Thèses : « Epigenetic biology »

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Kizaki, Seiichiro. « Chemical Biology Study on DNA Epigenetic Modifications ». 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225420.

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Rosselló, Tortella Margalida. « Epigenetic Regulation of tRNA Biology in Cancer ». Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/673026.

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Transfer RNAs (tRNAs) are essential molecules that allow the translation of the genetic code into amino acids. Extensive research during the last 50 years have revealed that, despite their apparently simple structure and function, tRNAs are more than simple adaptors in protein synthesis –they are of high importance in normal cell functions. Reinforcing this, tRNA levels are tightly regulated to match the codon usage patterns of a given cell type or cellular status to meet the cellular specific needs and adapt to stress. Moreover, tRNA nucleoside modifications are critical for their function at multiple levels, such as translation efficiency and fidelity, wobbling and fragmentation. The relevance of tRNA regulation in cell physiology is emphasized by the recent discovery that these molecules and their derived fragments are deregulated in cancer. Not only tRNA biology imbalance is associated to malignant transformation, but it also actively participates in it. These alterations occur at multiple levels of tRNA biology, such as expression, nucleoside modification and fragmentation, but many open questions remain unanswered. Cancer- specific tRNA deregulation is a very new and still unexplored discipline, and further studies are required to fully understand the molecular mechanisms that account for these alterations and their relevance in tumor biology. Because alterations in DNA methylation constitute a frequent mechanism by which transformed cells acquire their malignant characteristics, the cornerstone of this thesis is the description of epigenetic lesions that support the cancer-associated tRNA deregulation. To this end, we have designed and performed two independent studies to unveil the epigenetic regulation of tRNA biology in cancer. In the first study, we highlighted the tumor-specific epigenetic silencing of TYW2 as a mechanism to induce tRNAPhe hypomodification at position 37, a phenomenon that was observed for the first time more than forty years ago but whose cause and consequences have remained obscure. Our results established the connection between this epigenetic defect and a phenotype that enhances -1 ribosome frameshifting events to ultimately confer increased migratory capacities and mesenchymal features to the transformed colon cells. In the second study, we established a founded connection between cancer-associated DNA methylation defects with alterations in the expression of specific tRNAs. Our analyses also revealed that the oncogenic tRNA-Arg-TCT-4-1 overexpression in endometrial cancer was guided by DNA hypomethylation. Most importantly from the clinical perspective, the epigenetic alterations identified in both studies can anticipate the patients’ outcome, for which they may serve as biomarkers to allow the identification of high-risk patients that may benefit from a more comprehensive surveillance or complementary therapeutic strategies.
Els ARN de transferència (tRNAs) són d’una importància clau en la regulació de la síntesi proteica i l’expressió gènica. La seva rellevància en la fisiologia cel·lular es veu reforçada pel descobriment que aquestes molècules i els seus derivats estan alterats en patologies com el càncer, on contribueixen activament. Les alteracions dels tRNAs en càncer suposen una nova disciplina d’estudi on encara moltes preguntes romanen obertes per tal d’arribar a comprendre quines són les causes d’aquestes defectes i quin impacte tenen sobre la malaltia. Aquesta tesi té com objectiu identificar i caracteritzar alteracions en la metilació de l’ADN subjacents als desequilibris en la biologia dels tRNAs de les cèl·lules tumorals. En el primer estudi, hem descobert el silenciament epigenètic de l’enzim TYW2 en càncer colorectal com a causa de la hipomodificació del tRNAPhe, un fenomen que va ser descrit per primer cop fa més de quaranta anys però les causes i conseqüències del qual no van ser mai estudiades. Els nostres resultats estableixen una clara connexió entre aquest defecte epigenètic i un fenotip que és propens a potencial el frameshift dels ribosomes, cosa que augmenta la capacitat migratòria de les cèl·lules de càncer de colon. El segon estudi ha servit per caracteritzar la relació entre els canvis en la metilació de l’ADN i les alteracions en l’expressió dels tRNAs en càncer. Els nostres resultats han revelat que l’expressió de tRNA-Arg-TCT-4-1 augmenta en càncer d’endometri arrel de la hipometilació del seu gen. Més enllà d’aquests dos mecanismes epigenètics per modular la biologia dels tRNAs, els nostres estudis estableixen una connexió entre aquestes lesions epigenètiques i la prognosi dels pacients amb certs tipus de tumor, per la qual cosa podrien proposar-se com biomarcadors per identificar pacients de risc.

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Weaver, Ian Cassford Gordon. « Epigenetic programming by maternal behaviour ». Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=102231.

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Individual differences in gene expression and behaviour are the result of an interaction between a given set of genes and a variety of environmental conditions. The study of epigenetics focuses on the nature of this interaction. The early developmental period in the life of a mammal is exquisitely sensitive to environmental cues. One critical question is how is the genome capable of adapting to these developmental or environmental signals? Building on an established rodent model, in which the effects of maternal care have been demonstrated to regulate the development and expression of neurobiological and behavioural measures in offspring as adults, the current project concerns how events during the first week of life can have sustained effects on gene expression, which persist throughout the life of the organism.
The research presented in this thesis demonstrates how one facet of mothering style leads to a cascade of molecular and cellular changes, resulting in life-long alterations in the nature of stress responses and neuron survival. Frequent licking/grooming by rat mothers alters DNA methylation of the hippocampal glucocorticoid receptor (GR) gene and acetylation of histones early in life, providing a mechanism for these permanent changes in stress responses. Through postnatal cross-fostering studies, I was able to directly study how an identical gene within the same rat strain is expressed and regulated under the different developmental environments and how such effects on gene expression persist through life. I have also examined the potential for reversibility of the long-term consequences of postnatal environment and have demonstrated that both GR levels and the nature of stress responses exhibit a high degree of plasticity in adulthood in response to both pharmacological intervention and dietary amino-acid supplementation. These results demonstrate that the epigenomic marks established early in life through a behavioural mode of programming, are dynamically maintained and potentially reversible in the adult brain. These results contrast with the very dogmatic view that the genome is rendered fixed and immutable. I next questioned the global effects of early-in-life experience on the hippocampal transcriptome and anxiety-mediated behaviours in adulthood. Microarray analysis revealed > 900 different maternal care-responsive mRNA transcripts. These results suggest that effects of early life experience have a stable and broad effect on the hippocampal transcriptome, which may play a role in the development of anxiety-mediated behaviours through life. Finally, both in vivo and in vitro studies show that maternal behaviour increases GR expression in the offspring via increased hippocampal serotonergic tone accompanied by increased histone acetylase transferase activity, histone acetylation and DNA demethylation mediated by the transcription factor NGFI-A.
In summary, this research demonstrates that an epigenetic state of a gene can be established through early-in-life experience, and is potentially reversible in adulthood. We predict that epigenetic modifications of targeted regulatory sequences in response to variations in environmental conditions might serve as a major source of variation in biological and behavioural phenotypes. In the case of GR, the resulting individual differences in behavioural and physiological responses to stress are thought to be a major risk factor for the development of psychiatric and physical illness. Thus, in addition to contributing to our understanding of how gene-environment interactions shape development, our work provides a mechanism that can be targeted for therapeutic intervention to potentially reduce the prevalence of these disorders.

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Magnell, Albert T. (Albert Thomas). « Epigenetic Memory of Mouse Intestinal Inflammation ». Thesis, Massachusetts Institute of Technology, 2021. https://hdl.handle.net/1721.1/130670.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Biology, 2021
Cataloged from the official PDF version of thesis.
Includes bibliographical references (pages 29-31).
The gut, encompassing one of the largest epithelial surfaces in the body, interacts with both biological and non-biological agents that can cause regular injury. Fortunately, the small intestinal epithelium has a remarkable capacity to repair itself after severe injury, due to the abundance of highly replicative stem cells housed in the intestinal crypt regions. Much remains to be understood about the activation processes of the repair mechanisms and to what extent the stem cells themselves can adapt to certain forms of damage, including molecular mechanisms related to gene regulation. Here, I show that in response to acute inflammation, chromatin in intestinal stem cells has increased accessibility around specific loci and that this state is maintained in some regions even after the epithelium has recovered from damage, suggesting the possibility of memory. Such epigenetic memory may confer some adaptive resiliency to subsequent damage.
by Albert T. Magnell.
S.M.
S.M. Massachusetts Institute of Technology, Department of Biology

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Lezcano, Magda. « The Control of the Epigenome ». Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7190.

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The genetic information required for the existence of a living cell of any kind is encoded in the sequence information scripted in the double helix DNA. A modern trend in biology struggles to come to grip with the amazing fact that there are so many different cell types in our body and that they are directed from the same genomic blueprint. It is clear, that the key to this feature is provided by epigenetic information that dictates how, where and when genes should be expressed. Epigenetic states “dress up” the genome by packaging it in chromatin conformations that differentially regulate accessibility for key nuclear factors and in coordination with differential localizations within the nucleus will dictate the ultimate task, expression. In the imprinted Igf2/H19 domain, this feature is determined by the interaction between the chromatin insulator protein CTCF and the unmethylated H19 imprinting control region. Here I show that CTCF interacts with many sites genome-wide and that these sites are generally protected from DNA methylation, suggesting that CTCF function has been recruited to manifest novel imprinted states during mammalian development. This thesis also describes the discovery of an epigenetically regulated network of intra and interchromosomal complexes, identified by the invented 4C method. Importantly, the disruption of CTCF binding sites at the H19 imprinting control region not only disconnects this network, but also leads to significant changes in expression patterns in the interacting partners. Interestingly, CTCF plays an important role in the regulation of the replication timing not only of the Igf2 gene, but also of all other sequences binding this factor potentially by a cell cycle-specific relocation of CTCF-DNA complexes to subnuclear compartments. Finally, I show that epigenetic marks signifying active or inactive states can be gained and lost, respectively, upon exposure to stress. As many genes belonging to the apoptotic pathway are upregulated we propose that stress-induced epigenetic lesions represent a surveillance system marking the affected cells for death to the benefit of the individual. This important observation opens our minds to the view of new intrinsic mechanisms that the cell has in order to maintain proper gene expression, and in the case of misleads there are several check points that direct the cell to towards important survival decisions.

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Vadnal, Jonathan. « Epigenetic Mechanisms in Neurodegenerative Disease ». Kent State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=kent1353955013.

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

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The genetic information encoded by the DNA sequence, can be expressed in different ways. Genomic imprinting is an epigenetic phenomenon that results in monoallelic expression of imprinted genes in a parent of origin-dependent manner. Imprinted genes are frequently found in clusters and can share common regulatory elements. Most of the imprinted genes are regulated by Imprinting Control Regions (ICRs). H19/Igf2 region is a well known imprinted cluster, which is regulated by insulator function of ICR located upstream of the H19 gene. It has been proposed that the epigenetic control of the insulator function of H19 ICR involves organization of higher order chromatin interactions. In this study we have investigated the role of post-translational modification in regulating insulator protein CTCF (CCCTC-binding factor). The results indicated novel links between poly(ADP-ribosyl)ation and CTCF, which are essential for regulating insulators function. We also studied the higher order chromatin conformation of Igf2/H19 region. The results indicated there are different chromatin structures on the parental alleles. We identified CTCF-dependent loop on the maternal allele which is different from the paternal chromatin and is essential for proper imprinting of Igf2 and H19 genes. The interaction of H19 ICR with Differentially Methylated Regions (DMRs) of Igf2 in a parent-specific manner maintains differential epigenetic marks on maternal and paternal alleles. The results indicate that CTCF occupies specific sites on highly condensed mitotic chromosomes. CTCF-dependent long-range key interaction on the maternal allele is maintained during mitosis, suggesting the possible epigenetic memory of dividing cells. In this study, we developed a new method called Circular Chromosome Conformation Capture (4C) to screen genome-wide interactions with H19 ICR. The results indicated there are wide intra- and inter-chromosomal interactions which are mostly dependent on CTCF-binding site at H19 ICR. These observations suggest new aspects of epigenetic regulation of the H19/Igf2 imprinted region and higher order chromatin structure.

