Dissertations / Theses on the topic 'X-chromosome inactivation'
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1
Norris, Dominic Paul. "X chromosome inactivation in the mouse." Thesis, Open University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282142.
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Benjamin, Don. "Molecular studies of human X chromosome inactivation." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318784.
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Paterno, Gary David. "X chromosome inactivation in mouse embryonal carcinoma cells." Thesis, University of Ottawa (Canada), 1985. http://hdl.handle.net/10393/4629.
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Metello, de Napoles Mariana. "Epigenetic modifications during X-chromosome inactivation and reactivation." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.422058.
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Ager, Miranda. "Mechanisms of X chromosome inactivation : a transgenic approach." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342240.
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林德深 and Tak-sum Lam. "A biochemical study of mammalian x chromosome inactivation." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1987. http://hub.hku.hk/bib/B31981306.
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Dossin, François. "Mechanistic dissection of SPEN functionduring X chromosome inactivation." Thesis, Université Paris sciences et lettres, 2021. http://www.theses.fr/2021UPSLS042.
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Chez les mammifères placentaires femelles, la transcription d’un des deux chromosomes X est inactivée (ICX) au cours du développement embryonnaire. Cette inactivation est permise par Xist, un ARN non-codant qui recouvre le chromosome X à partir duquel il est exprimé, induisant ensuite l’extinction transcriptionnelle de tout ce chromosome. Les mécanismes moléculaires par lesquels Xist permet une telle répression des gènes liés à l’X demeurent globalement incompris. En 2015, la protéine SPEN a été identifiée comme interagissant directement avec l’ARN de Xist, mais sa fonction précise ainsi que son mécanisme d’action au cours de l’ICX restaient à découvrir.Au cours de mon travail de thèse, j’ai utilisé la technique du dégron inductible à l’auxine, une approche de type perte de function, permettant de dégrader SPEN à façon dans des cellules souches embryonnaires de souris (CSES) en cours d’ICX. Grâce à cette technique, je démontre que SPEN est absolument necessaire pour la repression transcriptionnelle de tout le chromosome X pendant l’ICX. Aussi, en ayant recours à des embryons de souris Spen KO, je montre que SPEN is tout autant essentiel pour l’inactivation du chromosome X paternel au cours de l’ICX soumise à empreinte. En revanche, la perte de SPEN dans des cellules différenciées, où l’ICX est déjà établie, révèle que SPEN n’est plus requis ni pour maintenir les gènes éteints, ni pour préserver l’organisation tridimensionnelle du chromosome X inactif.Par des approches de microscopie en cellules vivantes, je rapporte ensuite que SPEN est colocalisé avec l’ARN de Xist immédiatement après l’expression de ce dernier, suggérant que SPEN peut initier la répression transcriptionnelle très tôt pendand l’ICX. La caractérisation des sites de liaisons de SPEN à la chromatine révèle que SPEN est recruté uniquement au niveau des promoteurs et des enhancers des gènes actifs. Aussi, la magnitude du recrutement de SPEN aux promoteurs liés à l’X prédit la rapidité avec laquelle les gènes sont inactivés au cours de l’ICX. Enfin, une fois les genes inactivés, SPEN se dissocie de la chromatine, ce qui indique qu’une activité transcriptionnelle est requise pour l’association de SPEN à la chromatine.Par complémentation fonctionnelle, le domaine SPOC est identifié comme l’effecteur principal de l’activité répressive de SPEN pendant l’ICX, et le recrutement « forcé » de SPOC sur l’ARN de Xist suffit à entraîner l’inactivation des gènes à l’échelle du chromosome entier. L’identification de l’interactome protéique de SPOC par spectrométrie de masse révèle que SPOC interagit avec de nombreux complexes impliqués dans la répression transcriptionnelle : NCoR/SMRT (désacétylation des histones), NuRD (remodelage de la chromatine et désacétylation des histones) et la machinerie de méthylation m6A des ARN, ainsi qu’avec la machinerie de transcription (Pol2).En utilisant des approches de biophysique et de biologie structurale, je montre que SPOC interagit directement et spécifiquement avec le domaine C-terminal (CTD) de Pol2, seulement quand ce dernier est phosphorylé sur la Sérine 5. Ces résultats suggèrent que SPEN peut réprimer la transcription directement en interférant avec les évènements transcriptionnels dépendant de Pol2-CTD Ser5P.Ainsi, mon travail de these souligne l’essentialité de SPEN pour éteindre la transcription à l’échelle du chromosome X entier au cours de l’ICX, aussi bien in vitro que in vivo. Immédiatement après l’expression de Xist, SPEN est recruté aux promoteurs et enhancers de gènes actifs, réprime la transcription, puis se dissocie de la chromatin une fois les gènes éteints. Grâce à ses domaines RRMs et SPOC, SPEN joue un rôle d’intégrateur, asociant Xist à des désacétylases des histones, des remodeleurs de la chromatine, mais surtout, à la machinerie de transcriptionIn female placental mammals, dosage compensation of X-linked gene expression is achieved early during development through transcriptional inactivation of one of the two X chromosomes (XCI). This process is dependent on Xist, a long non-coding RNA which coats and silences the X chromosome from which it is transcribed. The mechanisms through which Xist initiates transcriptional silencing during XCI remain however completely unknown. In 2015, several studies identified that the SPEN protein binds Xist RNA directly, and its implication in mediating gene silencing was reported. However, its precise function and mechanism(s) of action during XCI are unclear.During my PhD, I made use of a conditional loss of function approach, the auxin inducible degron, to acutely deplete SPEN in mouse embryonic stem cells (mESCs) undergoing XCI. Using this approach, I demonstrate that SPEN is absolutely necessary for chromosome-wide Xist-mediated gene silencing during initiation of XCI. Furthermore, using conditional Spen KO mouse embryos, I show that SPEN is also required for the transcriptional inactivation of the paternal X chromosome during imprinted X inactivation. Depleting SPEN in differentiated cells, in which XCI has been established, reveals that SPEN is neither required to maintain gene silencing nor to preserve the spatial organization of the inactive X chromosome.By combining fixed and live cell imaging of Xist and SPEN, I show that SPEN colocalizes with Xist RNA, and accumulates on the X chromosome, immediately upon Xist upregulation, suggesting that SPEN can initiate gene silencing very early on during XCI. Profiling SPEN chromatin binding sites reveals that SPEN is recruited to promoters and enhancers of active genes specifically. The magnitude of SPEN recruitment to X-linked promoters dictates the efficiency with which these genes will be silenced. Remarkably, SPEN disengages from chromatin after gene silencing, indicating that active transcription required for SPEN’s association with chromatin.Using a functional complementation approach, I identify the SPOC domain as the effector of SPEN’s gene silencing activity during XCI. Artificial tethering of SPOC to Xist RNA results in transcriptional repression along the entire X chromosome, demonstrating that SPOC contains all the sufficient potential to instruct gene silencing during XCI. I further characterize the protein interactors of SPOC using mass spectrometry and reveal that SPOC interacts with several protein complexes involved in repressing transcription, including the NCoR/SMRT (histone deacetylation), the NuRD (nucleosome remodeling/histone deacetylation) and the m6A writing (governing mRNA fate) complexes. Finally, several transcription initiation and elongation factors are found to interact with SPOC, as well as the RNA polymerase II (RNAPII) transcription machinery.I identify that SPOC interacts directly and specifically with the C-terminal domain (CTD) of RNAPII only when the latter is phosphorylated on Ser5, and determine the 3D structure of the SPOC/RNAPII-CTD Ser5-P complex at 1.8Å resolution. These results suggest that SPEN could directly repress transcription during XCI by interfering with RNAPII-CTD Ser5-P templated processes.Altogether, my PhD work reveals that SPEN is essential for chromosome-wide transcriptional silencing during XCI, both in mESCs and in vivo. Following Xist upregulation, SPEN is immediately recruited to active gene promoters and enhancers, silences transcription, and subsequently disengages from chromatin. Through its RRMs and SPOC domains, SPEN acts as a molecular integrator, bridging Xist with histone deacetylases, nucleosome remodelers, RNA methyltransferases and most importantly, the transcription machinery
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Lam, Tak-sum. "A biochemical study of mammalian x chromosome inactivation." [Hong Kong : University of Hong Kong], 1987. http://sunzi.lib.hku.hk/hkuto/record.jsp?B12827186.
