analysed. All strains screened contained GFP-labelled tubulin (GFP-Atb2) allowing visualisation of the microtubule polymer network and its organisation in cells, a feature that is conserved across eukaryotes and simplified in S. pombe, making it easy to study. Examination of cell outlines and microtubule patterns was used to study three cell processes: the shape of cells, the organisational pattern of interphase microtubules and the cell cycle stage of cells, as judged by microtubule pattern. Comparison with extensive data from wild-type cells led to the identification of 262 factors that influence one or more of these cell processes. I go on to biologically validate some of the outcomes from the screen, leading to a publication in Developmental Cell reporting the screen, its findings and the online genomic resource SYSGRO. I then focus on a group of mutants that suggest a connection between the DNA damage response (DDR) and microtubule organisation. From here I show that the DDR induces elongation of microtubule bundles in response to the DDR kinases, ATM and ATR. I begin to reveal factors that may mediate this response and finally, I provide evidence to suggest that the same mechanism is conserved in cultured human cells (Hc3716-hTERT), which may go some way to explaining clinical results showing a beneficial effect of microtubule destabilisation in conjunction with cancer therapies.
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Guillemette, Shawna S. "Investigating Tumor Suppressors in the DNA Damage Response: Caretakers of the Genome and Biomarkers to Predict Therapeutic Response: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/712.
Full textAbstract:
Our genome is constantly challenged by sources that cause DNA damage. To repair DNA damage and maintain genomic stability eukaryotes have evolved a complex network of pathways termed the DNA damage response (DDR). The DDR consists of signal transduction pathways that sense DNA damage and mediate tightly coordinated reactions to halt the cell cycle and repair DNA with a collection of different enzymes. In this manner, the DDR protects the genome by preventing the accumulation of mutations and DNA aberrations that promote cellular transformation and cancer development. Loss of function mutations in DDR genes and genomic instability occur frequently in many tumor types and underlie numerous cancer-prone hereditary syndromes such as Fanconi Anemia (FA).
My thesis research applies candidate-based and unbiased experimental approaches to investigate the role of several tumor suppressor genes (TSGs) in the DDR. My dissertation will first describe a novel function for the breast and ovarian cancer tumor suppressor and FA-associated gene FANCJ in the DDR to ultraviolet (UV) irradiation. In response to UV irradiation FANCJ supports checkpoint induction, the arrest of DNA synthesis, and suppresses UV induced point mutations. Suggesting that FANCJ could suppress UV induced cancers, in sequenced melanomas from multiple databases I found somatic mutations in FANCJ previously associated with breast/ovarian cancer and FA syndrome.
The second part of my dissertation will describe an RNA interference screen to identify genes modulating cellular sensitivity to the chemotherapeutic drug cisplatin. The hereditary breast/ovarian cancer tumor suppressor BRCA2 is essential for DNA repair, thus BRCA2 mutant ovarian cancer cells are initially sensitive to cisplatin chemotherapy that induces DNA damage. However, drug resistance develops and remains a major problem in the clinic. My screen identified the chromatin remodeling factor CHD4 as a potent modulator of cisplatin sensitivity and predictor of response to chemotherapy in BRCA2 mutant cancers. Taken together, my investigations highlight the important contribution of the DDR and the role they play in tumorigenesis and predicting therapeutic response.
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Bianchi, Joy J. "Origin of somatic mutations in lymphoid cancers : role of the V(D)J recombinase Breakage-fusion-bridge events trigger complex genome rearrangements and amplifications in developmentally arrested T cell lymphomas End donation errors at antigen receptor loci trigger genome-wide instability in ATM-deficient T cell lymphomas." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCB057.
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Les cancers lymphoïdes présentent fréquemment des aberrations chromosomiques. Dans les lymphocytes, cette instabilité génomique peut découler d'une activité anormale de la recombinase V(D)J (i.e. RAG endonuclease), alors que des facteurs de réponse aux dommages à l'ADN (DDR), tels que les protéines Ataxia-telangiectasia mutated (ATM) et p53, sont connus pour empêcher l'apparition de réarrangements chromosomiques et la lymphomagénèse. Le but de ma thèse fut de tester la contribution relative de ces facteurs dans l'émergence des mutations somatiques dans le génome des lymphomes. Pour ce faire, j'ai réalisé du séquençage génome et transcriptome entier de différents lymphomes, issus de modèles murins génétiquement modifiés pour lesquels les activités RAG et DDR étaient altérées. Lors d'une première étude, j'ai identifié des lésions génomiques spécifiques et récurrentes, causées par l'activité « off-target » de RAG et, de manière plus surprenante, un pattern de réarrangements anormaux survenant en l'absence de RAG. J'ai mis en évidence un mécanisme de « Breakage-Fusion-Bridge », en l'absence de RAG, entrainant l'instabilité et