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Huang, Chieh-Ting. « Epigenetic involvement of GluR2 regulation in Epileptogenesis ». Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=106297.

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Epilepsy is one of the most common neurological disorders characterized by recurrent seizures. Currently, the underlying mechanisms are not well understood and therapies only serve to relieve the symptoms. A single episode of seizure can trigger epileptogenesis, a process in which the brain undergoes network reorganization including neurodegeneration and sprouting of axons. The mechanisms linking the first seizure to development of epilepsy are currently unknown. Interestingly, changes in neuronal circuitry in epilepsy are accompanied by chronic alterations in the normal brain gene expression profile. Epigenetic mechanisms, including DNA methylation and covalent histone modifications stably program the genome during gestation. However, recent studies suggest also that epigenetic mechanisms might be involved in modifying genome function in response to environmental stimuli. We therefore hypothesize that a single seizure can disrupt normal epigenetic programming in the brain, which results in altered gene expression profiles that drive the network reorganization events. In this study, we used in vitro and in vivo models of temporal lobe epilepsy (TLE) by kainic acid treatment to test whether DNA methylation changes are associated with epileptogenesis. DNA methylation is a covalent modification of DNA by adding a methyl group on the 5' position of cytosine by DNA methyltransferases. We focused our analysis on DNA methylation because of its importance role in gene regulation. Indeed there is an overall inverse correlation between DNA methylation of regulatory regions of genes and gene expression. We closely examined the DNA methylation changes associated with the promoters of the GriA2 gene (codes for glutamate receptor ionotropic AMPA 2 subunit), which has been demonstrated to be down-regulated in epilepsy and to be highly implicated in hyper-excitable neuronal circuitries. We detected rapid hypermethylation in GriA2 after a 2-hour period of epileptiform activity in the in vitro model. Similar changes in GriA2 DNA methylation were also observed in our in vivo model 10 weeks post-kainic acid injection. We also observed a significant positive correlation between the number of seizures recorded by video-EEG and severity assessed by Racine scale and the average GriA2 DNA methylation. Epileptogenic insults induced by kainic acid treatment led to rapid DNA methylation changes in GriA2 gene. This result suggests that alterations in DNA methylation may serve as a molecular memory of the insult, which can lead to the progressive changes in gene expressions, thus contributing to the development of epilepsy as well as the maintenance of an epileptic neuronal circuitry.
L'épilepsie est l'une des maladies neurologiques les plus fréquentes, caractérisée par des crises épileptiques répétées et chroniques. Les mécanismes sous-tendant les troubles neurologiques associés à la maladie sont encore mal compris et seuls des traitements symptomatiques sont actuellement disponibles. Une seule crise épileptique peut induire un processus d'épileptogenèse durant lequel une réorganisation des circuits neuronaux s'effectue, incluant une neurodégénérescence et un bourgeonnement anormal des axones. Les mécanismes conduisant au développement de la maladie épileptique en tant que telle à partir d'un premier épisode épileptique sont encore inconnus. De façon intéressante, les réarrangements des circuits neuronaux observés dans l'épilepsie sont accompagnés de changements stables de schémas d'expression de gènes. Les mécanismes épigénétiques, incluant la méthylation de l'ADN ou les modifications covalentes des histones, permettent une régulation stable des schémas d'expression des gènes se mettant en place durant la gestation. Cependant, de récentes études suggèrent que ces mécanismes épigénétiques permettent également une réorganisation des schémas d'expression de gènes en réponse à des stimuli environnementaux. Nous avons alors émis l'hypothèse qu'un seul épisode épileptique peut perturber les profils épigénétiques cérébraux normaux, aboutissant à des schémas d'expression de gènes altérés et aux réorganisations cérébrales caractéristiques de l'épilepsie. Lors de cette étude, nous avons utilisés des modèles in vitro et in vivo de l'épilepsie du lobe temporal (TLE), par traitements au kaïnate, afin de tester si des changements de méthylation de l'ADN sont associés au processus d'épileptogenèse. La méthylation de l'ADN est un processus épigénétique dans lequel les bases cytosines peuvent être modifiées par l'addition d'un groupement méthyle lors d'une réaction catalysée par des ADN méthyltransférases. Nous avons focalisé notre étude sur l'étude des changements de méthylation de l'ADN en raison de son rôle important dans la régulation de l'expression des gènes. En effet, le niveau de méthylation de régions régulatrices de l'ADN telles que les promoteurs est corrélé négativement au niveau d'expression génique. Nous avons en particulier mesuré les modifications des niveaux de méthylation des promoteurs du gène GriA2 (codant pour la sous-unité 2 du récepteur gutamatergique ionotropique AMPA), qui est sous-exprimé dans l'épilepsie et dont la protéine est fortement impliquée dans l'hyperexcitabilité neuronale observée dans les crises épileptiques. Nous avons mesuré une hyperméthylation du gène GriA2 à la suite d'une période de 2 heures d'activité épileptiforme dans le modèle in vitro. Des modifications similaires ont également été observées dans le modèle in vivo, 10 semaines après une injection intracérébrale de kaïnate. Nous avons également observé une corrélation positive significative entre le nombre de crises épileptiques, détectées par Electro-Encéphalogramme Vidéo, la sévérité des crises, évaluée grâce à l'échelle Racine, et le niveau moyen de méthylation du gène GriA2.Les crises épileptiques, induites par un traitement au kaïnate, conduisent à des changements rapides des niveaux de méthylation du gène GriA2. Ce résultat suggère que des modifications des schémas de méthylation de l'ADN pourraient être un mécanisme moléculaire de mémorisation des crises épileptiques, conduisant à des changements progressifs d'expression de gènes et contribuant au développement de l'épilepsie et au maintien de circuits neuronaux anormaux.

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Khan, Maria Mohammad. « Computational Biology in the Analysis of Epigenetic Nuclear Self-Organization ». Thesis, The University of Arizona, 2010. http://hdl.handle.net/10150/146042.

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The function of the nucleus is central to the survival of cells and thus life as a whole. Among other processes, it is the site of gene expression, DNA repair, and genome stability. These functions are carried in the context of a complex nuclear architecture. The nucleus is compartmentalized both spatially and functionally. These compartments are proteinaceous nuclear bodies or chromatin domains, both of which are not segregated from other compartments by membranes-as are the organelles of cells. Specifically, proteinaceous nuclear bodies are characterized as regions within the nucleus with distinct sets of inhabitant proteins. Examples of such proteinaceous nuclear bodies include the nucleolus, splicing factor compartments, and the Cajal body. The nucleolus is the location of the transcription and processing of ribosomal RNA and the Cajal body is the site of snRNP assembly, while the splicing factor compartments are a storage and assembly site for spliceosomal components.

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Nuthikattu, Saivageethi. « Diverse mechanisms of Athila retrotransposon epigenetic silencing in Arabidopsis thaliana ». The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1417685369.

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Chinaranagari, Swathi. « Epigenetic Silencing of ID4 in Prostate Cancer : Mechanistic Insight ». DigitalCommons@Robert W. Woodruff Library, Atlanta University Center, 2015. http://digitalcommons.auctr.edu/cauetds/13.

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Inhibitor of DNA binding/differentiation protein 4 (ID4) is a dominant negative regulator of basic helix loop helix (bHLH) family of transcription factors. ID4 shares the homology of HLH domain with other ID proteins (ID1, ID2, and ID3) and lack the basic DNA binding region. Evidence suggested that unlike ID1, ID2 and ID3, ID4 acts as a tumor suppressor in prostate cancer by attenuating cell proliferation and promoting apoptosis. Consistent with these observations ID4 is epigenetically silenced in DU145 prostate cancer cell line. In this study we investigated whether ID4 is also epigenetically silenced in prostate cancer. We also examined association between ID4 promoter hyper-methylation and its expression in prostate cancer cell lines. ID4 protein expression was analyzed in human prostate adenocarcinoma samples by Immunohistochemistry (IHC). ID4 promoter methylation pattern on prostate cancer cell lines was examined by methylation specific PCR. In addition, we performed methylation specific PCR on the human prostate tissues and genomic DNA to correlate cell line studies with clinical studies. IHC demonstrated decreased ID4 protein expression in human prostate tissue samples, whereas higher nuclear ID4 expression was found in normal prostate tissues. ID4 methylation specific PCR (MSP) on prostate cancer cell lines, showed ID4 methylation in DU145, but not in LNCaP and C33 cells. C81 and PC3 cells showed partial methylation. Increased ID4 methylation in C81 as compared to LNCaP suggests its epigenetic silencing as cells acquire androgen independence. Tumors with ID4 promoter hyper-methylation showed distinct loss of ID4 expression. However, the underlying mechanism involved in epigenetic silencing of ID4 is currently unknown. We hypothesized that ID4 promoter methylation is initiated by an EZH2 dependent tri-methylation of histone 3 at lysine 27 (H3K27Me3). ID4 expressing (LNCaP) and non-expressing (DU145 and C81) prostate cancer cell lines were used to investigate EZH2, H3K27Me3 and DNMT1 enrichment on ID4 promoter by Chromatin immuno-precipitation (ChIP). Increased enrichment of EZH2, H3K27Me3 and DNMT1 in DU145 and C81 cell lines was compared to ID4 expressing LNCaP cell line. Knockdown of EZH2 in DU145 cell line led to re-expression of ID4 and decrease in enrichment of EZH2, H3K27Me3 and DNMT1 demonstrating that ID4 is regulated in an EZH2 dependent manner. ChIP on prostate cancer tissue specimens and cell lines suggested EZH2 occupancy and H3K27Me3 marks on the ID4 promoter. Collectively, our data indicate a PRC2 dependent mechanism in ID4 promoter silencing in prostate cancer through recruitment of EZH2 and a corresponding increase in H3K27Me3. Increased EZH2, but decreased ID4 expression in prostate cancer strongly supports this model.