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Forrester, Lesley Margaret. "Murine haematopoiesis : studies using X chromosome-inactivation mosaics." Thesis, University of Edinburgh, 1987. http://hdl.handle.net/1842/28042.
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Blood erythrocytes and leukocytes were serially sampled over many months from female mice that were heterozygous at the X-chromosomal locusencoding the glycolytic enzyme phosphoglycerate kinase (PGK-1). PGK-1A andPGK-1B alloenzymes were identified and quantified electrophoretically. There was little variation in PGK-1 phenotype between serial samples from individual mice. This small amount of variation was discussed in terms of the number of clones participating in haematopoiesis and the contribution of technical factors. Similar studies were performed using radiation chimaeras, repopulated with either a high dose (107 cells) or a low dose (105 cells) of PGK-1AB bonemarrow. The variation in PGK-1 phenotype between serial samples taken fromthe animals repopulated with a high dose of bone marrow was comparable to that seen in normal animals. In contrast, the variation observed in the low- dose chimaeras was. relatively large. These animals were used to study the clonal organisation of the haematopoietic system. The development of B lymphocytes carrying the X-linked immunodeficiency mutation (xid) was studied in mice that were heterozygous at both the x[d and the Pgk-1 loci. An abnormallly large population of B lymphocytes, possessing an characteristic membrane phenotype, was observed in the peripheral blood of a group of experimental mice. This behaved as a transplantable neoplasia. Subsequently, similar populations were found in several aged (>2 years) CBA/Ca mice. A preliminary characterisation of these cells was carried out and their possible relevance to human chronic lymphocytic leukaemia (CLL) was discussed.
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Sprong, Amy Nicole. "X Chromosome Aneuploidy: A Look at the Effects of X Inactivation." Miami University Honors Theses / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=muhonors1209079846.
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Cotton, Allison Marie. "Patterns of DNA methylation on the human X chromosome and use in analyzing X-chromosome inactivation." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/40363.
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The process of X-chromosome inactivation achieves dosage compensation between
mammalian males and females. In females one X chromosome is transcriptionally silenced
through a variety of epigenetic modifications including DNA methylation. Most X-linked genes
are subject to X-chromosome inactivation and only expressed from the active X chromosome.
On the inactive X chromosome, the CpG island promoters of genes subject to X-chromosome
inactivation are methylated in their promoter regions, while genes which escape from Xchromosome
inactivation have unmethylated CpG island promoters on both the active and
inactive X chromosomes.
The first objective of this thesis was to determine if the DNA methylation of CpG island
promoters could be used to accurately predict X chromosome inactivation status. The second
objective was to use DNA methylation to predict X-chromosome inactivation status in a variety
of tissues. A comparison of blood, muscle, kidney and neural tissues revealed tissue-specific
X-chromosome inactivation, in which 12% of genes escaped from X-chromosome inactivation in
some, but not all, tissues. X-linked DNA methylation analysis of placental tissues predicted four
times higher escape from X-chromosome inactivation than in any other tissue. Despite the
hypomethylation of repetitive elements on both the X chromosome and the autosomes, no
changes were detected in the frequency or intensity of placental Cot-1 holes.
The third objective of this thesis was to use DNA methylation to investigate X-chromosome
inactivation in female samples with chromosomally abnormal karyotypes. The spread of Xchromosome
inactivation into the autosomal portion of six unbalanced X;autosome
translocations revealed similarities between X;autosome translocations involving the same
autosome and therefore suggested a role for DNA sequence in influencing X-chromosome
inactivation status of genes. Autosomal genes that escaped from inactivation were found to
have significantly lower L1 and LTR but higher Alu content than genes which were subject to
inactivation. Lastly, DNA methylation was used to predict the number of inactive X
chromosomes in triploid placental samples. Triploid samples provide an excellent system in
which to study the counting step of X-chromosome inactivation and DNA methylation analysis
provides a means to determine the number of inactive X chromosomes using only a DNA
sample.
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Adra, Chaker Nadim. "X chromosome inactivation and the phosphoglycerate kinase gene family." Thesis, University of Ottawa (Canada), 1988. http://hdl.handle.net/10393/5308.
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Sharp, Andrew James. "A molecular study of X chromosome inactivation in humans." Thesis, University of Southampton, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252456.
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Spotswood, Hugh Timothy. "Histone modification and the epigenetics of X chromosome inactivation." Thesis, University of Birmingham, 2003. http://etheses.bham.ac.uk//id/eprint/230/.
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Dosage compensation serves to equalise the levels of X-linked gene products between males and females. In mammals this occurs through the transcriptional silencing of the majority of the genes on one of the two female X chromosomes. The inactive X chromosome (Xi) differs from its active homologue in a number of ways, including the hypoacetylation of core histones, a common property of genetically inactive chromatin. This study has used Xi to explore the functional significance of hypoacetylation and patterns of histone methylation in silent chromatin. Xi was shown to be depleted for di- and tri-methylated lysine 4 of H3, but retained di-methylated lysine 9 of H3. I have examined the temporal order of these modifications as they become established using an in vitro model system for X inactivation; differentiating female embryonic stem cells. The results showed that the loss of tri-methylated lysine 4 of H3 preceded the loss of its di-methylated equivalent, which occurs during a time period of concurrent core histone deacetylation supporting a functional role to the level of lysine methylation. I have used cases of X;autosome translocation to examine how these modifications relate to late replication and transcriptional silencing. Results show that whilst the spread of X inactivation can occur in the absence of both of these properties, histone modifications are a more reliable indicator of the extent of spread of X inactivation than late replication. To explore mechanisms that drive changes in histone modification I have analysed the distribution of histone deacetylases across a region of defined histone deacetylation. The results showed a ubiquitous distribution that did not correlate with acetylated H3 or H4 suggesting that the global association of the Hdacs might serve to provide a rapid return the basal level of histone acetylation following specific targeting events.
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Apedaile, Anwyn Emily. "Dynamics of DNA methylation on the mammalian X-chromosome during X-inactivation." Thesis, Imperial College London, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444592.
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Luikenhuis, Sandra 1972. "Studies on X chromosome inactivation and the X-linked disease Rett syndrome." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28676.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2004.Includes bibliographical references.
(cont.) the RTT phenotype.
Deletion of the Xist gene results in skewed X-inactivation. To distinguish primary non-random choice from post-choice selection, we analyzed X-inactivation in early embryonic development in the presence of two different Xist deletions. We found that Xist is an important choice element, and that in the absence of an intact Xist gene, the X chromosome will never be chosen as the active X. To understand the molecular mechanisms that affect choice we analyzed the role of replication timing prior to X-inactivation. The X chromosomes replicated asynchronously before X-inactivation but analysis of cell-lines with skewed X-inactivation showed no preference for one of the two Xist alleles to replicate early, indicating that asynchronous replication timing prior to X-inactivation does not play a role in skewing of X-inactivation. Expression of the Xist is negatively regulated by its antisense gene, Tsix. In order to determine the role of transcription in Tsix function, we modulated Tsix transcription with minimal disturbance of the genomic sequence. Loss of Tsix transcription lead to non-random inactivation of the targeted chromosome, whereas induction of Tsix expression caused the targeted chromosome always to be chosen as the active X. These results for the first time establish a function for antisense transcription in the regulation of Xist expression. The X-linked disease Rett syndrome (RTT), a neurodevelopmental disorder, is caused by mutations in the MECP2 gene. We used a mouse model to test the hypothesis that RTT is exclusively caused by neuronal MeCP2 deficiency. Expression of an Mecp2 transgene in postmitotic neurons resulted in symptoms of severe motor dysfunction. Transgene expression in Mecp2 mutant mice, however, rescued
by Sandra Luikenhuis.