l'amplification d'une région génomique s'étendant sur plusieurs mégabases. Plus encore, j'ai également montré que cette amplification mène à son tour à la surexpression de multiples gènes connus ou candidats dans le cancer et se retrouve dans un sous-groupe de leucémies humaines. Afin de rétablir la différentiation des cellules T, bloquée en l'absence des RAG, j'ai utilisé un autre modèle murin exprimant un récepteur des cellules T (TCR) transgéniques. Ce travail a permis de montrer que le stade du développement et l'activité RAG tous les deux déterminent le paysage génomique des lymphomes T et guident la transformation maligne des cellules à travers différentes voies oncogéniques. De plus, j'ai également réalisé la première étude génome entier de lymphomes T déficients pour ATM et ai identifié un nombre important d'anomalies dans ces tumeurs, présentes aux loci des récepteurs aux antigènes mais aussi à des positions ectopiques. Mes résultats suggèrent, qu'en l'absence d'ATM, les cassures de l'ADN induites par les RAG (non réparées ou résolues de manière anormales) déclenchent une instabilité massive au niveau des loci des récepteurs aux antigènes. Cette instabilité se propage ensuite ailleurs dans le génome et affecte des gènes du cancer. De manière plus générale, ma thèse approfondie la compréhension des mécanismes générant des mutations somatiques dans les cancers lymphoïdes, suite à des défauts de recombinaison V(D)J ou de DDRLymphoid cancers frequently harbor chromosomal aberrations. Abnormal V(D)J recombinase (i.e RAG endonuclease) activity is thought to promote genomic instability in lymphocytes, while DNA damage response (DDR) factors such as Ataxia-telangiectasia mutated (ATM) and p53 have been shown to suppress aberrant chromosomal rearrangements and lymphomagenesis. During my thesis, to test the relative contribution of these factors in shaping the pattern of somatic mutations in lymphoma genome, I performed whole genome and transcriptome sequencing of several genetically modified mouse lymphoma models in which the activities of RAG and DDR were perturbed. In a first study, I have identified specific recurrent genomic lesions caused by off-target RAG activity and, more surprisingly, a unique pattern of aberrant rearrangements occurring in the absence of RAG. I provided evidence that, in the absence of RAG, Breakage-Fusion-Bridge triggers instability and amplification of a genomic region of several megabases leading to the overexpression of multiple known and putative cancer genes. Importantly, I also showed that this region is found amplified in a subset of human leukemia. Using additional animal models in which blocked T cell differentiation due to the absence of RAG was rescued by the expression of a transgenic T cell receptor, I could demonstrate that both developmental stage and RAG activity determine T cell lymphoma genome landscapes and mediate malignant transformation through distinct oncogenic paths. In addition, I have established the first genome-wide analysis of ATM-deficient T-cell lymphomas and identified a high number of aberrations localized at antigen receptor loci and ectopic locations in these tumors. My results suggest that, in the absence of ATM, aberrantly resolved RAG-induced DNA breaks at antigen receptor loci trigger massive complex rearrangements spreading to ectopic locations and affecting cancer genes. Overall, my studies provide new insights into the mechanisms of somatic mutations arising in lymphoid cancers in the context of aberrant V(D)J recombination and DDR
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Boyko, Oleksandr, and University of Lethbridge Faculty of Arts and Science. "The versatile role of homologous recombination in plant cell : repair of DNA damage, stress-directed genome evolution and foreign DNA integration." Thesis, Lethbridge, Alta. : University of Lethbridge, Faculty of Arts and Science, 2008, 2008. http://hdl.handle.net/10133/724.
Full textAbstract:
Homologous recombination represents a DNA repair pathway. Its role in a plant cell is not limited to double strand break repair. It also extends to genome evolution via rearranging of DNA sequences, and has an important application in foreign DNA integration in the plant genome. Our study demonstrated that effects exerted by stress on homologous recombination and genome stability are not restricted to the exposed generation. The progeny of plants exposed to stress exhibited elevated spontaneous homologous recombination, changes in DNA methylation and higher tolerance to stress. These heritable changes are mediated by an unknown stress-inducible epigenetic signal. Furthermore, we demonstrated that using factors that enhance homologous recombination can improve the efficiency of genetic transformation by Agrobacterium. We have developed and patented a plant growth medium enhancing homologous recombination and significantly increasing the transformation frequency. The role of several other chemicals for the improvement of transformation was also evaluated.xxi, 246 leaves : ill. ; 29 cm. --
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Kaku, Taijin. "RD1 region in mycobacterial genome is involved in the induction of necrosis in infected RAW264 cells via mitochondrial membrane damage and ATP depletion." Kyoto University, 2007. http://hdl.handle.net/2433/135912.
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Lyraki, Rodanthi. "Molecular mechanisms underlying Retinitis pigmentosa type 2." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31254.