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Eggan, Kevin C. (Kevin Carl) 1974. « Cloning, stem cells and epigenetic reprogramming after nuclear transfer ». Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/29931.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2003.
Includes bibliographical references (leaves 128-146).
The process by which a single totipotent cell becomes a complex organism is a unidirectional program, with each mitotic division generating new cells that gradually differentiate towards more specified fates and specialized functions. Nuclear transfer (NT) experiments have demonstrated the epigenetic nature of development and showed, that although differentiated cells have a very limited developmental potential, the nuclei of these cells retain the potency to direct embryogenesis after reintroduction into the unfertilized oocyte. Herein, we have used the mouse as a model system for understanding both the nature of epigenetic reprogramming that occurs after NT as well as the ramifications it has for the development of cloned animals. Specifically, we investigated how epigenetic states are reprogrammed after NT and demonstrated that the inactive X chromosome is reactivated in NT embryos, resulting in normal X inactivation in female clones. Additionally, investigations into the factors that influence the survival of cloned animals, indicate that there are considerable genetic influences on the cloning process. These genetic factors modify the survival of mice cloned from ES cells by influencing the developmental potential of the donor ES cells rather then the reprogramming process itself. This realization has subsequently led to the development of novel methods for the expedited production of complex mutant mice, which are also described. Finally, we have created cloned embryos by NT from both cortical and mature olfactory sensory neurons to address question of nuclear equivalence in the brain and to investigate whether generation of synaptic diversity or odorant receptor choice, are mediated by genetic as well as epigenetic events.
by Kevin C. Eggan.
Ph.D.

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Robertson, Marta. « Epigenetic Response to Challenging Environmental Conditions ». Scholar Commons, 2017. http://scholarcommons.usf.edu/etd/6939.

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The discovery of epigenetic mechanisms has ignited speculation into their role in ecological and evolutionary processes. In particular, the contribution of epigenetic variation to adaptation or phenotypic plasticity that is distinct from genetic variation would be an important addition to existing evolutionary mechanisms. Although the research of epigenetic mechanisms from an ecological and evolutionary (or eco-evolutionary) perspective has been growing, it is still unclear how epigenetic variation might function in natural populations and settings and to what extent it might serve to mediate population response to changing environmental conditions over time. Over the course of my dissertation, I explored the importance of DNA methylation in population response to a variety of environmental conditions. In the first chapter of my dissertation, I reviewed existing literature on the relationship between DNA methylation and environmental response. I argued that given the weight of current evidence, DNA methylation, in addition to other epigenetic mechanisms, needs to be included the evolutionary synthesis. Additionally, I identified a number of outstanding questions and outlined research directions that would help elucidate the role of epigenetic mechanisms in evolution. In my second chapter, I studied the genetic and epigenetic composition of populations of Spartina alterniflora that were impacted by the Deepwater Horizon oil spill in 2010. Current evolutionary theory predicts that following a severe environmental stressor, populations may experience a bottleneck effect, in which one or only a few genotypes survive to reproduce in subsequent generations. However, it is unclear whether these patterns are reflected in epigenetic variation as well, because novel environmental perturbations may serve to induce epigenetic variation rather than diminish it. We found a significant genetic signature of oil exposure in exposed populations, but did not see a similar effect in the epigenetic composition of exposed populations. These data suggest that epigenetic modifications, such as DNA methylation, may not always increase in number during stressful episodes, but may instead follow genetic variation. These results provide valuable information for the development of nascent population epigenetic theory, and may help parameterize expectations about conditions that provoke epigenetic variation, particularly when genetic variation may be limited. In addition to strong, unpredictable stressors, populations also respond via phenotypic changes over time through developmental stages and life histories that coincide with seasonal, regular environmental cues. Epigenetic mechanisms influence these regulatory and developmental changes that occur within an individual over time. In my third chapter, I examined the epigenetic response to seasonality in multiple coastal plant species. We found a weak signature of single methylation polymorphisms that was associated with seasonal environmental change within the studied species, as well as global patterns of methylation that were consistent across species. The results of this study indicate the possibility of conservation of methylation patterns across phylogenetic histories. In my fourth chapter, I explored in detail how the ability to maintain methylation might affect stress response. We compared individuals of the model plant Arabidopsis thaliana that were deficient in maintenance methylation machinery to control genotypes under both abiotic and biotic stresses, and then studied the growth of their offspring in the absence of stress. We found inherited phenotypic signatures of parental stress in the offspring generation and interactive effects of parental stress and genotype. This study not only reinforces the correlations that we observed in our field studies, but adds to the growing body of literature highlighting the importance of DNA methylation both in immediate environmental response and as a mechanism for heritability. Overall, this dissertation demonstrates that DNA methylation is highly abundant in natural populations and may be part of the response to various stressors at a number of time scales. The integration of DNA methylation in the evolutionary synthesis will aid in the explanation of phenomena such as phenotypic plasticity or adaptation, and will be an important contribution to the existing body of evolutionary mechanisms.

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Gocevski, Goran. « Interplay of Mye and Max with Epigenetic Regulator Bmi1 ». Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=114264.

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The polycomb group protein Bmi1 is an epigenetic regulator essential for the proliferation of many types of cancers. By impeding the expression of the tumor suppressor p53, Bmi1 is able to prevent apoptosis and senescence. c-Myc, a prominent oncogene, cooperates with Bmi1 to stimulate cellular transformation and tumorigenesis. Further investigation of the basic biological interplay between Bmi1 and c-Myc is crucial for our understanding of their tumorigenic ability. In my project I demonstrated that c-Myc and Bmi1 directly interact with each other and form nuclear foci. Overexpression of Max, a known partner of Myc, disrupts the Bmi1 and c-Myc interaction and prevents the formation of nuclear foci. Similar results were obtained with another member of the Myc family, L-Myc. Additionally, I found that HDAC3 interacts and co-localizes with Myc. HDAC3 also forms nuclear foci with Bmi1 and the addition of Max abrogates this interaction. In addition to the well-established role of Bmi1 as an epigenetic regulator, it has been recently shown that Bmi1 is part of an E3 ubiquitin-ligase complex, known as the Bmi1/RING1A or B complex. This complex controls the stability of many proteins. I showed that Bmi1 induces an L-Myc ubiquitination, which in turn causes the degradation of L-Myc. This data proposes a novel regulatory mechanism for the stability of the Myc oncogenes. The results of this thesis provide new insight into the basic biochemical interplay ofBmi1 with Myc and Max.
La protéine de groupe polycomb Bmi1 est essentielle pour la prolifération de nombreux types de cancers. En freinant l'expression du suppresseur de tumeur p53, Bmi1 est capable de prévenir l'apoptose et la sénescence. c-Myc, une autre oncogène, s'associe à Bmi1 pour stimuler la transformation et la tumorigenèse. Une enquête plus approfondie de l'interaction biologique fondamentale entre Bmi1 et c-Myc est crucial pour notre compréhension de leur capacité à promouvoir la tumorigène. Dans mon projet, j'ai démontré que c-Myc et Bmi1 interagissent directement et forment des foyers nucléaires. La surexpression de Max, un partenaire connu de Myc, perturbe l'interaction entre Bmi1 et c-Myc et empêche la formation de foyers nucléaires. Des résultats similaires ont été obtenus avec un autre membre de la famille Myc, L-Myc. En outre, j'ai constaté que HDAC3 interagi et se co-localise avec Myc. HDAC3 forme aussi des foyers nucléaires avec Bmi1 et l'ajout de Max abroge cette interaction. En plus du rôle bien établi de Bmi1 comme un régulateur épigénétique, il a été démontré récemment que Bmi1 fait partie d'une ubiquitine-ligase E3 complexe, connu sous le nom complexe Bmi1/RING1A ou B. Ce complexe contrôle la stabilité de nombreuses protéines. J'ai démontré que Bmi1 induit l'ubiquitination de L-Myc qui à son tour provoque la dégradation de celle-ci. Ces données proposent un nouveau mécanisme de règlementation pour la stabilité des oncogènes Myc. Les résultats de cette thèse fournissent un nouvel éclairage sur l'interaction biochimique de Bmi1 avec Myc et Max.

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Rhodes, Christopher. « Epigenetic Repression in the Context of Adult Neurogenesis ». Thesis, The University of Texas at San Antonio, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10686193.

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Neural stem progenitor cells (NSPCs) in the mammalian brain contribute to life-long neurogenesis and brain health. Adult mammalian neurogenesis primarily occurs in the subventricular zone (SVZ) and the subgranular zone (SGZ) of the dentate gyrus. Epigenetic repression is a crucial regulator of cell fate specification during adult neurogenesis. How epigenetic repression impacts adult neurogenesis and how epigenetic dysregulation may impact neoplasia or tumorigenesis remains poorly understood. Examination of epigenetic regulation in the adult mammalian brain is complicated by the heterogeneous nature of neurogenic niches and by the highly orchestrated fate specification processes within neural stem progenitor cells involving myriad intrinsic and extrinsic factors. To overcome these challenges, we utilized a cross-species approach. To model histone modifications as they exist in vivo for epigenetic profiling, we isolated neural stem progenitor cells from the adult SVZ and SGZ of non-human primate baboon brains. To determine cellular and molecular changes within the adult SVZ and SGZ following loss of epigenetic repression, we utilized multiple mouse models, including conditional Ezh2 and Suv4-20h1 knockouts. To model the non-cell type specific effects common to small molecule screening and brain chemotherapeutic agents, induction of conditional knockout utilized a recombinant Cre protein. Finally, to model epigenetic mechanisms during SVZ-associated glioblastoma (GBM) tumorigenesis, we conducted comparative analysis between healthy NSPCs and GBM specimens from humans. The convergence of baboon, mouse and human models of adult neurogenesis revealed that epigenetic repression is a critical mechanism regulating proper neural cell fate and that epigenetic dysregulation may be a driver of GBM.

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Rice, Judd Christopher. « Epigenetic silencing of BRCA1 and maspin in sporadic breast cancer ». Diss., The University of Arizona, 2000. http://hdl.handle.net/10150/289142.

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The RNA expression of the tumor suppressor genes BRCA1 and maspin are frequently decreased or lost in sporadic breast cancer. We hypothesized that inactivation of these genes was due to aberrant epigenetic silencing at the level of gene transcription. In this study we show that aberrant cytosine methylation of the BRCA1 and maspin CpG island promoters is a common event in the inactivation of these genes in sporadic breast cancer cell lines. Furthermore, we show that the methylation-associated inactivation of BRCA1 occurs in 15-30% of sporadic breast cancer patient specimens and our data suggests that the methylation-associated inactivation of maspin occurs in ∼70% of advanced sporadic breast cancers. Additional studies indicate that the methylation associated inactivation of these genes is coincident with the repressive epigenetic events of histone hypoacetylation and chromatin condensation. These data suggest that aberrant cytosine methylation, histone hypoacetylation and chromatin condensation act together in the BRCA1 and maspin promoters to inactivate their transcription, thereby, contributing to the progression of sporadic breast cancer.

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Felician, Giulia. « Regulation of Notch signaling in the heart by epigenetic modifications ». Doctoral thesis, Scuola Normale Superiore, 2015. http://hdl.handle.net/11384/85955.