Ph.D.
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Nora, Elphège-Pierre. "Architecture chromosomique du locus Xic : implications pour la régulation de l'inactivation du chromosome X." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA112130/document.
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Le développement embryonnaire précoce des mammifères femelles s’accompagne de l’inactivation transcriptionnelle d’un de leurs deux chromosomes X. Cet évènement est initié suite à l’expression mono-allélique de l’ARN non codant Xist, qui est contrôlée par de nombreux éléments cis-régulateurs présents dans le centre d’inactivation du chromosome X (Xic) – tel son anti-sens répresseur Tsix. Mon travail de thèse a consisté à développer des approches permettant d’appréhender le paysage structural dans lequel s’exerce cette régulation. La caractérisation de l’architecture tridimensionnelle du Xic, par des techniques basées sur la capture de conformation chromosomique (3C) et l’hybridation in situ en fluorescence (FISH), m’a permis de mettre en évidence que les promoteurs respectifs de Xist et Tsix sont engagés dans des interactions physiques intimes avec des loci distaux, localisés au sein du Xic, et de montrer qu’au moins certaines de ces régions exercent un effets régulateurs à longue-distance. Les éléments du Xic contactés par les régions promotrices de Xist et de Tsix sont en outre fondamentalement différents, chacune engageant des associations chromosomiques sur plusieurs centaines de kilobases dans leur direction 5’ respective.Ce travail a également permis de révéler des propriétés insoupçonnées de l’architecture chromosomiques. En effet, le Xic apparaît scindé en plusieurs sous-régions, couvrant chacune entre 200kb et 1Mb, à l’intérieur desquelles les interactions chromosomiques sont préférentiellement établies. L’existence de ces domaines d’interaction s’intègre avec d’autres propriétés structurales du génome, tels la composition de la chromatine sous-jacente et l’association à la lamine nucléaire, mais n’apparaît pas en dépendre directement. En étudiant la dynamique de la conformation chromosomique du Xic au cours de la différenciation cellulaire, j’ai pu constater la robustesse de cette organisation, sauf sur le chromosome X inactif, qui se distingue par la perte des contacts chromosomiques préférentiels détectables sur son homologue actif.Enfin, j’ai pu mettre en évidence que la variabilité du repliement général du chromosome X amène à un instant donné chaque allèle de Tsix à contacter physiquement des jeux de séquences distales différents, suggérant que l’environnement structural instantané de chacun de ces allèles à l’orée de l’activation mono-allélique de Xist est différent. Ce travail, combinant des approches à l’échelle de la population cellulaire d’une part et de la fibre de chromatine unique d’autre part, apporte une nouvelle vision du paysage structural et régulateur dans lequel s’inscrit le contrôle de l’activité transcriptionnelle de Xist, et fourni de nouvelles perspectives concernant les principes fondamentaux de l’organisation topologique des chromosomes chez les mammifèresEarly development of female mammals is accompanied by transcriptional inactivation of one of their two X chromosomes. This event is initiated following mono-allelic expression of the Xist non-coding RNA – what is achieved by the interplay of numerous cis-regulatory elements present within the X inactivation center (Xic), such as its repressive antisense Tsix. Our work aimed at throwing light on the structural landscape that underlies such long-range regulation. Characterization of the three-dimensional architecture of the Xic, by the means of Chromosome Conformation Capture (3C)-based techniques and in situ fluorescence hybridization (FISH), revealed that the respective promoters of Xist and Tsix contact many distal genomic elements within the Xic, and that at least one of such interacting region exerts long-range cis-transcriptional control. Noticeably, Xist and Tsix promoters associate with different sets of elements in their respective 5’ direction that are spread out over several hundreds of kilobases These experiments also revealed unforeseen properties of chromatin architecture. Indeed, the Xic appears to be partitioned in several sub-regions, each spanning between 200kb and 1Mb, inside which chromosomal interactions are preferentially established. The existence of these interaction domains integrates with other structural features of the genome, such as underlying chromatin composition and association with the nuclear lamina, but does not seem to directly depend on them. By analyzing chromosome conformation of the Xic during cell differentiation we document the robustness of this organizational principle, with the noticeable exception of the inactive X chromosome that assumes a folding pattern that is more random than its active homolog. Finally we also bring evidence that variability in the folding pattern of the two X chromosomes in the same cell brings each Tsix allele in association with different sets of chromosomal partners at a given moment, suggesting that the instantaneous structural environment of each allele at the onset of mono-allelic Xist up-regulation is different.By combining approaches at the scale of cell populations on the one hand, and at the single chromatin fiber level on the other, this study provides a first vision of the structural landscape in which Xist regulation takes place, and brings new insights concerning fundamental properties of chromosome organization in mammals
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Ensminger, Alexander Wilson. "Autosomal random asynchronous replication is analogous to X-chromosome inactivation." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/34197.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, February 2006.Includes bibliographical references.
A number of mammalian genes are expressed from only one of two alleles in either an imprinted or random manner. Those belonging to the random class include X-linked genes subject to X inactivation, as well as a number of autosomal genes, including odorant receptors, immunoglobulins, T-cell receptors, interleukins, natural killer-cell receptors, and pheromone receptors. Random asynchronous replication of DNA in S-phase represents an epigenetic mark that often parallels monoallelic expression. All randomly monoallelically expressed genes discovered to date replicate asynchronously in S-phase, though not all of the genes contained within asynchronous domains are monoallelically expressed. The focus of my work has been on understanding this random choice that cells make between two sequence-identical alleles. Using two-color fluorescent in situ hybridization (FISH) analyses, the random asynchronous replication of a large number of human and mouse genes appears to be coordinated at the level of entire chromosomes. This regulatory scheme is reminiscent of random X-chromosome inactivation, the dosage compensation machinery in mammals. We have shown that autosomal coordination responds to trisomy in a fashion similar to X inactivation, with one copy of the trisomic chromosome marked for early replication and the other two rendered late replicating.
(cont.) These observations raise the intriguing possibility that the mechanistic underpinnings of X inactivation and autosomal coordination may also be similar. Furthermore, the existence of chromosome-wide epigenetic differentiation between autosomes has evolutionary implications concerning the establishment of X inactivation as the approach to mammalian dosage compensation. A crucial event in X inactivation is the random monoallelic expression of a noncoding RNA, Xist from one of the two X chromosomes. Noncoding RNA transcripts are enticing candidates for regulating chromatin structure within the mammalian nucleus. We have initiated a screen for novel nuclear, noncoding RNA transcripts. Using expression array profiling, we have identified several broadly expressed nuclear enriched transcripts. In addition to Xist, this approach identified two noncoding transcripts, NEATI and NEAT2 that are located near one another on human chromosome 1 I and chromosome 19 of mice. Using a variety of techniques, including RNA FISH and RNA-mediated interference, we have explored the potential regulatory functions of these transcripts.
by Alexander Wilson Ensminger.
Ph.D.
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Liu, Mengning. "Evolutionary landscape of CpG island methylation in X chromosome inactivation." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611328.
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Farazmand, Ali. "X-inactive specific transcript (XIST) and X chromosome inactivation in the bovine species." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/NQ56279.pdf.
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Vigneau, Sébastien. "Etude fonctionnelle de l'inactivation du chromosome X au moyen de délétions ciblées dans le centre d'inactivation du chromosome X murin." Paris 6, 2007. http://www.theses.fr/2007PA066271.