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The term 'Retinitis pigmentosa' (RP) represents a group of inherited, late-onset diseases characterised by progressive retinal degeneration due to photoreceptor death. Mutations in the RP2 gene are found in 7-18% of patients with X-linked RP, one of the most severe forms. The RP2 gene product is a membrane-associated protein which encompasses two distinct domains. The N-terminal domain is well characterised as possessing GTPase-activating protein (GAP) activity towards the small GTPase ARL3 and thus regulate the transport of lipid-modified proteins within the photoreceptor cell. However, it is not known if the loss of this particular function of RP2 is the sole reason that causes the disease, while the role of the protein's C-terminus remains unknown. This thesis focuses on the characterisation of two novel protein-protein interactions of RP2 with the aim to investigate novel roles of the protein. Firstly, evidence is provided that a highly-conserved cluster of RP2 residues that span both the N- and C-terminus participate in direct interaction with Osteoclast-stimulating factor 1 (OSTF1). Two hypotheses are explored about the potential role of the complex in SRC-mediated RP2 phosphorylation and the regulation of cell motility. Secondly, the catalytic subunit of DNA-dependent protein kinase (DNA PK) is identified as a novel interaction partner of RP2 in cultured cells. The two proteins are shown to co-localise in the nuclear and membrane compartments of a retinal-derived cell line and might engage in a kinase-substrate relationship. So far, no evidence was found that RP2 participates in the canonical function of DNA PK which is the regulation of DNA double-stranded breaks. Finally, the CRISPR/Cas9 genome editing method was applied on zebrafish embryos to generate a novel vertebrate animal model for the loss of RP2 function. One out of three different zebrafish lines with rp2 mutations was shown by histology to have mild late-onset thinning of the photoreceptor outer segments. The present thesis reports previously unexplored aspects of RP2's function and will, therefore, contribute to understanding the molecular mechanisms that underlie RP. Moreover, this thesis will contribute to the discussion about the usefulness of zebrafish as an RP model.
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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 bypasses with high accuracy and efficiency. Thus, the accuracy and efficiency of translesion synthesis depends on which non-classical DNA polymerase within the mutasome is chosen to bypass the damage. In this thesis, I discuss how the most appropriate polymerase is chosen. In so doing, I examine the components of the mutasome; the structural motifs that mediate the protein interactions in the mutasome; the methods used to study translesion synthesis; the definition of a cognate lesion; the intrinsically disordered regions that tether the polymerases to PCNA and to one another; the multiple architectures that the mutasome can adopt, such as PCNA tool belts and Rev1 bridges; and the kinetic selection model in which the most appropriate polymerase is chosen via a competition among the multiple polymerases within the mutasome. Taken together, this thesis provides and inclusive review of the current state of what is known about translesion synthesis with conclusions at its end suggesting what major questions remain and ideas of how to answer them.
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Meisenberg, Cornelia. "The role of ubiquitylation in regulating apurinic/apyrimidinic endonuclease 1." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:9a6582d4-6fc0-48c9-9c13-6c99e23e66e9.
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Apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair factor involved in the DNA base excision repair (BER) pathway that is required for the maintenance of genome stability. In this pathway, APE1 cleaves DNA at an abasic site to generate a DNA single strand break, allowing for repair completion by a DNA polymerase and a DNA ligase. High levels of APE1 have been observed in multiple cancer types however it is not understood if this contributes to cancer onset and development. What is known is that these cancers tend to display increased resistance to DNA damaging treatments and APE1 is therefore considered a key target for inhibition in the treatment of APE1-overexpressing cancers. Considering the relevance of modulating APE1 levels in disease and cancer treatment, very little is known about how cellular APE1 levels are regulated. Our lab has previously shown that the levels of the BER factors Pol β, XRCC1 and DNA Lig IIIα are regulated by ubiquitylation-mediated proteasomal degradation. The aim of this doctoral thesis was therefore to determine if ubiquitylation also regulates APE1 stability in cells. I present evidence that APE1 is ubiquitylated in cells and have identified the UBR3 E3 ligase that is responsible for this activity. Using mouse embryonic fibroblasts generated from Ubr3 knockout mice, I demonstrate that UBR3 regulates APE1 cellular levels. I furthermore show that a loss of cellular UBR3 leads to the formation of DNA double strand breaks and genome instability.
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Walz, Paul S. "Influence of pathogenic bacterial determinants on genome stability of exposed intestinal cells and of distal liver and spleen cells." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biology, c2011, 2011. http://hdl.handle.net/10133/3405.
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Most bacterial infections can be correlated to contamination of consumables such as food and water. Upon contamination, boil water advisories have been ordered to ensure water is safe to consume, despite the evidence that heat-killed bacteria can induce genomic instability of exposed (intestine) and distal cells (liver and spleen). We hypothesize that exposure to components of heat-killed Escherichia coli O157:H7 will induce genomic instability within animal cells directly and indirectly exposed to these determinants. Mice were exposed to various components of dead bacteria such as DNA, RNA, protein or LPS as well as to whole heat-killed bacteria via drinking water. Here, we report that exposure to whole heat-killed bacteria and LPS resulted in significant alterations in the steady state RNA levels and in the levels of proteins involved in proliferation, DNA repair and DNA methylation. Exposure to whole heat-killed bacteria and their LPS components also leads to increased levels of DNA damage.xiv, 132 leaves : ill. (chiefly col.) ; 29 cm
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Kosicki, Michal Konrad. "Cas9-induced on-target genomic damage." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/289911.