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Synopsis: Understanding the molecular mechanisms regulating cardiac cell proliferation during the embryonic, fetal and adult life is of paramount importance in view of developing innovative strategies aimed at inducing myocardial regeneration after cardiac damage. The Notch pathway plays a key role in the regulation of cardiomyocyte proliferation during mammalian embryonic life. Moreover, it is essentially involved in the cardiac regeneration process after injury in Zebrafish. Therefore, we assessed the efficacy of Notch pathway activation to sustain cardiac regeneration in a model of myocardial infarction in mice. During early postnatal life, cardiomyocytes exit the cell cycle. We demonstrated that this event is paralleled by a decrease of Notch signaling and by the establishment of a repressive chromatin environment at Notch target genes, characterized by Polycomb Group protein 2-mediated silencing. The stimulation of the Notch pathway through Adeno-associated virus-mediated gene transfer of activated Notch1 or of the soluble form of the ligand Jagged1 prolonged the capacity of cardiomyocytes to replicate, which correlated with an increased rate of Notch target gene expression and the maintenance of an open chromatin conformation at Notch target gene promoters. However, the same vectors were ineffective in stimulating cardiac repair in a model of myocardial infarction in adult mice, despite efficient transgene expression. We identified the molecular cause of the lack of action of Notch signaling stimulation in adults in the increased DNA methylation at Notch target gene promoters, which correlated with permanent switch off of the Notch pathway. Our results confirm that the Notch pathway is an important regulator of neonata adults, due to the permanent epigenetic modifications at the DNA level at Notch responsive genes l.

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JnBaptiste, Courtney K. (Courtney Kenneil). « Dicer loss induces an oncogenic epigenetic switch in mesenchymal stem cells ». Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/103163.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis. Vita.
Includes bibliographical references.
MicroRNAs (miRNAs) are post-transcriptional regulators that tune gene expression. Despite the modest 2-fold repression that miRNA activity generally confers on a target, miRNAs are critical for many biological processes including development and differentiation. Due to this mild repression directly conferred by miRNA activity, miRNAs coordinate with other regulators such as transcription factors to shape the gene expression landscape and phenotypes of a cell. To understand the function of global miRNA activity in regulating the specification of the somatic state, we deleted Dicer in a murine mesenchymal stem cell model. Upon exploring the consequences of Dicer deletion, we identify a specific let-7 regulated mid-embryonic program within the global de-repression of miRNA targets accompanying Dicer loss. We further observe within the landscape of let-7 regulated targets, an activation of greater than 50-fold of known oncofetal (Igf2bp1/2/3) genes, an effect much greater than that typically reported for miRNA-mRNA interactions. This suggests a requirement of let-7 for the continual suppression of mid-embryonic programs in adult cells. To investigate the regulation of these oncofetal genes, we restored miRNAs through re-expression of Dicer. Despite complete reconstitution of the posttranscriptional activity of miRNAs, the activated oncofetal genes are incompletely suppressed. Igf2bp1-3 are components of a larger set of irreversible oncogenes whose chromatin signature indicate that they are transcriptionally activated upon Dicer deletion. This transcriptional activation is maintained, despite miRNA restoration in Dicer rescued cells. Consistent with this expression pattern, Dicer rescued cells are able to form tumors in mice, a phenotype absent in the parental wild-type and Dicer knockout cells. Moreover, the irreversible gene set is amplified in human cancers and is predictive of patient survival indicating that our observations are relevant to human disease. Finally, we develop a computational method to decipher the indirect, transcription factor mediated effects of miRNAs on gene expression. Through comprehensive analysis of ChIP-Seq, CLIP-Seq and RNA-Seq datasets, we quantitatively assess the relative contributions of direct posttranscriptional miRNA activity and transcriptional activity on gene expression changes resulting from Dicer deletion. We find that transcriptional changes contribute significantly to perturbations in gene expression resulting from global miRNA loss upon Dicer deletion. In summary, our work expands the current knowledge of fundamental roles for miRNAs in differentiated mammalian cells. As further work builds on our observations, the increased understanding of miRNA-mediated regulation will inform therapeutic strategies for human disease.
by Courtney K. JnBaptiste.
Ph. D.

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Alzrigat, Mohammad. « Targeted Inhibition of Polycomb Repressive Complexes in Multiple Myeloma : Implications for Biology and Therapy ». Doctoral thesis, Uppsala universitet, Experimentell och klinisk onkologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-312250.

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Multiple myeloma (MM) is a hematological malignancy of antibody producing plasmablasts/plasma cells. MM is characterized by extensive genetic and clonal heterogeneity, which have hampered the attempts to identify a common underlying mechanism for disease establishment and development of appropriate treatment regimes. This thesis is focused on understanding the role of epigenetic regulation of gene expression mediated by the polycomb repressive complexes 1 and 2 (PRC1 and 2) in MM and their impact on disease biology and therapy. In paper I the genome-wide distribution of two histone methylation marks; H3K27me3 and H3K4me3 were studied in plasma cells isolated from newly diagnosed MM patients or age-matched normal donors. We were able to define targets of H3K27me3, H3K4me3 and bivalent (carry both marks) which are, when compared to normal individuals, unique to MM patients. The presence of H3K27me3 correlated with silencing of MM unique H3K27me3 targets in MM patients at advanced stages of the disease. Notably, the expression pattern of H3K27me3-marked genes correlated with poor patient survival. We also showed that inhibition of the PRC2 enzymatic subunit EZH2 using highly selective inhibitors (GSK343 and UNC1999) demonstrated anti-myeloma activity using relevant in vitro models of MM. These data suggest an important role for gene repression mediated by PRC2 in MM, and highlights the PRC2 component EZH2 as a potential therapeutic target in MM. In paper II we further explored the therapeutic potential of UNC1999, a highly selective inhibitor of EZH2 in MM. We showed that EZH2 inhibition by UNC1999 downregulated important MM oncogenes; IRF-4, XBP-1, BLIMP-1and c-MYC. These oncogenes have been previously shown to be crucial for disease establishment, growth and progression. We found that EZH2 inhibition reactivated the expression of microRNAs genes previously found to be underexpressed in MM and which possess potential tumor suppressor functions. Among the reactivated microRNAs we identified miR-125a-3p and miR-320c as predicted negative regulators of the MM-associated oncogenes. Notably, we defined miR-125a-3p and miR-320c as targets of EZH2 and H3K27me3 in MM cell lines and patients samples. These findings described for the first time PRC2/EZH2/H3K27me3 as regulators of microRNA with tumor suppressor functions in MM. This further strengthens the oncogenic features of EZH2 and its potential as a therapeutic target in MM. In paper III we evaluated the therapeutic potential of targeting PRC1 in MM using the recently developed chemical PTC-209; an inhibitor targeting the BMI-1 subunit of PRC1. Using MM cell lines and primary cells isolated from newly diagnosed or relapsed MM patients, we found that PTC-209 has a potent anti-MM activity. We showed, for the first time in MM, that PTC-209 anti-MM effects were mediated by on-target effects i.e. downregulation of BMI-1 protein and the associated repressive histone mark H2AK119ub, but that other subunits of the PRC1 complex were not affected. We showed that PTC-209 reduced MM cell viability via significant induction of apoptosis. More importantly, we demonstrated that PTC-209 shows synergistic anti-MM activity with other epigenetic inhibitors targeting EZH2 (UNC1999) and BET-bromodomains (JQ1). This work highlights the potential use of BMI-1 and PRC1 as potential therapeutic targets in MM alone or in combination with other anti-MM agents including epigenetic inhibitors.

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Bayles, Ian Matthew. « SCREENING FOR EPIGENETIC INHIBITORS OF OSTEOSARCOMA METASTASIS ». Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1579859055599871.

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Gimple, Ryan Christopher. « Epigenetic Landscapes Identify Functional Therapeutic Vulnerabilities in Glioblastoma ». Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1587732572817921.

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Nelson, Jonathan M. « Identification of drug sensitive gene motifs using "epigenetic profiles" derived from bioinformatics databases ». Thesis, The University of North Carolina at Greensboro, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10123750.

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The use of epigenetic modifying drugs such as DNA methyltransferase inhibitors (DNMTi) and histone deacetylase inhibitors (HDACi) is becoming more common in the treatment of cancer. Currently, there is a profound interest in determining predictive biomarkers for patient response and the efficacy of known and novel drugs. There are likely distinct “epigenetic profiles” defined by the location and abundance of DNA methylation patterns and histone modifications. Here we propose to investigate the response of a selected subset of genes to particular DNMTi and HDACi treatments, in two human cancer cell lines, colorectal carcinoma HCT-116 and liver adenocarcinoma HepG2. In this study we identified unique epigenetic profiles based on microarray and bioinformatics derived epigenetic data that are predictive of the response to epigenetic drug treatment. Microarray studies were used to identify re-activated genes common in two different cancer cell types treated with epigenetic drugs. Bioinformatics data was compiled on these genes and correlated against re-expression to construct the genes’ “epigenetic profile”. We then verified the response of the select group of genes in HCT-116 and HepG2 upon treatment at varying concentrations of epigenetic drugs and illustrated that selective reactivation of the target gene. Additionally, two novel genes were introduced and one selectively activated over another.

Further research would prove invaluable for the medical and drug development communities, as a more extensive model would certainly be of use to determining patient response to drug treatment based on their individual epigenetic profile and leading to more successful novel drug design.

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

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Epigenetic states constitute heritable features of the chromatin to regulate when, where and how genes are expressed in the developing conceptus. A special case of epigenetic regulation, genomic imprinting, is defined as parent of origin-dependent monoallelic expression. The Igf2-H19 locus is considered as paradigm of genomic imprinting with a growth-promoting gene, Igf2, expressed paternally and a growth antagonist, H19 encoding a non-coding transcript, expressed only from the maternal allele. The monoallelic expression patterns are regulated by the epigenetic status at an imprinting control region (ICR) in the 5´-flank of the H19 gene. The chromatin insulator protein CTCF interacts with only the maternal H19 ICR allele to prevent downstream enhancers to communicate with the Igf2 promoters. Mutations of these CTCF binding sites lead to biallelic Igf2 expression, increased size of the conceptus and predisposition for cancer. Reasoning that these effects cannot be explained by the regulation of Igf2 expression alone, a technique was invented to examine long-range chromatin interactions without prior knowledge of the interacting partners. Applying the circular chromosomal conformation capture (4C) technique to mouse neonatal liver cells, it was observed that 114 unique sequences interacted with the H19 ICR. A majority of these interactors was in complex with only the maternal H19 ICR allele and depended on the presence of functional CTCF binding sites. The functional consequence of chromosomal networks was demonstrated by the observation that the maternal H19 ICR allele regulated the transcription of two genes on another chromosome. As the chromosomal networks underwent reprogramming during the maturation of embryonic stem cells, attention was turned to human cancer cells, displaying features common with mouse embryonic stem cells. Subsequently, chromatin folding at the human H19 ICR suggested that stable chromatin loops were organized by synergistic interactions within and between baits and interactors. The presence of these interactions was linked to DNA methylation patterns involving repeat elements. A "flower" model of chromatin networks was formulated to explain these observations. This thesis has unravealed a novel feature of the epigenome and its functions to regulate gene expression in trans. The identified roles for CTCF as an architectural factor in the organization of higher order chromatin conformations may be of importance in understanding development and disease ontogeny from novel perspectives.

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Alholle, Abdullah. « Genetic and epigenetic alterations of sarcoma ». Thesis, University of Birmingham, 2017. http://etheses.bham.ac.uk//id/eprint/7301/.