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Chez les mammifères, l'un des deux chromosomes X est transcriptionnellement inactif chez les femelles, ce qui permet l'expression à un niveau équivalent dans les deux sexes des gènes liés au chromosome X. L'inactivation est initiée par le recouvrement du futur chromosome X inactif par l'ARN Xist exprimé en cis, qui est lui-même réprimé par l'expression de l'ARN antisens Tsix. Grâce à une stratégie de délétions ciblées en 3' de Xist dans des cellules souches embryonnaires mâles, nous avons montré que l'expression de Tsix est régulée par le minisatellite DXPas34, et qu'elle est essentielle pour empêcher l'inactivation chez les mâles. Les profils de modification d'histones et d'expression des gènes en 5' de Xist suggèrent en outre que Tsix régule une région plus étendue que le seul locus Xist/Tsix. Enfin, nous avons généré des souris recombinantes dans lesquelles DXPas34 est délété, ce qui nous permet désormais d'étudier la fonction de ce minisatellite au cours du développement embryonnaire
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Royce-Tolland, Morgan Elizabeth. "Investigation into the molecular mechanisms that control random X chromosome inactivation." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3378505.
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Hore, Timothy Alexander, and timothy hore@anu edu au. "THE EVOLUTION OF GENOMIC IMPRINTING AND X CHROMOSOME INACTIVATION IN MAMMALS." The Australian National University. Research School of Biological Sciences, 2008. http://thesis.anu.edu.au./public/adt-ANU20081216.152553.
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Genomic imprinting is responsible for monoallelic gene expression that depends on the sex of the parent from which the alleles (one active, one silent) were inherited. X-chromosome inactivation is also a form of monoallelic gene expression. One of the two X chromosomes is transcriptionally silenced in the somatic cells of females, effectively equalising gene dosage with males who have only one X chromosome that is not complemented by a gene poor Y chromosome. X chromosome inactivation is random in eutherian mammals, but imprinted in marsupials, and in the extraembryonic membranes of some placentals. Imprinting and X inactivation have been studied in great detail in placental mammals (particularly humans and mice), and appear to occur also in marsupial mammals. However, both phenomena appear to have evolved specifically in mammals, since there is no evidence of imprinting or X inactivation in non-mammalian vertebrates, which do not show parent of origin effects and possess different sex chromosomes and dosage compensation mechanisms to mammals.¶
In order to understand how imprinting and X inactivation evolved, I have focused on the mammals most distantly related to human and mouse. I compared the sequence, location and expression of genes from major imprinted domains, and genes that regulate genomic imprinting and X-chromosome inactivation in the three extant mammalian groups and other vertebrates. Specifically, I studied the evolution of an autosomal region that is imprinted in humans and mouse, the evolution of the X-linked region thought to control X inactivation, and the evolution of the genes thought to establish and control differential expression of various imprinted loci. This thesis is presented as a collection of research papers that examines each of these topics, and a review and discussion that synthesizes my findings.¶
The first paper reports a study of the imprinted locus responsible for the human Prader-Willi and Angelman syndromes (PWS and AS). A search for kangaroo and platypus orthologues of PWS-AS genes identified only the putative AS gene UBE3A, and showed it was in a completely different genomic context to that of humans and mice. The only PWS gene found in marsupials (SNRPN) was located in tandem with its ancient paralogue SNRPB, on a different chromosome to UBE3A. Monotremes apparently have no orthologue of SNRPN. The several intronless genes of the PWS-AS domain also have no orthologues in marsupials or monotremes or non-mammal vertebrates, but all have close paralogues scattered about the genome from which they evidently retrotransposed. UBE3A in marsupials and monotremes, and SNRPN in marsupials were found to be expressed from both alleles, so are not imprinted. Thus, the PWA-AS imprinted domain was assembled from many non-imprinted components relatively recently, demonstrating that the evolution of imprinting has been an ongoing process during mammalian radiation.¶
In the second paper, I examine the evolution of the X-inactivation centre, the key regulatory region responsible for X-chromosome inactivation in humans and mice, which is imprinted in mouse extraembryonic membranes. By sequencing and aligning flanking regions across the three mammal groups and non-mammal vertebrates, I discovered that the region homologous to the X-inactivation centre, though intact in birds and frogs, was disrupted independently in marsupial and monotreme mammals. I showed that the key regulatory RNA of this locus (X-inactive specific transcript or XIST) is absent, explaining why a decade-long search for marsupial XIST was unsuccessful. Thus, XIST is eutherian-specific and is therefore not a basic requirement for X-chromosome inactivation in all mammals.¶
The broader significance of the findings reported in these two papers is explored with respect to other current work regarding the evolution and construction of imprinted loci in mammals in the form of a review. This comparison enabled me to conclude that like the PWS-AS domain and the X-inactivation centre, many domains show unexpected construction from disparate genomic elements that correlate with their acquisition of imprinting.¶
The fourth and last paper examines the evolution of CCCTC-binding Factor (CTCF) and its parologue Brother Of Regulator of Imprinted Sites (BORIS) which contribute to the establishment and interpretation of genomic imprinting at the Insulin-Like Growth Factor 2/H19 locus. In this paper I show that the duplication of CTCF giving rise to BORIS occurred much earlier than previously recognised, and demonstrate that a major change in BORIS expression (restriction to the germline) occurred in concert with the evolution of genomic imprinting. The papers that form the bulk of this thesis show that the evolution of epigenetic traits such as genomic imprinting and X-chromosome inactivation is labile and has apparently responded rapidly to different selective pressures during the independent evolution of the three mammal groups. I have introduced these papers, and discussed them generally in terms of current theories of how and why these forms of monoallelic expression have evolved in mammals.
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Yang, Christine. "DNA methylation demonstrates spread of X-chromosome inactivation to human transgenes." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/43045.
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X-chromosome inactivation is the process by which mammalian females achieve dosage compensation with males by silencing one of the two X chromosomes in female cells. Despite the chromosome-wide inactivation, a significant proportion of genes on the X chromosome in humans remain expressed on the inactive X chromosome. It has been long hypothesized that the genomic context plays an important role in influencing whether a gene is subject to or escapes from X-chromosome inactivation; however, cis-regulatory elements involved in X-chromosome inactivation have not yet been identified.
The objective of this thesis was to identify DNA elements that promote the escape of genes from X-chromosome inactivation in the human genome, through analyzing the X-chromosome inactivation statuses of human transgenes integrated at the Hprt locus on the mouse X chromosome and identifying the transgenes that escape from X-chromosome inactivation. DNA methylation was used to assess the inactivation status of 74 human reporter constructs comprising over 1.5 Mb of DNA. Transgenes that show low promoter DNA methylation in males and females would be potential escape genes. Of the 47 genes examined, only the PHB gene showed female DNA hypomethylation approaching the level seen in males, and escape from X-chromosome inactivation was verified by the demonstration of expression from the inactive X chromosome in females with non-random X-chromosome inactivation. Analysis on the repeat element content of five BAC-derived transgenes subject to X-chromosome inactivation suggested that local LINE-1 and Alu densities were insufficient to determine whether a gene would be subject to X-inactivation. Interestingly, CpG islands not associated with promoters also showed female-specific DNA hypermethylation, suggesting a dominant effect of X-chromosome inactivation on the regulation of DNA methylation. Different human transgenes show a differential capacity to accumulate DNA methylation when integrated into the identical location on the inactive X chromosome, indicating the presence of additional cis-acting epigenetic modulators. As only one of the human transgenes analyzed escaped from X-chromosome inactivation, we conclude that elements involved in ongoing expression from the inactive X are rare in the human genome and that mouse X-chromosome inactivation is very effective in silencing human transgenes.
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Rosspopoff, Olga. "Evolution of the human & mouse X-chromosome inactivation regulatory network." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC295.