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CRISPR/Cas9 is the gene editing tool of choice in basic research and poised to become one in clinical context. However, current studies on the topic suffer from a number of shortcomings. Mutagenesis is often assessed using bulk methods, which means rare events go undetected, unresolved or are discarded as potential sequencing errors. Many of the genotyping methods rely on short-range PCR, which excludes larger structural variants. Other methods, such as FISH, do not provide basepair resolution, making the genotype assessment imprecise. Furthermore, it is not well understood how Cas9 delivery format influences the dynamics of indel introduction. Finally, many studies of on-target activity were conducted in cancerous cell lines, which do not accurately model the mutagenesis of normal cells in the therapeutic context. In my thesis, I have investigated on-target lesions induced by Cas9 complexed with single gRNAs and no exogenous template. I have followed the time dynamics of Cas9-induced small indels as a function of reagent delivery methods, established an assay for quantification of Cas9-induced genomic lesions that are not small indels ("complex lesions") and used this assay to isolate and genotype complex lesions, many of which would be missed by standard methods. I found that DNA breaks introduced by single guide RNAs frequently resolved into deletions extending over many kilobases. Furthermore, lesions distal to the cut site and cross-over events were identified. Frequent and extensive DNA damage in mitotically active cells caused by CRISPR/Cas9 editing may have pathogenic consequences.
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Damasceno, Jeziel Dener. "Caracterização molecular do envolvimento das proteínas LmHus1 e LmRad9 em mecanismos de reconhecimento e reparo de DNA no parasito Leishmania major." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/17/17136/tde-04042013-114550/.
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A estabilidade genômica é condição essencial à sobrevivência e ao funcionamento dos organismos vivos. No entanto, várias situações podem provocar danos no DNA. Por exemplo, cerca de 104 lesões podem ocorrer no material genético de uma célula de mamífero a cada dia. No intuito de preservar a integridade genômica e contornar os efeitos deletérios destas modificações, uma maquinaria constituída de proteínas especializadas em reconhecer e reparar estes danos foi selecionada ao longo do curso evolutivo. Defeitos em proteínas destas maquinarias causam instabilidade genômica e pode resultar em elevada taxa de mutações e quebras do DNA que resultam em eventos de amplificação gênica, como em células cancerosas. De uma maneira aparentemente contrária ao requerimento de estabilidade genômica como condição primordial para a perpetuação da vida, Leishmania apresenta um genoma notavelmente maleável e explora a amplificação gênica como recurso de sobrevivência. Ainda que a plasticidade genômica em Leishmania seja facilmente demonstrada, nós não conhecemos os mecanismos precisos pelos quais este parasita coordena a ação da maquinaria de detecção de danos no DNA e a consumação dos eventos de amplificação gênica. No intuito de contribuir para a compreensão deste processo, nós identificamos proteínas homólogas do complexo 9-1-1 (Rad9-Hus1-Rad1) em Leishmania major. As proteínas LmHus1 e LmRad9 apresentam marcada divergência estrutural em relação aos seus homólogos em outros eucariotos e nenhuma proteína obviamente homóloga a Rad1 foi identificada neste parasita. Análises filogenéticas indicam que LmHus1 e LmRad9 são relacionadas ao complexos heterotriméricos envolvidos na detecção de danos no DNA. Em acordo com isso, nossos experimentos demonstram que alteração nos níveis destas proteínas interfere na capacidade do parasita em lidar com estresse genotóxico. LmHus1 localiza-se no núcleo, é requerida para o crescimento normal deste parasita e a diminuição de sua expressão compromete mecanismos de controle de ciclo celular e manutenção de telômeros. LmRad9 também localiza-se no núcleo e sua superexpressão causa defeito de crescimento e de resposta ao estresse genotóxico em L. major. Nós observamos que LmHus1 e LmRad9 formam um complexo responsivo ao dano no DNA in vivo, uma forte indicação de que o complexo 9-1-1 tenha sido conservado em L. major. As peculiaridades estruturais destas proteínas sugerem que o complexo 9-1-1 de L. major possua uma arquitetura distinta em comparação aos eucariotos superiores. Em adição a isto, outras proteínas, tais como a LmRpa1, também apresentam uma marcante divergência estrutural. Isso sugere que a via de sinalização de danos no DNA envolvendo o complexo 9-1-1 e Rpa1 de L. major possua mecanismos peculiares de ação. Estas observações podem permitir entender como ocorreu o processo evolutivo da sinalização mediada pelo complexo 9-1-1 nos eucariotos, além de ajudar para o entendimento das bases moleculares de como este parasito conduz os eventos de amplificação gênica.Genome stability is a essential condition for survival and proper functioning of living organisms. However, a broad range of elements may lead to DNA damage. For instance, about 104 DNA lesions may be inflicted upon any given mammalian cell everyday. In order to maintain the genome integrity and circumvent the deleterious effects of these lesions, a molecular machinery composed of proteins specialized in detecting and repairing DNA damage has been selected in evolution. Defects of the proteins that constitute such machineries may result not only in a high mutation rate, but also in breaks in the DNA structure that can mediate gene amplification as observed in cancer cells. In an apparent opposition to such requirement for stability as an essential condition to life, the protozoan Leishmania presents a highly malleable genome and explores genome amplification as a survival and adaptation tool. Despite of the fact that the Leishmania genome plasticity can be easily demonstrated, the precise mechanisms that coordinate the molecular machineries involved in the detection and signaling of DNA damage, and in the regulation of gene amplification is still largely unknown. In order to contribute to a better understanding of these processes, we identified and studied the Leishmania major proteins that are homologues of those proteins that compose the 9-1-1 complex (Rad9-Hus1-Rad1). The proteins LmHus1 and LmRad9 present a high structural divergence when compared to its homologues from other eukaryotes and no obvious homologue of Rad1 was identified in the parasite genome. Phylogeny analysis indicated that LmHus1 and LmRad9 are closely related to heterotrimeric complexes involved in the detection of DNA damage. In accordance to that, our experiments demonstrated that altered levels of these proteins interfere with the parasite ability to deal with genotoxic stress. Moreover, LmHus1 was localized to the parasite nucleus and is a required protein for normal parasite proliferation. Besides, we showed that decreased levels of LmHus1 compromise cell cycle regulation and the maintenance of telomeres. LmRad9 was also shown to be localized to the cell nucleus and its overexpression led to growth defects and affected the L. major response to genotoxic stress. We also observed that LmHus1 and LmRad9 interact with each other to for a protein complex that is responsive to DNA damage in vivo, which strongly suggested that the 9-1-1 complex was conserved in L. major. The structural peculiarities of these proteins indicate that the possible L. major 9-1-1 complex has a different architecture when compared to the complex found in higher eukaryotes. In addition to that, other proteins, such as LmRpa1, also present a marked structural divergence. Altogether, these findings suggest that the DNA damage signaling pathway involving the 9-1-1 complex and LmRpa1 in L. major, may present a peculiar mode of action. These observations may contribute to a better understanding not only of the evolution of the signaling pathway mediated by the 9-1-1 complex in eukaryotes, but also of the molecular basis of the genome plasticity and the gene amplification phenomenon.