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Primary malignant bone tumours are rare cancers that are characterised by different genetic and epigenetic alterations. A functional epigenomic approach was combined with the Illumina HumanHT-12.v4-BeadChip expression microarray in three Ewing Sarcoma (ES) cell lines to identify genome-wide functional methylation changes in these cells and ES primary samples. This study revealed eight frequently methylated genes in ES patients’ samples, where NPTX2 and PHF11 promoter methylation was associated with poor patient prognosis. The second methylation study involved genome-wide DNA methylation profiling of chordoma samples using the Infinium-HumanMethylation450-BeadChip microarray. This study identified a list of 8,819 loci which were differentially methylated between chordomas and controls and eight genes which were differentially methylated between recurrent and non-recurrent chordoma samples. RNA sequencing (RNA-seq) analysis of primitive small blue round cell tumour (SBRCT) samples was also carried out in order to identify gene fusions in this type of cancer. Three different somatic gene fusions in SBRCT samples were identified using RNA-Seq (CRTC1-SS18;BCR-UPB1 and KHDRBS2-CIC). Moreover, two other gene fusions were identified in unpaired SBCRT samples. Overall, this study used high-throughput technologies to identify novel genetically and epigenetically altered genes in different types of bone sarcoma which may, therefore, provide unique insight into bone sarcoma tumorigenesis.

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Gerrard, Diana Lea. « Characterization Of Epigenetic Plasticity And Chromatin Dynamics In Cancer Cell Models ». ScholarWorks @ UVM, 2019. https://scholarworks.uvm.edu/graddis/1060.

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Cancer progression is driven by cumulative changes that promote and maintain the malignant phenotype. Epigenetic alterations are central to malignant transformation and to the development of therapy resistance. Changes in DNA methylation, histone acetylation and methylation, noncoding RNA expression and higher-order chromatin structures are epigenetic features of cancer, which are independent of changes in the DNA sequence. Despite the knowledge that these epigenetic alterations disrupt essential pathways that protect cells from uncontrolled growth, how these modifications collectively coordinate cancer gene expression programs remains poorly understood. In this dissertation, I utilize molecular and informatic approaches to define and characterize the genome-wide epigenetic patterns of two important human cancer cell models. I further explore the dynamic alterations of chromatin structure and its interplay with gene regulation in response to therapeutic agents. In the first part of this dissertation, pancreatic ductal adenocarcinoma (PDAC) cell models were used to characterize genome-wide patterns of chromatin structure. The effects of histone acetyltransferase (HAT) inhibitors on chromatin structure patterns were investigated to understand how these potential therapeutics influence the epigenome and gene regulation. Accordingly, HAT inhibitors globally target histone modifications and also impacted specific gene pathways and regulatory domains such as super-enhancers. Overall, the results from this study uncover potential roles for specific epigenomic domains in PDAC cells and demonstrate epigenomic plasticity to HAT inhibitors. In the second part of this dissertation, I investigate the dynamic changes of chromatin structure in response to estrogen signaling over a time-course using Estrogen Receptor (ER) positive breast cancer cell models. Accordingly, I generated genome-wide chromatin contact maps, ER, CTCF and regulatory histone modification profiles and compared and integrated these profiles to determine the temporal patterns of regulatory chromatin compartments. The results reveal that the majority of alterations occur in regions that correspond to active chromatin states, and that dynamic chromatin is linked to genes associated with specific cancer growth and metabolic signaling pathways. To distinguish ER-regulated processes in tamoxifen-sensitive and in tamoxifen-resistant (TAMR) cell models, we determined the corresponding chromatin and gene expression profiles using ER-positive TAMR cancer cell derivatives. Comparison of the patterns revealed characteristic features of estrogen responsiveness and show a global reprogramming of chromatin structure in breast cancer cells with acquired tamoxifen resistance. Taken together, this dissertation reveals novel insight into dynamic epigenomic alterations that occur with extrinsic stimuli and provides insight into mechanisms underlying the therapeutic responses in cancer cells.

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Thornton, Seraphim R. « The role of Polycomb-mediated epigenetic regulation in embryonic stem cell differentiation ». Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/89838.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2014.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references.
During mammalian development, a single founding cell must produce all of the different types of cells in the adult organism. What are the regulatory mechanisms required to coordinate the necessary gene expression networks for this process? Polycomb group (PcG) proteins are epigenetic regulators necessary for proper differentiation of cells and for mammalian development. Notably, faulty regulation of PRC2 has been associated with a broad range of cancers, suggesting that it has a critical role in maintaining cell identity. Polycomb Repressive Complex 2 (PRC2) catalyzes the posttranslational histone modification H3K27me3, a histone modification associated with transcriptional repression. Although PRC2 has critical functions in lineage commitment and in mediating cell fate transitions, it has proved difficult to study its precise role in these processes since complete loss of H3K27me3 leads to an inability of embryonic stem cells (ESCs) to properly undergo directed differentiation in vitro. PRC2 functions with additional regulators and regulatory pathways, including PRC1, accessory PcG subunits, and DNA methylation, among others; however, we know little about how they work together to coordinate gene expression programs during lineage commitment. Thus, dissecting the function of PRC2 is critical to improve our understanding of mammalian development and disease. Here, we analyzed gene expression and DNA methylation levels in several PRC2 mutant ESC lines that maintained varying levels of H3K27me3. We found that while a partial reduction of H3K27me3 levels allowed for proper temporal activation of lineage genes during directed differentiation of ESCs to spinal motor neurons (SMNs), genes that function to specify other lineages failed to be repressed, suggesting that PRC2 activity is necessary for regulating lineage fidelity. We also found that H3K27me3 is antagonistic to DNA methylation in cis. Thus, these data suggest a role for PRC2 in coordinating gene repression while protecting against inappropriate promoter DNA methylation during differentiation. Our work provides novel insights into the functional relationship between two distinct epigenetic regulatory mechanisms, as mediated by PRC2 and DNA methylation, in regulating lineage decisions during development.
by Seraphim R. Thornton.
Ph. D.

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Salamé, Patrick-Georges. « The epigenetic mechanism involved in MBD2-mediated induction of interleukin-33 ». Thesis, McGill University, 2010. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=95057.

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Il-33, the most recently discovered member of the il-1 family of cytokines, is mainly expressed by fibroblasts, epithelial cells, and endothelial cells and signals via the ST2 receptor to promote Th2 type immune responses. This newly discovered cytokine has a well established role in airways inflammation, most notably asthma, and is involved in a wide range of diseases such a s atherosclerosis and atopic dermatitis, but its role in cancer remains unknown. Previous studies in our lab have demonstrated that expression of ectopic MBD2 transforms mouse fibroblasts NIH3T3 cells into highly invasive metastatic cancerous cells. Il-33 is the top gene induced by upregulation of the putative DNA demethylase MBD2 suggesting an undiscovered role of this new cytokine in tumorigenesis. The aim of this thesis is to assess the mechanisms underlying MBD2-mediated induction of il-33. We identify here using high-density tiling arrays with a combination of mDIP and ChIP-on-chip a regulatory region of il-33 which is partially demethylated by increasing the levels of methylated DNA binding protein domain 2 (MBD2) in the cell. Luciferase reporter assays confirm that this region bearing promoter activity is silenced upon in vitro methylation as well as show MBD2-dependent activation of a reporter gene. We further demonstrate using bisulfite pyrosequencing that similar methylation patterns are observed in murine tissues and cell types expressing il-33. Taken all together, our data suggest that il-33 is silenced by DNA methylation and activated by MBD2 triggering cell transformation and invasion. Thus, the new mechanism of il-33 regulation discovered in our studies might have important therapeutic implications in cancer growth and metastasis.
Il-33, le plus récemment découvert membre de la famille il-1 des cytokines, est principalement exprimé par les fibroblastes, les cellules épithéliales et les cellules endothéliales et signale via le récepteur ST2 pour promouvoir des réponses immunitaires de type Th2. Cette cytokine nouvellement découverte a un rôle bien établi dans l'inflammation des voies respiratoires notamment l'asthme et est impliquée dans un large éventail de maladies comme l'athérosclérose et la dermatite atopique, mais son rôle dans le cancer reste inconnu. Des études antérieures dans notre laboratoire ont démontré que l'expression ectopique de MBD2 transforme des cellules NIH3T3 fibroblastes de souries en cellules cancéreuses hautement envahissantes et métastatiques. Il-33 est à la tête des gènes induits par la régulation positive de la putative ADN déméthylase MBD2 suggérant un rôle inconnu de cette nouvelle cytokine dans la tumorigenèse. L'objectif de cette thèse est d'évaluer les mécanismes sous-jacents l'induction d'il-33 médiée par MBD2. Nous avons identifié en utilisant des puces à ADN de carrelage haute densité avec une combinaison de mDIP et ChIP-on-chip une région de régulation d'il-33 qui est partiellement déméthylée en augmentant les niveaux de methylated DNA binding protein domain 2 (MBD2) dans la cellule. Les dosages rapporteurs de la luciférase confirment que l'activité de cette région du promoteur est réduite au silence avec la méthylation in vitro ainsi que l'activation d'un gène rapporteur par MBD2. Nous montrons également à l'aide du pyroséquencage bisulfite que des modèles de méthylation similaires sont observés dans les tissus murins et des types de cellules exprimant il-33. Prises dans leur ensemble, nos données suggèrent qu'il-33 est réduit au silence par la méthylation de l'ADN et activé par la déméthylation par MBD2 déclenchant la transformation cellulaire et l'invasion. Ainsi, le nouveau mécanisme de

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Lee, Jennifer Sohn. « Epigenetic Regulation of Lytic and Latent Herpes Simplex Virus 1 Infection ». Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467322.

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Epigenetic regulation plays a major role in whether the herpes simplex virus 1 (HSV-1) will initiate viral gene expression and lytic infection or instead suppress its gene expression and establish a latent infection. Prior to this study, it was known that cells respond to naked DNA by assembling chromatin to silence foreign genetic material. However, during lytic infection of epithelial cells, viral proteins VP16 and ICP0 have been implicated in limiting chromatin association and promoting euchromatic histone modifications on the HSV-1 genome. We hypothesized that the viral genome would also be subject to silencing by heterochromatin modification during lytic infection. To test this we examined the association of chromatin and heterochromatic modifications during lytic infection with WT viruses and ICP0-null mutant viruses. We found that heterochromatin modifications H3K9me3 and H3K27me3 associate initially with all viruses, but were removed rapidly during infection with WT HSV-1. ICP0-null viruses were not able to remove histones or heterochromatin, indicating a role for ICP0 in reversing epigenetic silencing. In latent infection, HSV-1 undergoes epigenetic silencing as a means to suppress gene expression and persist in neurons. Surprisingly, in this study, we find that ICP0-null viruses accumulate less heterochromatin on lytic gene promoters relative to WT viruses. This suggests that ICP0 may function to promote infection of neurons, or assist in the establishment or maintenance of latent infection. Additionally, during latency the viral genome maintains active expression from the latency-associated transcript (LAT) region, and this region retains markers of euchromatin that are excluded from the lytic viral genes. The insulator protein, CTCF, binds to a site downstream of this region between the LAT and ICP0 promoters. We find that during latent infection, deletion of this site promoted accumulation of H3K27me3 at the LAT promoter and reduced reactivation competence of the virus, but surprisingly enhanced LAT expression. This suggests that CTCF balances epigenetic repression to promote latency and maintain reactivation competence. In summary, this dissertation suggests that during lytic infection HSV reverses cell-mediated epigenetic repression and promotes viral gene expression, while during latency, the virus co-opts epigenetic mechanisms to maintain a silenced but poised genome.
Medical Sciences

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Sakatos, Alexandra J. « Beyond Mutation : Epigenetic Drivers of Phenotypic Diversity and Survival in Mycobacteria ». Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493309.