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L’émergence des nouvelles techniques de séquençage à haut débit a permis d’appréhender la complexité du transcriptome des eucaryotes supérieurs. La majeure partie du génome des mammifères est transcrite, et les longs ARN non codants (lARNnc) en occupe une place prépondérante, dont la fonction est encore largement énigmatique. L’étude d’une minorité d’entre eux a révélé que leur fonction peut être médiée par diverses entités telles que le transcript, l'acte de leur transcription ou les éléments régulateurs compris au sein du locus. Une caractéristique de ces lARNnc est leur faible conservation au cours de l’évolution, ce qui pose la question de leur contribution à des mécanismes de régulation spécifique à chaque espèce. L'inactivation du chromosome X (ICX) est un paradigme des processus épigénétiques médiés par les gènes des lARNnc et un puissant modèle pour explorer leurs aspects fonctionnels, mécanistiques et évolutifs. L’ICX se met en place précocement au cours du développement embryonnaire et assure la compensation de dose des gènes du chromosome X entre les individus mâles et femelles chez les mammifères. Chez la souris, l’ICX résulte de l'action combinée de multiples gènes produisant des lARNnc, parmi lesquels Xist est l’acteur majeur de l’inactivation. L’accumulation de Xist sur le chromosome à partir duquel il est transcript permet de déclencher la répression transcriptionnelle du chromosome X. Xist se situe au coeur d’une région génomique, le centre d'inactivation du chromosome X, qui comprend de nombreux autres lARNnc tantôt activateurs ou répresseurs, dont la fonction dans l’ICX dans d’autres espèces est largement méconnue. Dans cette étude, nous avons étudié la conservation fonctionnelle de deux lARNnc JPX et FTX, et leur contribution à la régulation XIST chez l'homme et la souris.Chez la souris, nous avons montré que l'ARN Jpx est nécessaire à la régulation post-transcriptionnelle de Xist, probablement en affectant son accumulation ou sa stabilité. Chez l'homme, c'est la transcription de JPX, mais pas le transcrit lui-même, qui contrôle le recrutement de l’ARN polymérase II au niveau de la région promotrice de XIST. En conséquence, alors que la fonction de JPX/Jpx dans la régulation de l'accumulation XIST/Xist est conservée chez l'humain et la souris, les mécanismes sous-jacents divergent nettement. D'autre part, les résultats préliminaires sur la fonction FTX chez l'homme suggèrent qu'il pourrait être impliqué dans la maintenance de XCI chez l'homme dans des contextes cellulaires spécifiques. Ces résultats apportent un éclairage nouveau sur l'évolution fonctionnelle du réseau de régulation XIST/Xist entre la souris et l'homme, qui pourrait être spécifiquement adaptée aux exigences de l’ICX dans chaque espèce. Ce travail met en évidence la plasticité fonctionnelle des lARNnc dans l'évolution et la façon dont il pourrait jouer un rôle important dans le mécanisme de régulation des gènes spécifique d’une espèce à l’autreLong non-coding RNAs (lncRNAs) have emerged as the major output of mammalian transcriptomes. As of today, the function of the majority of lncRNAs remains largely enigmatic and importantly may be mediated by various entities such as the transcript itself, the act of transcription or key regulatory elements within the locus. A remarkable characteristic of lncRNAs is their poor evolutionary conservation, which raises the question of their contribution to species-specific regulatory mechanisms.X chromosome inactivation (XCI) is a paradigm for epigenetic processes mediated by lncRNA genes (LRGs) and a powerful model to explore their functional, mechanistic and evolutionary aspects. XCI is a process initiated early during embryonic development, which ensures the dosage compensation of X-linked genes between male and female in mammals. In the mouse, XCI is triggered by the combined action of several LRGs, among which Xist is the key regulator of the process. Xist is produced from a genomic region, the X-chromosome inactivation center (Xic), that is enriched for LRGs described either as positive or negative XCI regulators. In the present study, we investigated the evolutionary conservation of two candidate LRGs, JPX and FTX, and their contribution to XIST regulation in both human and mouse.In the mouse, we demonstrated that the Jpx RNA is required for proper Xist expression and acts as a post-transcriptional regulator of Xist, most likely by affecting its accumulation or stability. In striking contrast, in human, it is JPX transcription, but not the transcript itself, that controls the RNA Polymerase II (RNAPII) recruitment at XIST promoter. Accordingly, the two genes are interacting through local chromosome conformation, emphasized by RNAPII bridges in between the two loci. While the function of JPX/Jpx in promoting XIST/Xist accumulation is conserved between human and mouse, the underlying mechanisms diverge markedly. On the other hand, preliminary results on FTX function in human, suggest that it might be involved in XCI maintenance in human in very specific cellular contexts. Altogether, these results shed a new light on the functional evolution of XIST regulatory network between mouse and human that might be specifically adapted to XCI requirements in each species. This work highlights the functional plasticity of lncRNAs in evolution and how it might play important roles in species-specific mechanism of gene regulation
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Hore, Timothy Alexander. "The evolution of genomic imprinting and X chromosome inactivation in mammals /." View thesis entry in Australian Digital Theses Program, 2008. http://thesis.anu.edu.au/public/adt-ANU20081216.152553/index.html.
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Amos-Landgraf, James. "A HUMAN POPULATION STUDY OF THE GENETIC CONTROL OF X-INACTIVATION." Case Western Reserve University School of Graduate Studies / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=case1089861669.
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Häfner, Sophia Julia. "Study of X-inactivation independent functions of the conserved long noncoding RNA Ftx." Paris 7, 2014. http://www.theses.fr/2014PA077015.
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Mon travail de thèse se focalise sur l'étude du 1ARNnc Ftx, dont le gène est situé dans le centre d'inactivation du chromosome X , région riche en gènes codant pour des IARNncs et responsable du processus d'inactivation du chromosome X chez les mammifères femelles. Le laboratoire a montré que l'expression de Ftx favorise l'expression des gènes voisins, lui conférant ainsi un rôle activateur dans le processus d'inactivation. Ftx est également exprimé dans l'organisme murin adulte, plus spécifiquement dans le cerveau, suggérant ainsi des fonctions indépendantes du processus d'inactivation. Ainsi, je me suis focalisée sur l'étude de l'implication potentielle d( Ftx dans le développement et/ou le fonctionnement du cerveau. L'expression de Ftx dans le cerveau est relativement homogène entre différentes régions, en revanche elle s'instaure que durant la période postnatale, plus précisément entre P7 et P21, où elle augmente brusquement. Cette période correspond à une importante phase de structuration du cerveau murin, à la fois en termes de myélination et de remaniement synaptique. Il est envisageable que Ftx participe à un de ces processus. En utilisant un modèle cellulaire basé sur des cellules souches embryonnaires murines sauvages et portant une délétion constitutive de Ftx, j'ai développé une technique de différenciation neurale in vitro. Malgré le fait que la perte de Ftx n'a pas d'impact majeur sur le potentiel de différenciation neurale des cellules, une analyse par puce ADN a révélé qu'elle induit une surexpression d'une grande quantité de gènes Hox. L'ensemble de ces travaux fortifient l'hypothèse initiale et donnent naissance à des pistes excitantesMy PhD project focuses on the study of the long RNAnc Ftx, whose gene is located in the X chromosome inactivation center, a region rich in genes encoding long RNAncs and in charge of the inactivation process of one X chromosome in female mammals. The team has shown that the expression of Ftx favors the expression of the neighboring genes, conferring it the role of an activator of the inactivation process. Ftx is also expressed in the adult murine organism, more specifically in the brain, suggesting thus functions independent of the inactivation process. As a consequence, I focused on the potential implication of Ftx in de development and/or the functions of the brain. Ftx expression in the brain is relatively homogeneous among different regions, although it is established only during the postnatal period, between P7 and P21, when it increases suddenly. This period corresponds to an important phase of restructuring of the murine brain like myelination and synaptic reorganization. Thus it is conceivable that Ftx takes part in one of these processes. Using a cellular model based on wild-type and Ftx-deleted mouse embryonic stem cells? I developed a technique of in vitro neural differentiation. Although the lors of Ftx does not impact in a visible way on the neural differentiation potential of the cells, an analysis by microarray revealed that it causes the overexpression of several Hox genes. These combined results reinforce the initial hypothesis and lay numerous exciting tracks
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Simpson, T. Ian T. Ian. "An investigation into the role of methylation in mammalian X-chromosome inactivation." Thesis, University of Oxford, 1999. http://ora.ox.ac.uk/objects/uuid:5fd37c27-af19-4bbd-92a7-4c5b846b3a31.