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Ozols, Agris. "Low-dose studies of genomic instability-mechanisms and targets." Thesis, Queen Mary, University of London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271260.
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Perl, Abbey Leigh. "Leveraging Small Molecule Activators of Protein Phosphatase 2A (PP2A) toElucidate PP2As Role in Regulating DNA Replication and Apoptosis." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1574418174603893.
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Costa, Natalia Layane Badaró. "Improved procedures to assess plant protoplast viability: evidencing cytological and genomic damages." Universidade Federal de Viçosa, 2017. http://www.locus.ufv.br/handle/123456789/11949.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
Fundação de Amparo a Pesquisa do Estado de Minas Gerais
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Em todas as aplicações, o teste de viabilidade e necessario para medir a taxa de protoplastos viáveis, possibiltando decidir os procedimentos de isolamento e purificação mais adequados e verificar se ha celulas suficientes para as etapas subsequentes. A microscopia de fluorescência geralmente é empregada para o teste de viabilidade. No entanto, alguns problemas têm sido apontados: longo tempo necessário para contar um número relativamente pequeno de protoplastos, aglomerados de células que impedem a observação dos protoplastos e percepção visual da fluorescência subjetiva ao observador. Este estudo teve como objetivo estabelecer procedimentos para teste de viabilidade adaptado para citometria de fluxo (FCM), MuseTM cell analyzer (Muse) e Ensaio cometa (CA). Para isso, Capsicum annuum foi escolhido devido a natureza morfogênica recalcitrante dos protoplastos. Após o isolamento e a purificação, as aplicações permitiram avaliar um grande número de protoplastos (FCM e MUSE) e núcleos dos protoplastos (CA) em um curto período de tempo. A partir das adaptações nos procedimentos, foram evidenciados diferentes tipos e níveis de danos citológicos (FCM e Muse) e genômicos (Muse e CA), possibilitando discriminar e mensurar os protoplastos viãveis. Considerando os resultados, este estudo introduz procedimentos quantitativos melhorados para o teste de viabilidade. Alem disso, visando a regeneração de plântulas, diferentes métodos podem ser aplicados para avaliar a viabilidade de protoplastos, definindo os procedimentos de isolamento e purificação mais adequados. Corraborando para este propósito, foram mostrados guias para FCM, Muse e CA visando a padronizaçao dos testes de viabilidade em protoplastos de plantas.
Plant protoplasts are valuable in biotechnology, enabling the plantlet regeneration until the gene function determination. In all applications, viability test is required to measure the rate of viable protoplasts, allowing to decide on the most adequate isolation and purification procedures and to verify whether there are sufficient cells for subsequent steps. Fluorescence microscopy is usually employed for viability test. However, some problems have been pointed out: long time required to count a relatively small number of protoplasts, cell clumps preventing their observation, and the subjective visual perception of the fluorescence by observer. This study aimed to establish procedures for viability test adapted for flow cytometry (FCM), MuseTM cell analyzer (Muse) and Comet Assay (CA). For this, Capsicum annuum was chosen due to recalcitrant morphogenic nature of its protoplasts. After isolation and purification, the applications allowed assessing large numbers of protoplasts (FCM and MUSE) and protoplasts nuclei (CA) in a short time period. From the adjusted procedures, different types and levels of cytological (FCM and Muse) and genomic damages (Muse and CA) were evidenced, allowing to discriminate and measure the viable protoplasts. Considering the results, this study introduces improved quantitative procedures for viability test. Besides of these and aiming the plantlet regeneration, different methods can be applied to assess the protoplast viability, defining the more adequate isolation and purification procedures. Contributing with this purpose, guides were showed for FCM, Muse and CA to standardization of viability tests in plant protoplasts
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Yamazaki, Hiroyuki. "APOBEC3B promotes genomic instability in myeloma cells." Kyoto University, 2020. http://hdl.handle.net/2433/259004.