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M. tuberculosis is the causative agent of a global health epidemic that kills ~1.5 million people each year. The outcomes of infection with Mtb are highly variable. Although many patients are able to control the infection in a quiescent state, others develop active disease. Furthermore, the progression of TB lesions has been shown to vary within a single individual. This phenotypic variability in the infecting population of Mtb may be responsible for the high rate of treatment failures, which can exceed 20% in some endemic areas (World Health Organization, 2015). Although genetic mutation can drive a portion of the observed phenotypic variability, mutation rates in mycobacteria are exceedingly low. Epigenetic factors are therefore likely to be responsible for the majority of observed diversity in infection and treatment outcomes. Here, we investigated epigenetic drivers of phenotypic variability and survival in mycobacteria. We found evidence of high rates of phenotypic variability in response to drug treatment of M. smegmatis, a non-pathogenic, model for TB. Specifically, we found that two distinct subpopulations are able to grow in the presence of drug. These subpopulations exhibited heritability of their transcriptional profiles, growth properties, and ability to grow on drug across generations. We next found that hupB, a histone-like protein, is critical for the formation of these epigenetically regulated subpopulations. We also show that hupB regulates gene expression and is post-translationally modified, and that modification of hupB may drive the formation of one of these phenotypically drug-resistant subpopulations. These findings suggest that modification of a histone-like protein may drive epigenetic inheritance and phenotypic variability in mycobacteria, which allows it to withstand antibiotic treatment. Finally, we also investigated alternative post-transcriptional mechanisms of hupB regulation.
Biological Sciences in Public Health

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Octavio, Leah M. (Leah Mae Manalo). « Molecular systems analysis of a cis-encoded epigenetic switch ». Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/68433.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references.
An ability to control the degree of heterogeneity in cellular phenotypes may be important for cell populations to survive uncertain and ever-changing environments or make cell-fate decisions in response to external stimuli. Cells may control the degree of gene expression heterogeneity and ultimately levels of phenotypic heterogeneity by modulating promoter switching dynamics. In this thesis, I investigated various mechanisms by which heterogeneity in the expression of FLO 11 in S. cerevisiae could be generated and controlled. First, we show that two copies of the FLOJ1 locus in S. cerevisiae switch between a silenced and competent promoter state in a random and independent fashion, implying that the molecular event leading to the transition occurs in cis. Through further quantification of the effect of trans regulators on both the slow epigenetic transitions between a silenced and competent promoter state and the fast promoter transitions associated with conventional regulation of FLO11, we found different classes of regulators affect epigenetic, conventional, or both forms of regulation. Distributing kinetic control of epigenetic silencing and conventional gene activation offers cells flexibility in shaping the distribution of gene expression and phenotype within a population. Next, we demonstrate how multiple molecular events occurring at a gene's promoter could lead to an overall slow step in cis. At the FLO] 1 promoter, we show that at least two pathways that recruit histone deacetylases to the promoter and in vivo association between the region -1.2 kb from the ATG start site of the FLO11 ORF and the core promoter region are all required for a stable silenced state. To generate bimodal gene expression, the activator Msnlp forms an alternate looped conformation, where the core promoter associates with the non-coding RNA PWR1's promoter and terminator regions, located at -2.1 kb and -3.0 kb from the ATG start site of the FLO]1 ORF respectively. Formation of the active looped conformation is required for Msnlp's ability to stabilize the competent state without destabilizing the silenced state and generate a bimodal response. Our results support a model where multiple stochastic steps at the promoter are required to transition between the silenced and active states, leading to an overall slow step in cis. Finally, preliminary investigations of heterozygous diploids revealed possible transvection occurring at FLO] 1, where a silenced allele of FLO 11 appeared to transfer silencing factors to a desilenced FLO11 allele on the homologous chromosome. These observations suggest a new mechanism through which heterogeneity in FL011 expression could be further controlled, in addition to the molecular events at the FL011 promoter we elucidated previously.
by Leah M. Octavio.
Ph.D.

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Chen, Liying Michelle. « Targeting the Epigenetic Lesion in MLL-Rearranged Leukemia ». Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10663.

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It has become increasingly apparent that the misregulation of histone modification actively contributes to cancer. The histone H3 lysine 79 (H3K79) methyltransferase Dot1l has been implicated in the development of leukemias bearing translocations of the Mixed Lineage Leukemia (MLL) gene. We studied the global epigenetic profile for H3K79 dimethylation and found abnormal H3K79 dimethylation profiles exist not only in leukemias driven by MLL-fusion proteins with nuclear partners like AF9, but also in leukemia with MLL-fusions containing cytoplasmic partners like AF6. Genetic inactivation of Dot1l led to downregulation of fusion target genes and impaired both in vitro bone marrow transformation and in vivo leukemia development by MLL-AF10, CALM-AF10 as well as MLL-AF6, suggesting that aberrant H3K79 methylation by DOT1L sustains fusion-target gene expression in MLL rearranged leukemias and CALM-AF10 rearranged leukemias. Pharmacological inhibition of DOT1L selectively killed MLL-AF10 and MLL-AF6 transformed cells but not Hox9/Meis1 transformed cells, pointing to DOT1L as a potential therapeutic target in MLL-rearranged leukemia. We further characterized the DOT1L complex under physiological conditions from human leukemia cells and identified AF10 as a key DOT1L complex component. Given the importance of H3K79 methylation in MLL-rearranged leukemia, we sought to study the role of DOT1L complex component AF10 in H3K79 methylation and MLL leukemia. We generated conditional knockout mice in which the Dot1l-interacting octapeptide-motif leucine-zipper (OM-LZ) domain of Af10 was flanked by LoxP sites. Cre induced deletion of \(Af10^{OM-LZ}\) is predicted to abrogate the Af10-Dot1l interaction. Our histone mass spectrometry data demonstrated that deletion of the endogenous \(Af10^{OM-LZ}\) domain abrogated global H3K79 dimethylation but retained H3K79 monomethylation. Interestingly, bone marrow transformation by MLLAF6 and MLL-AF9 is abrogated by induced deletion of endogenous \(Af10^{OM-LZ}\), while bone marrow transformation by MLL-AF10 and CALM-AF10 is not affected by deletion of endogenous \(Af10^{OM-LZ}\), confirming the importance of Af10-Dot1l interaction in MLL- or CALM fusion-leukemias. Moreover, we showed \(Af10^{OM-LZ}\) deletion prolonged survival of MLL-AF9 leukemia in vivo and led to chromotin compaction and downregulation of MLL fusion targets in MLL-AF9 leukemia. Therefore our results demonstrate a role for Af10 in the conversion of H3K79 monomethylation to dimethylation and reveal the AF10-DOT1L interaction as an attractive therapeutic target in MLL-rearranged leukemias.

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Mukhopadhyay, Rituparna. « Chromatin Insulators and CTCF : Architects of Epigenetic States during Development ». Doctoral thesis, Uppsala University, Department of Animal Development and Genetics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4241.

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A controlled and efficient coordination of gene expression is the key for normal development of an organism. In mammals, a subset of autosomal genes is expressed monoallelically depending on the sex of the transmitting parent, a phenomenon known as genomic imprinting.

The imprinted state of the H19 and Igf2 genes is controlled by a short stretch of sequences upstream of H19 known as the imprinting control region (ICR). This region is differentially methylated and is responsible for the repression of the maternally inherited Igf2 allele. It harbors hypersensitive sites on the unmethylated maternal allele and functions as an insulator that binds a chromatin insulator protein CTCF. Hence the H19 ICR, which plays an important role in maintaining the imprinting status of H19 and Igf2, was shown to lose the insulator property upon CpG methylation.

Another ICR in the Kcnq1 locus regulates long-range repression of p57Kip2 and Kcnq1 on the paternal allele, and is located on the neighboring subdomain of the imprinted gene cluster containing H19 and Igf2, on the distal end of mouse chromosome 7. Similarly to the H19 ICR, the Kcnq1 ICR appears to possess a unidirectional and methylation-sensitive chromatin insulator property in two different somatic cell types. Hence, methylation dependent insulator activity emerges as a common feature of imprinting control regions.

The protein CTCF is required for the interpretation and propagation of the differentially methylated status of the H19 ICR. Work in this thesis shows that this feature applies genomewide. The mapping of CTCF target sites demonstrated not only a strong link between CTCF, formation of insulator complexes and maintaining methylation-free domains, but also a network of target sites that are involved in pivotal functions. The pattern of CTCF in vivo occupancy varies in a lineage-specific manner, although a small group of target sites show constitutive binding.

In conclusion, the work of this thesis shows that epigenetic marks play an important role in regulating the insulator property. The studies also confirm the importance of CTCF in maintaining methylation-free domains and its role in insulator function. Our study unravels a new range of target sites for CTCF involved in divergent functions and their developmental control.

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Holmgren, Claes. « Epigenetic Regulation of the H19 Chromatin Insulator in Development and Disease ». Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3405.

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The coordinated regulation of gene expression must be tightly controlled for normal development to occur. In mammals, this issue is further complicated by the requirement of both the maternal and paternal genomes for normal development, reflecting the fact that a subset of genes are monoallelically expressed depending on parental inheritance, a phenomenon known as genomic imprinting. The imprinted H19 and Igf2 genes are often considered as paradigms of genomic imprinting, since their monoallelic expression patterns are coordinated via a short stretch of sequence upstream of H19, known as the imprinting control region (ICR). This region is differentially methylated, with specific CpG methylation on the paternal allele. It is shown here that the ICR harbours several maternal-specific hypersensitive sites, located in linker regions between positioned nucleosomes. Furthermore, this region functions as an orientation-dependent insulator, that binds the chromatin insulator factor CTCF. The hypothesis that the methylation status of the ICR dictates the activity of the Igf2 gene 90 kb further upstream was confirmed by the demonstration that the insulator function is lost when the ICR is CpG methylated. The ICR has previously been shown to act as a silencer when positioned in a promotor-proximal position. The cause of this silencing was shown to be distance-dependent, suggesting that the silencing features of the ICR depend on a chromatin conformation that renders adjacent sequences inaccessible to the RNA polymerase. These data issue a cautionary note with respect to the interpretation of silencer functions. In several forms of cancer, the normally silent maternal IGF2 gene is expressed, possibly as a result of loss of insulator function at the ICR. The utilisation of CTCF target-sites was analysed in different tumours, and was shown to be highly variable. Methylation analysis showed that potential loss of insulator function and gain of methylation at the maternal ICR did not always correlate with biallelic expression of IGF2. Further investigations uncovered a novel mechanism, in which the activation of the IGF2 promoter was independent of insulator function in some cancers. This thesis shows that the regulation of the imprinted state of Igf2 depends on the formation of an epigenetically regulated chromatin insulator, and that the loss of IGF2 imprinting in human cancer can be attributed to several mechanisms, including a novel mechanism that neutralises chromatin insulator function.

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Gifford, Casey. « Transcriptional and Epigenetic Dynamics Observed During Lineage Specification of Human Embryonic Stem Cells ». Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11228.