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X-chromosome inactivation achieves dosage compensation of X-linked genes between male (XY) and female (XX) mammals. This process involves the down-regulation of most, but not all genes on one of the two X-chromosomes in the nucleus of each female somatic cell. The mechanism of X-inactivation has yet to be elucidated in full, but is known to involve the noncoding transcript of theXist gene, DNA methylation, histone hypo-acetylation and the condensation of higher order chromatin. Recent studies have established mechanisms linking methylation to repressive chromatin structures through methyl-binding proteins and histone deacetylase complexes. In order to better understand the role of methylation in X-inactivation, the promoters of the human Pyruvate dehydrogenase El a (PDHA1) and the human and murine Norrie disease protein (NDP/Ndp) genes were subjected to direct methylation sequencing, allowing the definition of methylation profiles at nucleotide resolution. The promoter of the PDHA1 gene was found to be hyper-methylated on the inactive X-chromosome and hypo-methylated on the active X-chromosome in agreement with studies at the promoters of other X-linked housekeeping genes. Methylation at the promoters of the NDP/Ndp genes was extensively investigated in a range of primary tissues and cell lines. The Ndp promoter was found to be methylated on both active and inactive X-chromosomes, but hypo-methylated in the proximal promoter exclusively in tissues that expressed the Ndp gene. The NDP promoter was found to be unmethylated on the active X-chromosome and hyper-methylated across the proximal promoter on the inactive X-chromosome in expressing cell lines and human retinal tissues. The novel promoter sequences of the human and murine SMCX/Smcx genes were isolated for comparative analysis and to provide a future resource for studying methylation at the promoters of genes which escape the X-inactivation process. Promoter sequences of the PDHA1, NDPI Ndp and SMCX/Smcx genes were screened for putative transcription factor binding sites and for conserved CpG-dinucleotide content. Promoter-reporter gene constructs for these genes were transfected into mammalian cells establishing that the sequences studied were functional promoters. Artificial methylation of these constructs was shown to repress their promoter activities.
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Romer, Justyna Teodora. "Studies on the role of the Xist gene in X chromosome inactivation." Thesis, Institute of Cancer Research (University Of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391361.
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Pollex, Tim. "Analysis of the role of nuclear organization during random X chromosome inactivation." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112192.
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Chez les mammifères femelles, le processus d’inactivation du chromosome X (XCI) assure la compensation de dose entre les deux sexes. Chez la souris, l’inactivation du X est établie de manière aléatoire dans l’épiblaste au stade blastocyste et peut être récapitulée in vitro dans les cellules souches embryonnaires. L’ARN non-codant Xist, exprimé à partir du centre d’inactivation du X (Xic), est le régulateur principal de ce processus. Il décore en cis le chromosome choisi pour être inactivé et initie la répression de ses gènes. Ainsi, de manière remarquable, les deux chromosomes X sont traités différemment pendant l’initiation de la XCI malgré leur homologie de séquence et leur localisation au sein d’un même noyau. De manière remarquable, ce processus implique le traitement différentiel de deux chromosomes homologues au sein d’un même noyau, avec des changements d’environnements nucléaires et chromatiniens entre le X actif et le X inactif. Il a été proposé que la localisation nucléaire pourrait jouer un rôle important dans l’initiation de l’expression monoallélique des gènes, non seulement pour l’initiation de la XCI mais aussi pour des processus tels que l’exclusion allélique dans les cellules lymphoides. Par exemple, l’association de loci avec des compartiments hétérochromatiques nucléaires et l’association en trans de loci homologues pourraient être impliquées dans la régulation des gènes monoalléliques. Ainsi, j’ai utilisé le système bactérien TetR/TetO afin d’analyser le rôle de l’organisation nucléaire du chromosome X et du Xic dans l’initiation de la XCI. J’ai pu montrer que si le recrutement des protéines de fusion TetR-LaminB1 ou -Cbx5 au niveau de la cassette TetO insérée dans le Xic permet la répression des gènes à proximité, cet évènement n’est pas toujours accompagné d’une relocalisation nucléaire. De plus, l’association forcée du Xic avec la périphérie nucléaire (TetR-LaminB1) n’a pas d’influence sur le choix du chromosome X à inactiver. Enfin, si la relocalisation des deux Xic à la périphérie nucléaire induit une réduction des évènements d’association en trans entre les deux loci, elle n’a pas d’effet sur l’initiation de l’inactivation. En résumé, ces résultats suggèrent que l’organisation nucléaire du chromosome X et du Xic et l’association des Xic en trans ne sont pas des facteurs déterministes pour le choix et l’initiation de la XCI, mais pourraient être le résultat des changements d’expression des gènes liés à l’X au cours de la différenciation des cellules souches ainsi que de l’augmentation de l’expression de Xist.Enfin, j’ai également analysé le rôle de la protéine CTCF, qui a été proposée pour être importante dans l’organisation structurale du génome, dans le contexte du Xic et de l’initiation de l’inactivation. Ainsi, le recrutement de CTCF au niveau de cassette TetO insérée dans le Xic induit localement une réduction mineure des interactions en cis et la répression des gènes du Xic, à l’exception de Xist dont l’expression est augmentée. Pour autant, la présence ectopique de CTCF n’a pas d’incidence majeure sur l’organisation générale du XicX-chromosome inactivation (XCI) ensures dosage compensation in female mammals. Random XCI is established in the epiblast of female mouse embryos and can be recapitulated in vitro in differentiating embryonic stem cells (ESCs). The major regulator of XCI is the long non-coding RNA Xist, which is expressed from the X-inactivation center (Xic), covers the chromosome in cis and initiates gene silencing. During XCI, the two X chromosomes are treated very differently, despite their homology and the fact that they reside in the same nucleus. Nuclear localization has been hypothesized to play a role in monoallelic gene regulation, not only during XCI but also in other contexts. For example, association with heterochromatin and homologous trans interactions (“pairing”) have been implicated in the establishment of monoallelic gene expression in lymphoid cells and transient pairing has been suggested to participate in symmetry breaking during random XCI. Using the bacterial tetO/tetR system to alter the subnuclear localization and environment of one or both Xics, we have tested the function of subnuclear localization and trans interactions between the Xic loci during initiation of XCI. Using stable expression and reversible binding of TetR fusion proteins (e.g. LaminB1, Cbx5) we show that binding of these proteins can induce local gene repression and chromatin changes, although this is not always associated with subnuclear relocalization. We further show that the forced association of the Xic with the nuclear envelope, does not impact on the choice-making process during XCI. In particular, tethering both Xics to the nuclear lamina during early ESC differentiation resulted in a substantial reduction of homologous pairing events, but had no obvious impact on the onset of random, monoallelic Xist expression. Taken together, our results suggest that nuclear localization and trans interactions of the Xic may be downstream events rather than causal in the regulation of the XCI process.Furthermore, we recruited CTCF, a protein suggested to be involved in structural organization of the genome, to the Xic using the tetO/tetR system. Upon binding of CTCF the overall structure of the Xic remained unaltered though few cis interactions appeared to be weakened, which was accompanied by gene repression in the Xic. Surprisingly, the only upregulated gene in the Xic was Xist in ESCs and during differentiation, which demonstrates that the induced minor changes of cis interactions might impact on gene regulation in the Xic
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Csankovszki, Györgyi 1971. "The role of Xist RNA in the maintenance of X chromosome inactivation." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/8209.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2001.Includes bibliographical references.