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Chau, P. Y. Pauline. "Mechanism of genomic instability in Prelamin A based premature ageing." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/HKUTO/record/B39557352.
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Chau, P. Y. Pauline, and 周珮然. "Mechanism of genomic instability in Prelamin A based premature ageing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B39557352.
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Li, Han. "Impact of KU80 in genomic stability, cancer and aging: a dissertation /." San Antonio : UTHSC, 2007. http://proquest.umi.com/pqdweb?did=1324370271&sid=2&Fmt=2&clientId=70986&RQT=309&VName=PQD.
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Bankoglu, Ezgi Eylül [Verfasser], and Helga [Gutachter] Stopper. "Oxidative status and genomic damage in an obesity model / Ezgi Eylül Bankoglu. Gutachter: Helga Stopper." Würzburg : Universität Würzburg, 2016. http://d-nb.info/1112466339/34.
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Nandi, Saikat. "Deciphering the molecular mechanism by which Fml1 promotes and constrains homologous recombination." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.561123.
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Homologous Recombination (HR) can promote genome stability through its capacity to faithfully repair DNA gouble 2trand !;!reak2 (DSBs) and preventing the demise of stalled replication forks in part by catalysing template switching to enable DNA polymerase to bypass lesions. Despite these beneficial roles, inappropriate or untimely HR events can have deleterious consequences. HR can cause genome instability by recombining "inappropriate" homologous sequences, especially if the recombination intermediates are resolved to form crossovers. Over the past few years, study of the rare inherited chromosome instability disorder, Eanconi Anaemia (FA), has uncovered a novel DNA damage response pathway. Although the FA pathway is required primarily for interstrand DNA cross link repair, its precise role in DNA repair reactions is still unclear. FA.Qomplementation group M (FANCM) is the sole component within the FA core complex which possesses a DNA helicase/ATPase domain and an endonuclease domain (albeit non-functional), suggesting that FANCM could translocate along DNA and target the FA core complex to blocked replication forks. To further elucidate the role of FANCM in HR, I have purified Fm11, the FANCM orthologue in the fission yeast Schizosaccharomyces pombe and tested its activity on a range of synthetic replication and recombination intermediates in vitro. Fml1 binds both replication forks and Holliday Junctions (HJs) which are key intermediates of HR.
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Chen, Hong, and 陳紅. "A study of male accessory sex glands in protecting: the genomic integrity of sperm in the golden hamster(Mesocricetus auratus)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B31245195.
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Rajaraman, Gnana Oli [Verfasser], and Helga [Akademischer Betreuer] Stopper. "Oxidative stress : role in genomic damage and disease = Oxidativer Stress / Gnana Oli Rajaraman. Betreuer: Helga Stopper." Würzburg : Universitätsbibliothek der Universität Würzburg, 2012. http://d-nb.info/1024851885/34.
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Wang, Zhenxing [Verfasser]. "Early genomic response to X-ray induced DNA damage and transposon regulation in Arabidopsis thaliana / Zhenxing Wang." Berlin : Freie Universität Berlin, 2015. http://d-nb.info/1077211910/34.
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Nyberg, Kara Ann. "Analysis of RAD9 functions: Roles in the checkpoint response, DNA damage processing, and prevention of genomic instability." Diss., The University of Arizona, 2003. http://hdl.handle.net/10150/280312.
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In the 15 years since Rad9's discovery, we have come to understand a great about Rad9 biology, yet numerous questions still remain. Especially intriguing questions include: (a) How does Rad9 get localized and/or recognize DNA damage? (b) How does Rad9 activate downstream checkpoint proteins? and (c) Does Rad9 play additional roles in recognizing and/or repairing DNA damage that have yet to be discovered? In an effort to try to answer some of these questions, I analyzed the effects of various RAD9 mutations. To assess the contribution of RAD9 to inhibiting DNA degradation and its role in the cell cycle arrest and DNA damage repair responses, I performed a pentapeptide mutagenesis screen in order to obtain RAD9 separation-of-function mutants that were proficient for one known phenotype and deficient in the other. I was able to obtain 2 such mutants that were hypomorphic in their ability to prevent DNA degradation and completely proficient for arresting the cell cycle in the presence of DNA damage and for repairing such damage. Despite many efforts, I was unable to enhance the hypomorphic dysfuntion of these mutants in preventing DNA degradation such that a suppressor screen to identify other genes in this pathway could be performed. In another effort to try to understand the role of the BRCT domains for RAD9 functions, I analyzed the effects of other various RAD9 mutants. By deletion analysis, I was able to determine that the predominant function of RAD9's BRCT domains is to mediate concentration of the Rad9 protein for function by two means: (1) by conferring stability to the Rad9 protein, and (2) by homodimerizing Rad9 to increase its local concentration to enable interactions with downstream checkpoint components.
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Kinvi-Dossou, Gbèssiho Raphaël. "Étude de la résistance à l’impact et de l’endommagement des composites stratifiés à matrice Elium acrylique : caractérisation expérimentale et modélisation numérique multi-échelle." Thesis, Université de Lorraine, 2018. http://www.theses.fr/2018LORR0249/document.