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Epigenetic regulation of gene expression is essential for faithful cellular specification during embryonic development. Directed differentiation of pluripotent human embryonic stem cells (hESCs), which maintain the ability to give rise to each cell type found within the human body, provides a tractable system to study both the epigenetic mechanisms that facilitate cellular transitions, and the transcription factors (TFs) that dictate these events. To understand molecular events associated with major lineage decisions, we performed comprehensive genomic profiling, including RNA-Sequencing, Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) for six histone modifications and whole genome bisulfite-sequencing (WGBS) to interrogate DNA methylation levels, on three populations derived through directed differentiation of hESCs. Expression profiling detected signatures that resembled the three embryonic germ layers, namely ectoderm, mesoderm and endoderm. Integration of ChIP-Seq and WGBS data revealed widespread remodeling, predominantly at intergenic regions. To understand the impact of TF binding on epigenetic remodeling, we then complemented the epigenetic information with binding profiles for the pluripotency TFs OCT4, SOX2 and NANOG (O/S/N) in hESCs, and FOXA2 in the endoderm population. O/S/N binding was identified near pluripotency genes as expected, as well as regions that exhibited lineage specific remodeling during differentiation and are linked to later stages of development. We also discerned a novel epigenetic trend, in which H3K27me3 was unexpectedly gained at regions of low CpG density that exhibit high levels of DNA methylation in hESCs. These events overlapped with FOXA2 binding sites in the dEN that lose DNA methylation. Notably, these events were detected near genes associated with later stages of development, such as AFP. We postulate that these FOXA2-associated epigenetic remodeling events lead to acquisition of a transient, facultative heterochromatic state necessary to foster efficient differentiation of subsequent stages. Integration of these data sets yielded an unprecedented perspective of the orchestrated transcriptional and epigenetic events that occur during cell state transitions. Future studies that compare epigenomic profiles of in vitro derived cell types to their primary counterparts may identify regulatory elements that are held in improper epigenetic states, and ultimately lead to improved differentiation protocols and the in vitro derivation of therapeutically relevant cell types.

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Lu, Yizhen. « Physical interation of parathyroid hormone-related protein with the epigenetic regulator Bmi1 ». Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96929.

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As a cause of malignancy-induced hypercalcemia, PTHrP (parathyroid hormone-related protein) plays an important role in cell growth and differentiation. This peptide is unique in that it not only acts through membrane receptors but also translocates directly to the nucleus. Studies have shown that the repression of target gene expression is achieved through chromatin modifications induced by the PcG complex. As a core protein of the PcG complex, Bmi1 functions as a transcriptional repressor for various genes involved in development and cell proliferation. Recent studies have indicated that the skeletal phenotypes of PTHrP(1-84) knock-in mice are consistent with ones observed in Bmi1-/- mice in vivo. In addition, the down-regulation of Bmi1 expression was detected in PTHrP(1-84) knock-in mice. Both phenotypes indicate that there is correlation between Bmi1 and PTHrP. However, the molecular mechanism involved in correlation of PTHrP and Bmi1 regulation is poorly understood. The aim of this study was to gain insight into the underlying molecular mechanism of the way of PTHrP regulating Bmi1. We focused on the interaction between PTHrP and Bmi1 in vitro and in vivo system and the consequences exerted by this interaction. At first, co-localization of PTHrP and Bmi1 was demonstrated and the N-terminus of PTHrP was found to be responsible for the interaction both in vivo and in vitro. Second, we set up the repression assays in vivo to identify the promoters' activities and cell survival influenced by this direct interaction. As a result, overexpression of PTHrP and Bmi1 in HEK293 cells was shown to have an effect on p19Arf and Gal4 promoter activities in vivo. Thirdly, increased cell proliferation was detected in HEK293 cells and NIH 3T3 cells with overexpressed PTHrP and Bmi1 together. At the same time, I also discovered the elevation of cell survival rate in HEK293 and NIH 3T3 cells when PTHrP and Mel18 were expressed together. This study provides evidence that the hormone PTHrP physically and functionally interacts with Bmi1 and Mel18 to affect the activities of promoters in the nucleus and regulate cell proliferation.
La protéine Parathyroid hormone related-protein (PTHrP) joue un rôle très important dans la croissance et la différentiation cellulaire en plus d'être responsable de l'hypercalcémie induite par la malignité. Ce peptide est unique non seulement parce qu'il agit par l'intermediate de récepteurs transmembranaires, mais aussi parce qu'il est transloqué directement au noyau. Bmi-1, un peptide essentiel du PcG complexe, fonctionne comme un répresseur de transcription pour plusieurs gènes importants dans le développement et de l'organisme de la prolifération cellulaire. Cette fonction répressive régule l'expression des gènes cibles en induisant des modifications sur la chromatine (73). Des études publiées récemment démontrent que PTHrP influence l'expression moléculaire de Bmi-1 (95). Cependant, le mécanisme par lequel Bmi-1 contrôle PTHrP n'est pas encore bien documenté. Mon but premier est d'élucider les mécanismes moléculaires de cette interaction ensuite de trouver quelles conséquences fonctionnelles peuvent résulter de cette interaction. Au départ, la colocalisation de PTHrP et Bmi-1 a été démontrée dans le noyau de cellules HEK293. Ensuite, l'interaction entre Bmi-1 et PTHrP a été illustrée in vivo et in vitro. On a trouvé que c'est le N-Terminal qui est responsable des interactions in vivo et in vitro. De plus, la surexpression de PTHrP et Bmi-1 dans les cellules HEK293 provoque des effets minimes sur l'activité transcriptionelle des gènes et de l'expression du gène P19arf. En outre, la surexpression de PTHrP et Bmi-1 cause une augmentation du niveau de prolifération cellulaire dans les cellules HEK293 et NIH 3T3. En parallèle, j'ai découvert une augmentation du taux de survie des cellules HEK 293 et NIH 3T3 suite à surexpression des peptides PTHrP et Mel18. A été noteé ces études démontrent que l'hormone PTHrP interagit physiquement et est attaché fonctionnellement avec Bmi-1.

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Pant, Vinod. « CTCF and Epigenetic Regulation of the H19/Igf2 Locus ». Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3540.

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Mariano, Piero. « Epigenetic Regulation and Reprogramming of the H19 Imprinting Control Region ». Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6299.

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The development of a new individual from the fertilized oocyte can ultimately be seen as the consequence of the establishment and maintenance of specific patterns of gene expression. Although regulation of gene activity occurs at different levels, cellular specialization and differentiation are the results of developmental cues that essentially take place at the transcriptional level. The involvement of epigenetics in this process has become increasingly clear during the last decade. Imprinted genes constitute an excellent example as monoallelic expression seems to reflect differential epigenetic marks on the two alleles. This is the case of the imprinted H19 and Igf2 genes were the monoallelic expression is coordinated through a differentially methylated region (hypermethylated on the paternal allele), known as ICR (imprinted control region). In the mouse the ICR harbours four binding sites for the methylation sensitive insulator protein CTCF. Previous studies with episomal constructs had shown that this region behaved as an insulator and that CTCF is required for the insulator activity of the H19 ICR This thesis establish a clear link between the insulator function and the chromatin structure at the H19 ICR and indicates that the precise allocation of the CTCF target sites in the linker regions can play a critical role in this process. The importance of the CTCF interaction at the ICR was also confirmed in vivo using a mouse model that showed how intact CTCF target sites are needed to manifest insulator activity and methylation protection. We have investigated the role of CTCF and a related protein BORIS in establishing the maternal to paternal imprint transition in chromatin structure at the H19/Igf2 locus in the male germline. This thesis also describe the development of a new technique for the localization of chromatin associated factors and modifications with higher sensitivity and resolution compared to existing approaches.

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Miller, Tyler Eugene. « Identifying Novel In Vivo Epigenetic Dependencies in Glioblastoma ». Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1464856610.

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Dubovsky, Jason A. « Epigenetic Modifiers to Augment the Immunogenicity of Chronic Lymphocytic Leukemia ». Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4623.

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Cancer cells employ a litany of immunosuppressive and immunevasive strategies to avoid detection and elimination by the various arms of the innate and adaptive immune system. Many hematologic and solid tumors progressively develop a specialized microenvironment which promotes tissue restructuring inflammation while masking the immune signature of the tumor cells themselves. Chronic lymphocytic leukemia, a malignancy of mature B lymphocytes must constantly balance on the precipice of immune recognition. A mature antigen presenting cell themselves, CLL clonal growth is dependent on the very interactions which, if effective, could potentially lead to their demise. To circumvent this, CLL clones set up unique signatures which promote immune recognition yet provide diversionary signals to the remaining immune armament resulting in profound immune dysfunction. While the aforementioned immune dysfunction is widespread, the B cell and T cell repertoire are severely impaired during leukemic progression. The lack of healthy B cells due to displacement by malignant B cells results in the obvious loss of an important antigen presenting cell as well as antibody-based immunity. Additionally, deficient interactions with T cells result in anergy and the preponderance of improperly polarized T lymphocytes which are impotent to eliminate both pathogens and leukemic cells. The result of such severe immune dysfunction is chronic infection and progressive disease which is the primary cause of death in CLL patients. Our research was focused on the premise that alleviating immune dysfunction and providing immunotherapeutic tools will significantly benefit CLL therapy. To this end we developed methods to improve the cellular interaction between CLL cells and T cells a critical step towards improving the antigen presentation capacity of the diseased B cell repertoire. We also identified a therapeutic strategy which can revert the anergic or improperly polarized state of T cells already in circulation allowing those cells to more effectively perform the effector functions necessary to fight pathogenic attack and malignant transformation. Finally, we identified a number of novel targets in CLL which could be used in a vaccinate-induce method to license the elimination of CLL cells by the patient's adaptive immune system. To achieve our goals we utilized a relatively new class of drugs called epigenetic modifiers which specifically alter the chromatin structure resulting in novel genetic signatures which are heritable over cellular generations. The unique properties of these drugs allow for the elicitation of suppressed genetic programs which, when properly controlled, have the potential to reassert healthy lymphocyte functions. Our studies provide a comprehensive therapeutic initiative which, by simultaneously alleviating the major causes of immune dysfunction in addition to facilitating the use of novel active immunotherapeutic strategies could potentially impact clinical therapy for CLL.

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Tazi, Mia Farrah. « Improving Autophagy in Cystic Fibrosis : The Effects of Epigenetic Regulation ». The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429668388.

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Respuela, Patricia. « Gene Regulation and Epigenetic Mechanisms in the Parasite Trypanosoma cruzi ». Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-100265.

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Deliard, Sandra. « THE ROLE OF SPLICING FACTOR SF3B1 IN TRANSCRIPTIONAL AND EPIGENETIC REGULATION ». Diss., Temple University Libraries, 2019. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/583882.