The role of Xist RNA in silencing the inactive X of female somatic cells was investigated by generating a conditional allele of the Xist gene. A system was set up in which reactivation of two X-linked genes, the endogenous Hprt gene and an X-linked GFP transgene, can be quantitatively assessed. Mouse embryonic fibroblasts derived from mice carrying the conditional Xist mutation were cultured and infected with an adenovirus vector carrying the gene for Cre recombinase. After Cre mediated deletion of Xist, the inactive X remained transcriptionally silent, late replicating, and hypoacetylated on histone H4, confirming that X-inactivation can be maintained in the absence of Xist RNA. However, the Xist mutant inactive X was no longer enriched in histone macroH2A 1. Furthermore, the reactivation rate of GFP and Hprt increased, indicating Xist RNA does contribute to gene repression on the inactive X. DNA methylation, histone hypoacetylation and Xist RNA were found to act synergistically in X chromosome silencing. To investigate whether Xist RNA can also silence the active X chromosome of male somatic cells, Xist expression on the active X was induced by demethylation. Demethylation was achieved by Cre mediated deletion of a conditional mutant allele of DNA methyltransferase-l (Dnmtl) in male fibroblasts. In these cells, Xist RNA coated the active X chromosome, in a pattern indistinguishable from coating of the inactive X of female cells. Although many Xist expressing chromosomes also transcribed X-linked genes Pgk-i and Hprt, in a small percent of cells Xist expression led to X chromosome inactivation. The proportion of chromosome expressing X-linked genes declined, and occasionally the X became late replicating, indicating that X-inactivation can be initiated in male somatic cells.
by Györgyi Csankovszki.
Ph.D.
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Khalil, Ahmad M. "Histone modifications and chromatin dynamics of the mammalian inactive sex chromosomes title." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0008329.
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Thesis (Ph.D.)--University of Florida, 2004.Typescript. Title from title page of source document. Document formatted into pages; contains 102 pages. Includes Vita. Includes bibliographical references.
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Shen, Yin. "Regulation of DNA methylation and X chromosome inactivation in human embryonic stem cells." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1709018911&sid=16&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Champion-Suntharalingam, K. M. "Aspects of molecular analysis in myeloproliferative disorders and myelodysplastic syndromes." Thesis, Anglia Ruskin University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342919.
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Augui, Sandrine. "Interactions chromosomiques et inactivation du chromosome X : éléments génétiques et mécanismes impliqués dans la reconnaissance du nombre de chromosomes X et dans la coordination des centres d'inactivation." Paris 11, 2009. http://www.theses.fr/2009PA112373.
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Le locus Xic contrôle l'initiation de l'inactivation du chromosome X. Il est nécessaire à la reconnaissance du nombre de chromosomes X (Sensing) et au déclenchement de l'expression monoallélique de Xist. Nous avons étudié la dynamique nucléaire des Xics au cours de la mise en place de l'inactivation dans les cellules ES. Nous avons montré que lors de l'initiation de l'inactivation, les deux Xics interagissent physiquement. Cet appariement transitoire permettrait la coordination des Xics afin de ne mettre en place l'inactivation qu'en présence de deux chromosomes X et au niveau d'un seul. Nous avons montré que cet appariement impliquait une région du Xic nommée Xpr pour "X-pairing region". Des expériences de transgénèse montrent que cette région est capable d'induire la trans-interaction des Xics de façon autonome et peut aussi induire l'activation du gène Xist endogène. Xpr serait ainsi le premier activateur en trans de Xist identifié à ce jour. La présence ectopique de Xpr semble en outre associée à une instabilité génétique dans les cellules ES. Notre modèle propose que l'appariement homologue des régions Xpr serait impliqué dans la coordination des Xics en ne permettant l'activation de Xist qu'en présence de plusieurs chromosomes X, et au niveau du nombre de X nécessaires pour rétablir la compensation de dose. En l'occurrence, des lignées males double transgéniques pour Xpr et Xist/Tsix semblent mettre en place au cours de leur différenciation un processus aléatoire d'inactivation, comparable à celui observé dans des lignées femelles, suggérant que Xpr+Xist/Tsix récapitulerait l'ensemble des fonctions du Xic et représenterait donc la région minimum du XicIn mammals, dosage compensation is achieved by the inactivation of one of the two X-chromosome during early development in females. X inactivation process is controlled by a complex locus, the X-inactivation centre (Xic), which includes the Xist gene and its antisense transcription unit Tsix/Xite. The Xic senses X chromosome number and initiates inactivation by triggering mono-allelic up-regulation of Xist RNA, and reciprocally, down-regulation of Tsix from one of the two X chromosomes in females. However, the mechanisms underlying sensing and reciprocal Xist/Tsix regulation remain obscure. We recently showed that a previously untested segment of the Xic, lying several hundred kilobases upstream of Xist and enriched in histone H3K27me3 and H3K9me2 marks, brings the two Xic's together prior to the onset of X inactivation (Augui et al, Science 318:1362, 2007). This X-pairing-region (Xpr) can autonomously drive Xic trans-interactions even as an ectopic single copy transgene. Furthermore its presence in male ES cells is selected against, suggesting that it may have a role in triggering Xist up regulation. We proposed that the pairwise interactions driven by this novel X-pairing-region (Xpr) of the Xic might enable a cell to sense that more than one X-chromosome is present in an XX cell, by activating biallelic Xist expression. Furthermore we believe that Xpr pairing then facilitates association between the Tsix/Xite regions, thus rendering biallelic Xist expression monoallelic. Finally, we think that Xpr could be the missing functional region of the Xic since Xpr + Xist/Tsix transgenes seem to recapitulate all Xic function in a male cell line
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Prudhomme, Julie. "Étude de la reprogrammation du chromosome X dans les cellules souches embryonnaires et extra-embryonnaires au cours du développement préimplantatoire murin." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066486.
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Chez les Mammifères femelles, l’extinction transcriptionnelle d’un des deux chromosomes X pendant l’embryogénèse précoce compense le déséquilibre de dose des gènes liés à l’X entre les sexes. L’inactivation aléatoire du chromosome X est mise en place dans la masse cellulaire interne du blastocyste et maintenue jusqu’à l’âge adulte dans le soma. Chez certains Euthériens incluant la souris, les tissus extra-embryonnaires (trophectoderme et endoderme primitif) montrent une inactivation soumise à empreinte du X paternel. Le statut inactif du Xp peut être étudié ex vivo dans les cellules souches trophoblastiques (TS) dérivées du trophectoderme. Nous avons pu sélectionner des cellules TS montrant une réactivation partielle du Xp ou bien une inversion complète du profil d’inactivation. Ceci révèle une plasticité épigénétique accrue de l’inactivation dans le trophectoderme par au soma.L’inactivation aléatoire du chromosome X est récapitulée pendant la différenciation des cellules souches embryonnaires (ES), qui servent de modèle cellulaire. Ce processus est déclenché par l’accumulation en cis du long ARN non codant Xist qui crée un domaine nucléaire répresseur autour du futur chromosome X inactif. Avant la différenciation, l’accumulation de Xist est réprimée par un autre long ARN non codant, Tsix, qui est transcrit en antisens de Xist. Afin d’adresser la dynamique fonctionnelle des ARN Xist et Tsix, nous avons inséré différents motifs d’étiquetage au locus Xist/Tsix endogène. Incorporés dans l’ARN sens ou antisens, ces étiquettes sont reconnues spécifiquement par des molécules fluorescentes, permettant ainsi la visualisation de ces transcrits dans les cellules vivantesIn female Mammals, the transcriptional silencing of one of the two X chromosomes during early embryogenesis compensates the dosage disequilibrium of X-linked genes between sexes. Random X chromosome inactivation occurs in the inner cell mass of the blastocyst and is maintained through adult life in the soma. In some Eutherian species including mice, extraembryonic tissues (trophectoderm and primitive endoderm) exhibit imprinted inactivation of the paternal X. The inactive state of the Xp can be extensively studied ex vivo in Trophoblast Stem (TS) cells derived from the trophectoderm. We were able to select from the general cell population, TS cells exhibiting partial reactivation of the Xp or showing a complete switch of imprinted X-inactivation pattern. This reveals an accrued epigenetic plasticity of imprinted X-inactivation in the trophectoderm as compared to random X-inactivation in the soma.Random X-chromosome inactivation is recapitulated during the differentiation of female Embryonic Stem (ES) cells – which serves as cellular model. This process is triggered by the cis-accumulation of Xist long non coding RNA molecules which create a nuclear repressive domain around the future inactive X chromosome. Before differentiation, the accumulation of Xist is repressed by another lncRNA, Tsix, that is transcribed antisense to Xist. In order to address the functional dynamics of Xist and Tsix RNAs, we inserted different types of tag sequences in the endogenous Xist/Tsix locus. Incorporated in the sense or antisense RNA, these tags are specifically recognized by fluorescent molecules, thereby allowing live cell imaging of these transcripts
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Grön, M. (Mathias). "Effects of human X and Y chromosomes on oral and craniofacial morphology:studies of 46,XY females, 47,XYY males and 45,X/46,XX females." Doctoral thesis, University of Oulu, 1999. http://urn.fi/urn:isbn:9514253744.