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Face aux défis environnementaux actuels, les industriels ont mis en œuvre de nouveaux matériaux recyclables et permettant une réduction significative de la masse. Le développement de la résine thermoplastique Elium par ARKEMA s’inscrit dans cette problématique. L’utilisation de cette résine pour la fabrication de pièces composites qui peuvent être sujettes à des dommages d’impact, nécessite au préalable des études, dans le but de comprendre leurs mécanismes de ruine sous ce type de sollicitation. Ainsi, la présente thèse propose une contribution à l’analyse multi-échelle de la tenue à l’impact des composites stratifiés à base de la résine Elium. Une étude expérimentale préliminaire a permis de confirmer la meilleure résistance à l’impact des composites à matrice Elium acrylique, comparativement à celles des composites thermodurcissables conventionnels. Ensuite, les performances à l’impact des composites stratifiés ont été améliorées par l’introduction de copolymères à blocs dans la matrice. Ces derniers sont capables de former des micelles de tailles nanométriques et ainsi d’améliorer la ténacité de la matrice acrylique. Les effets de l’énergie d’impact, de la température et de la composition en nanocharges sur la réponse du matériau composite ont été analysés. Afin de proposer un outil d’aide à la prédiction de la réponse à l’impact des matériaux fibres de verre/Acrylique, deux stratégies de modélisation ont été retenues. La première modélisation (macroscopique) considère le pli tissé du stratifié comme un matériau homogène tandis que la seconde (mésoscopique) utilise une description géométrique de l’ondulation et de l’entrecroisement des torons noyés dans la résine Elium. Ces deux modèles considèrent des zones cohésives à l’interface entre les plis adjacents pour simuler le délaminage interlaminaire. Des essais de délaminage (expérimentaux et numériques) ont permis d’alimenter le modèle d’endommagement de l’interface interplis. D’autre part, des essais de caractérisation du comportement mécanique et de l’endommagement du matériau couplés à l’homogénéisation multi-échelle des matériaux par la Mécanique du Génome de Structure ont permis d’identifier les paramètres du modèle macroscopique. A l’échelle mésoscopique, le modèle géométrique a été réalisé grâce au logiciel Texgen. Ce logiciel permet d’obtenir une description approchée mais réaliste de l’ondulation des torons de fibres. La même description a servi à l’homogénéisation numérique multi-échelle des stratifiés étudiés. La simulation numérique de l’impact basse vitesse a été effectuée au moyen du logiciel d’éléments finis ABAQUS/Explicit. Les modèles de comportement du matériau ont été implémentés via la routine utilisateur VUMAT. Les résultats obtenus offrent une bonne corrélation avec les données expérimentalesIn the race for light materials able of meeting modern environmental challenges, an acrylic resin (Elium) has been developed. Elium is a thermoplastic resin able to replace thermosetting matrices, which are widespread nowadays in the industrial world. The present study aims to evaluate the impact resistance and to understand the failure mechanisms of composite laminates based on acrylic matrix under impact loading. We provide a contribution to the multiscale analysis of the impact resistance of laminated composite.First, the impact resistance and the damage tolerance of the acrylic resin based composites were compared with those of conventional composites. Then, the impact performance of the laminated composites has been enhanced by adding copolymer blocks to the liquid acrylic resin. These copolymers are able to form micelles of nanometer sizes, which lead to the improvement of both the acrylic matrix fracture toughness and the impact resistance. The effects of the impact energy, temperature, and composition in nano-copolymers have also been investigated.In order to provide a numerical tool for the prediction of the impact response of the glass fiber/Acrylic laminates, two strategies have been analyzed. The first one, performed at the macroscopic scale, considers the woven ply of the laminate as homogeneous material, and the second one (at the mesoscopic scale), deals with a realistic geometrical description of the yarns undulation. Both models use cohesive zones at the interface between the adjacent plies, to simulate the delamination. For this purpose, experimental and numerical delamination tests were performed to feed the inter-ply damage model. Mechanical tests for material characterization were also performed on specimens in order to identify the ply-damage model parameters. The Mechanics of Structure Genome (MSG) and a finite element based micromechanics approaches were then conducted to evaluate the effective thermomechanical properties of the yarns and the plain woven composite laminate. The realistic topological and morphological textures of the composite were accounted through Texgen software. These numerical impact simulations were performed using the finite element software ABAQUS/Explicit. Both models were implemented through a user material subroutine VUMAT. The obtained results appear in a good agreement with the experimental data and confirm the relevance of the proposed approach
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Awad, Eman Da'as [Verfasser], and Helga [Gutachter] Stopper. "Modulation of insulin-induced genotoxicity in vitro and genomic damage in gestational diabetes / Eman Da'as Awad ; Gutachter: Helga Stopper." Würzburg : Universität Würzburg, 2019. http://d-nb.info/1185983120/34.
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Kirk, Austin J. "The partial development of novel assays for the analysis of distribution and quantification of oxidative damage in genomic DNA." Thesis, University of Liverpool, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288302.