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Biomedical Sciences
Ph.D.
Epigenetic silencing is often altered in cancer and is a target for drug discovery. Unbiased screens in live cells are performed to identify potential novel targets of epigenetic therapy, and these screens have identified drugs that were not previously recognized to be involved in epigenetic reactivation of gene silencing such as cardiac glycosides and a CDK9 inhibitor. Recently, our lab performed a whole genome siRNA screen in combination with DNMT inhibition. One of the top targets revealed in this screen was the splicing factor SF3B1. SF3B1 is a well-known crucial splicing factor and is mutated in several cancers. However, its role in epigenetic regulation has not been well studied. I propose SF3B1 is a novel target for epigenetic therapy in cancer. In the YB5 colon cancer cell line where GFP is under the control of a methylated CMV promoter, I validated the screen results and found 0%, 1.0% and 5.3% GFP+ cells after treatment with siControl, siSF3B1 or the DNA methyltransferase inhibitor decitabine (DAC), respectively. DAC and siSF3B1 were synergistic, inducing 17.2% GFP+ cells. This synergy was also seen in an additional live cell assay and with other SF3B and SF3A family proteins. RNA-Seq analyses showed 423 genes upregulated by siSF3B1, 430 genes induced by DAC, and 1190 induced by the combination. siSF3B1 resulted in aberrant splicing of 695 genes, but there were only 27 genes overlapping between splicing alterations and gene expression changes, suggesting different mechanisms. Genes regulated upon siSF3B1 treatment were enriched for the TATA motif in their promoters, and the TATA-Box binding protein (TBP) was among the genes differentially spliced after siSF3B1. DNA methylation analyses showed demethylation synergy between siSF3B1 and DAC. Finally, the effects of siSF3B1 were phenocopied by treatment with the pan-SF3B inhibitor Pladienolide B (PB). GFP was reactivated in two separate colon cancer cell lines upon treatment with PB with synergistic activation when combined with DAC in YB5 cells. Thousands of genes were regulated and alternatively spliced with PB treatment alone, and among the differentially spliced genes was TBP. Furthermore, PB treatment with DAC induced demethylation significantly more than with DAC treatment alone. Genes regulated upon SF3B1 loss and inhibition were enriched for p53 target genes. Indeed, there was reduced cell proliferation and cell cycle arrest when SF3B1 was inhibited. This study demonstrates that the splicing factor SF3B1 has unexpected effects on gene transcription and targeting SF3B1 is synergistic with DNA methylation inhibition suggesting clinical potential for the combination.
Temple University--Theses

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Koutzamani, Elisavet. « Chromatin, histones, and epigenetic tags ». Doctoral thesis, Linköping : Linköping University, 2006. http://www.bibl.liu.se/liupubl/disp/disp2006/med960s.pdf.

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Frühwald, Michael C. « Medulloblastoma, a developmental abnormality of the cerebellum : a comprehensive analysis of genetic and epigenetic alterations / ». The Ohio State University, 1999. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488191124570489.

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Shi, Wei. « Growth and Behaviour : Epigenetic and Genetic Factors Involved in Hybrid Dysgenesis ». Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4784.

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In mammals, the most frequently observed hybrid dysgenesis effects are growth disturbances and male sterility. Profound defects in placental development have been described and our work on hybrids in genus Mus has demonstrated putative hybrid dysgenesis effects that lead to defects in lipid homeostasis and maternal behavior. Interestingly, mammalian interspecies hybrids exhibit strong parent-of-origin effects in that offspring of reciprocal matings, even though genetically identical, frequently exhibit reciprocal phenotypes. Recent studies have provided strong link between epigenetic regulation and growth, behavior and placental development. Widespread disruption of genomic imprinting has been described in hybrids between closely related species of the genus Peromyscus. The studies presented in this thesis aim to investigate the effects of disrupted epigenetics states on altered growth, female infanticide and placental dysplasia observed in Mus hybrids. We showed that loss-of-imprinting (LOI) of a paternally expressed gene, Peg1, was correlated with increased body weight of F1 hybrids. Furthermore, we investigated whether LOI of Peg1 in F1 females would interfere with maternal behavior. A subset of F1 females indeed exhibited highly abnormal maternal behavior in that they rapidly attacked and killed the pups. By microarray hybridization, a large number of differentially expressed genes in the infanticidal females as compared to normally behaving females were identified. In addtion to Peg1 LOI, we studied allelic expression of numerous imprinted genes in adult Mus interspecies hybrids. In contrast to the study from Peromyscus, patterns of LOI were not consistent with a direct influence of altered expression levels of imprinted genes on growth. Finally, we investigated the allelic interaction between an X-linked locus and a paternally expressed gene, Peg3, in placental defects in Mus hybrids. This study further strengthened the notion that divergent genetic and epigenetic mechanisms may be involved in hybrid dysgenesis in diverse groups of mammals.

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Azoulay, Nelson. « Epigenetic modulation of glucocorticoid receptors in posttraumatic stress disorder : examining child vs. adult trauma ». Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=104876.

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PTSD is a devastating disorder that affects 7-12% of individuals who experience a traumatic event in their lives. Individuals suffering from the disorder show a dysfunctional HPA axis with decreased basal cortisol release and increased glucocorticoid receptor sensitivity. Recently, epigenetic studies have shown associations between trauma and the subsequent effects on the HPA axis in abused participants who committed suicide. Importantly, findings also showed child trauma as being a significant factor in DNA methylation levels in promoter region 1F in the hippocampus. This thesis shows the possible role of epigenetic programming of glucocorticoid receptors in PTSD while examining the effects of different timing of trauma. Methods included the measurements of salivary basal cortisol levels, the expression of glucocorticoid receptors in whole blood and the DNA methylation levels in two promoter regions of the glucocorticoid receptors by sequenome epityper. Results showed that individuals suffering from PTSD have decreased salivary cortisol release in the morning, increased glucocorticoid receptors and increased total methylation levels in promoter region 1C in whole blood. Additionally, adulthood trauma seemed to be of greater importance with regards to HPA axis activity while childhood trauma showed to be more significant with regards to epigenetics. These results indicate that 1) individuals suffering from a lifetime PTSD have a dampened HPA axis activity, 2) epigenetics play a different role in PTSD compared to abused individuals who have committed suicide and 3) timing of trauma has a significant effect on both the HPA axis activity and the epigenetic modifications.
Le TSPT est un syndrome dévastateur qui touche entre 7 et 12% de gens qui vivent un événement traumatique. Les personnes qui souffrent du syndrome ont un axe HPA dysfonctionnel avec moins de cortisol salivaire et une augmentation de sensitivité des récepteurs glucocorticoïdes. Il y a récemment eu des études épigénétiques qui ont montré une association entre les traumas et les effets sur l'axe HPA chez des patients abusés qui ont commis un suicide. De plus, les résultats indiquent qu'un trauma durant l'enfance est un facteur significatif pour la méthylation d'ADN dans la région promoteur 1F de l'hippocampe. Cette thèse présente le possible rôle modulateur de l'épigénétique des récepteurs glucocorticoïdes chez les personnes touchées du TSPT tout en examinant les effets du temps du trauma. Les résultats montrent que les individus qui souffrent du TSPT ont moins de cortisol salivaire le matin, une augmentation des récepteurs glucocorticoïdes et une augmentation de niveaux de méthylation totale dans la région promoteur 1C du sang. Il semblerait aussi qu'un trauma vécu durant l'âge adulte soit plus significatif pour l'axe HPA, alors qu'un trauma durant l'enfance semblerait prendre le dessus pour les modifications épigénétiques. Ces résultats montrent que 1) les personnes souffrant du TSPT ont une activité HPA atténuée, 2) l'épigénétique joue un rôle différent chez les TSPT comparés aux patients abusés qui ont commis un suicide et 3) le temps du trauma a des effets significatifs pour l'axe HPA et les modifications épigénétiques.

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Giannoukakis, Nick. « The genetic and epigenetic regulation of insulin-like growth factor II gene expression in humans ». Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0014/NQ36977.pdf.

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Saladi, SrinivasVinod. « SWI/SNF Chromatin Remodeling Enzymes : Epigenetic Modulators in Melanoma Invasiveness and Survival ». University of Toledo Health Science Campus / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=mco1310065995.

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Fristedt, Duvefelt Charlotte. « Tumour Survival Signals and Epigenetic Gene Silencing in Multiple Myeloma : Implications for Biology and Therapy ». Doctoral thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-242571.

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This thesis is focused on multiple myeloma (MM), a haematological malignancy that still remains incurable. The pathogenesis of MM is not fully understood and there is a large intra-tumour and interclonal genetic variation in MM patients. One of the most challenging areas in MM research is to find mechanisms for initiation and progression of MM, but also to overcome the arising resistance to therapy. In paper I, a signature of under-expressed genes in MM was found to significantly correlate with already defined Polycomb target genes. In selected genes from the profile we found an enrichment of H3K27me3, a repressive mark catalysed by Polycomb repressive complex 2 (PRC2), in MM patients and MM cell lines. Treatment with LBH589 (HDAC inhibitor) and DZNep (methyltransferase inhibitor) reactivated the H3K27me3 target genes and induced apoptosis in MM cell lines. LBH589 reduced tumour load and increased overall survival in the 5T33MM mice. These results suggest an important role for Polycomb complex in MM development and highlight PRC2 as a drug target in MM. In paper II, the insulin-like growth factor type 1 receptor tyrosine kinase (IGF-1RTK) inhibitor picropodophyllin (PPP) in combination with LBH589 synergistically inhibited cell proliferation and enhanced the apoptotic effect in MM. Since the bone marrow microenvironment has an important role in MM disease and also contributes to drug-resistance, we therefore evaluated the drug combination in the immunocompetent 5T33MM murine model. The drug combination significantly prolonged the survival of the 5T33MM mice compared to single drug treatment. We conclude that the combination of PPP and LBH589 has a therapeutic potential in MM. In paper III, the role of the cellular inhibitor of apoptosis protein 2 (cIAP2) was evaluated in MM cells harbouring TRAF3 deletion/mutation. By overexpressing cIAP2 in these cells we found an increased resistance to proteasome inhibitors. cIAP2 over-expression by lentiviral constructs led to decreased caspase activation, activation of the canonical NF-κB pathway, and down-regulation of tumour suppressor genes and genes that contribute to apoptosis. Supporting the role of cIAP2 mediated drug-resistance, we here demonstrate that inhibiting cIAP2 using an IAP antagonist, increased the sensitivity to the proteasome inhibitor, bortezomib.

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Seshadri, Chitra. « Genome wide epigenetic analyses of Araptus attenuatus, a bark beetle ». VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4167.

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Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This research examines spatial genetic structure using paired nucleotide and methylation genetic markers in the Sonoran bark beetle, Araptus attenuatus, for which we have a considerable knowledge about its neutral demographic history, demography, and factors influencing ongoing genetic connectivity. Using the msAFLP approach, we attained 703 genetic markers. Of those, 297 were polymorphic in both nucleotide (SEQ) and methylation (METH) were assayed from 20 populations collected throughout the species range. Of the paired SEQ and METH locis, the METH were both more frequent (16% vs. 7%), maintained more diversity (Shannon IMeth = 0.361 vs. ISeq=0.272), and had more among-population genetic structure (ΦST; Meth = 0.035 vs. ΦST; Seq= 0.008) than their paired SEQ loci. Interpopulation genetic distance in both SEQ and METH markers were highly correlated, with 16% of the METH loci having sufficient signal to reconstruct phylogeographic history. Allele frequency variation at five loci (two SEQ and three METH) showed significant relationships with at-site bioclimatic variables suggesting the need for subsequent analysis addressing non-neutral evolution. These results suggest that methylation can be as informative as nucleotide variation when examining spatial genetic structure for phylogeography, connectivity, and, identifying putatively adaptive genetic variance.

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Thèses sur le sujet « Epigenetic biology »

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