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Ramey, Christopher Joshua. "The role of histone H3/H4 chaperone anti-silencing function1 in maintaining genomic integrity /." Connect to full text via ProQuest. IP filtered, 2006.
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Thesis (Ph.D. in Molecular Biology) -- University of Colorado at Denver and Health Sciences Center, 2006.Typescript. Includes bibliographical references (leaves 119-130). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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Núñez, Ollé Marc 1984. "The Role of cyclin O in the DNA damage response." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/459302.
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Cyclin O, a novel identified CDK1 and CDK2-binding cyclin, has been demonstrated to be required for γ-radiation induced apoptosis in a lymphoid cell line. Ɣ-radiation induces the formation of DSBs in the DNA what activate the DDR in order to mitigate the consequences of this insult and repair the DNA damage. The aim of this thesis has been to study the role of Cyclin O in activation of the DDR in response to γ-radiation and the consequences in the cell survival. Using Cyclin O deficient cells as a cellular model, we have found that the Cyclin O limits the DNA resection, a process that drives the cell to repair the DNA damage by HR. Moreover, we have seen that ATM activation and some of its downstream targets are not properly activated after DNA damage in Cyclin O deficient cells. We also have found that Cyclin O complexes are able to phosphorylate ATM in vitro opening the door to study a new mechanism of the DDR regulation by Cyclin O.La Ciclina O és una nova ciclina que interacciona amb CDK1 i CDK2, i que s’ha demonstrat ser necessària per l’apoptòsi induïda per radiació gamma en una linia cel·lular d’origen linfoide. La radiació gamma indueix la formació de talls de doble cadena (DSBs) al DNA activant la resposta per dany al DNA (DDR) per tal de reduïr-ne les conseqüències citotòxiques i reparar el dany al DNA. L’objectiu d’aquesta tesi ha esta el d’estudiar el paper de la Ciclina O en l’activació de la resposta per dany al DNA i les conseqüències sobre la supervivència cel·lular. Utilitzant cèl·lules deficients en Ciclina O com a model, hem trobat que la Cyclina O limita el processament dels talls de doble cadena necessaris per a la reparació del dany al DNA per recombinació homologa. També hem una deficient activació d’ATM i la fosforil·lació d’alguns substrats d’aquesta proteína en cèl·lules deficients per la Ciclina O. Finalment, hem vist que els complexes de Ciclina O fosforil·len ATM in vitro, un fet que obre una porta a l’estudi de nous mecanismes de regulació de la resposta per dany al DNA mitjançant la Ciclina O.
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Bolton, Elisabeth Spring. "Genomic Instability Originates From Leukemia Stem Cells In a Mouse Model of CML-CP." Diss., Temple University Libraries, 2013. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/234916.
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Microbiology and ImmunologyPh.D.
In chronic myelogenous leukemia (CML), activation of BCR-ABL, the product of the bcr-abl chimeric gene, leads to constitutive activation of pathways that increase genomic instability through endogenous production of reactive oxygen species (ROS) that cause oxidative DNA damage and inactivate the function of repair proteins leading to unfaithful DNA repair. If misrepaired, oxidative DNA damage, such as 8-oxoguanine (8-oxoG), may result in point mutations and/or DNA double-strand breaks (DSBs) leading to drug resistance to the BCR-ABL kinase inhibitor imatinib mesylate (IM) and accumulation of chromosomal aberrations associated with malignant CML progression from a benign chronic phase (CP) to a fatal blast phase (BP). To determine which population of CML-CP cells, leukemia stem cells (LSCs) and/or leukemia progenitor cells (LPCs), displays elevated levels of ROS and oxidative DNA damage, and whether these elevated levels of ROS and oxidative DNA damage in CML-CP subpopulations result in the accumulation of genomic instability, we employed the tetracycline-inducible SCLtTA/BCR-ABL transgenic mouse model. We showed that LSCs, including the quiescent subpopulation, but not LPCs, displayed elevated levels of ROS and oxidative DNA damage, perhaps due to deregulated expression of genes involved in ROS metabolism, resulting in genomic instability manifested by both point mutations and genetic alterations. We also examined the effect of IM on ROS, oxidative DNA damage and genomic instability displayed by CML-CP subpopulations, and determined that elevated ROS and oxidative DNA damage were not inhibited by IM in quiescent LSCs, nor was genomic instability and deregulated gene expression prevented. To explore underlying mechanisms, i.e. BCR-ABL expression levels, by which CML-CP cells accumulate genomic instability, we examined the effect of low and high BCR-ABL expression on ROS and oxidative DNA damage in BCR-ABL-transduced human CD34+ cells. We detected elevated ROS and oxidative DNA damage in high BCR-ABL-expressing CD34+ cells compared to low BCR-ABL-expressing cells. Furthermore, BCR-ABL exerted a kinase-dependent effect on ROS-dependent DNA damage. These data support the hypothesis that genomic instability may originate from LSCs, but do not exclude the potential role of LPCs, and may have important clinical implications for CML treatment since additional genetic aberrations that encode primary resistance may protect LSCs, including the quiescent subpopulation, from eradication by tyrosine kinase inhibitors (TKIs), and the continuous accumulation of genetic errors may trigger disease relapse and progression.
Temple University--Theses