Full textAbstract:
Abstract
The influence of the X and Y chromosomes on the size and shape
of the dental arches and occlusion as well as on craniofacial cephalometric
dimensions, angles and dimensional ratios is studied. The material
consists of Finnish patients with sex chromosome aneuploidies and
normal population controls from the "Kvantti Study" series,
which was collected in the 1970's and 1980's at
the Institute of Dentistry, University of Turku. The patients are
five individuals with complete testicular feminization (CTF), eight
47,XYY males, and fourteen 45,X/46,XX females. The controls
are population female and male controls, as well as five first degree
relatives of the individuals with CTF, three of the 47,XYY males
and nine of the 45,X/46,XX females studied. Dental arch
dimensions and occlusion as well as craniofacial cephalometric dimensions,
angles and dimensional ratios are measured from dental study casts
and standardized lateral cephalograms.
The results show that the presence of the Y chromosome in
46,XY females and the supernumerary Y chromosomal gene(s) in 47,XYY
males result in the enlargement of the dental arches and craniofacial
dimensions without substantial effects on dimensional ratios and
plane angles, but with special influence on the growth of the mandibular
corpus. The reduction of X chromosomal genetic material in 45,X/46,XX
females results in the reduction of craniofacial dimensions, affecting dimensional
ratios and especially plane angles of the cranial base.
39
Furlan, Giulia. "Investigating the contribution of the non-coding gene Ftx to X-chromosome inactivation in mammals." Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC191/document.
Full textAbstract:
L’inactivation du chromosome X (XCI) est un mécanisme qui permet l’extinction transcriptionelle d’un des deux chromosomes X chez la femelle. XCI est régulé par une région spécifique nommée centre de l’inactivation du chromosome (Xic), contenant plusieurs gènes produisant de longs ARNs non codants (lncRNAs). Parmi ces lncRNAs, le transcrit Xist est l’effecteur principal pour l’XCI. Xist peut s’accumuler en cis sur le chromosome et recruter la machinerie qui permettra l’initiation et la propagation de l’extinction transcriptionnelle à l’échelle du chromosome.Le laboratoire d’accueil a identifié un nouveau gène du Xic qui produit le lncRNA Ftx. Dans cette étude, on a pu montrer que l’inactivation du chromosome X est fortement perturbée dans les cellules Ftx-/- et s’accompagne par une forte baisse du niveau d’expression et d’accumulation de Xist. Dans ce contexte, certaines cellules parviennent à maintenir l’expression de Xist mais le profil de couverture du chromosome X par Xist est anormal, présentant un profil diffus ; ceci est associé à une extinction transcriptionnelle déficiente des gènes liés à l’X. Dans les lignées hétérozygotes Ftx+/-, l’expression et l’accumulation de Xist est aussi affectée mais dans une moindre mesure, si bien qu’il apparaît que le nombre de copies de Ftx soit important pour sa fonction. Par ailleurs, l’inactivation du chromosome X dans les cellules Ftx+/- est biaisée de telle sorte que le chromosome X portant une copie fonctionnelle de Ftx est préférentiellement inactivé, suggérant un rôle en cis de Ftx. Ces résultats montrent que Ftx est un activateur de Xist et qu’il est essentiel pour la mise en place de l’inactivationX-chromosome inactivation (XCI) is a female-specific, chromosome-wide regulatory process that, in eutherians, ensures dosage compensation for X-linked genes between sexes. XCI is controlled by a cis-acting locus on the X-chromosome, the X-inactivation center (Xic), enriched in genes producing long non-coding RNAs (lncRNAs). The Xic-linked gene Xist is the master player of XCI, and produces a lncRNA that accumulates in cis on the X-chromosome and recruits the machinery responsible for initiation and propagation of silencing.The laboratory has identified an additional Xic-linked non-coding gene, Ftx. In this study, we could find that, in female Ftx-/- lines, XCI is strongly impaired, with a significant decrease in the levels of Xist expression and in the percentage of cells showing normal Xist accumulation patterns. Importantly, a high proportion of the cells that still retain Xist expression show abnormal X-chromosome coating and a decreased ability to silence X-linked genes. These data reveal that Ftx is a positive Xist regulator and it is required for proper XCI establishment. In female Ftx+/- lines, the levels of Xist expression and the percentage of cells showing normal Xist accumulation patterns are also decreased, albeit to a lower extent compared to Ftx-/- lines, suggesting that Ftx works in a copy-dependent manner. In addition, a high proportion of Ftx+/- cells display skewed X-inactivation, with preferential inactivation of the wild-type X chromosome. This suggests that Ftx role on Xist accumulation is mostly restricted in cis. Taken together, these results demonstrate that Ftx is required for XCI establishment, where it functions as a strong Xist activator
40
Prudhomme, Julie. "Étude de la reprogrammation du chromosome X dans les cellules souches embryonnaires et extra-embryonnaires au cours du développement préimplantatoire murin." Electronic Thesis or Diss., Paris 6, 2014. http://www.theses.fr/2014PA066486.
Full textAbstract:
Chez les Mammifères femelles, l’extinction transcriptionnelle d’un des deux chromosomes X pendant l’embryogénèse précoce compense le déséquilibre de dose des gènes liés à l’X entre les sexes. L’inactivation aléatoire du chromosome X est mise en place dans la masse cellulaire interne du blastocyste et maintenue jusqu’à l’âge adulte dans le soma. Chez certains Euthériens incluant la souris, les tissus extra-embryonnaires (trophectoderme et endoderme primitif) montrent une inactivation soumise à empreinte du X paternel. Le statut inactif du Xp peut être étudié ex vivo dans les cellules souches trophoblastiques (TS) dérivées du trophectoderme. Nous avons pu sélectionner des cellules TS montrant une réactivation partielle du Xp ou bien une inversion complète du profil d’inactivation. Ceci révèle une plasticité épigénétique accrue de l’inactivation dans le trophectoderme par au soma.L’inactivation aléatoire du chromosome X est récapitulée pendant la différenciation des cellules souches embryonnaires (ES), qui servent de modèle cellulaire. Ce processus est déclenché par l’accumulation en cis du long ARN non codant Xist qui crée un domaine nucléaire répresseur autour du futur chromosome X inactif. Avant la différenciation, l’accumulation de Xist est réprimée par un autre long ARN non codant, Tsix, qui est transcrit en antisens de Xist. Afin d’adresser la dynamique fonctionnelle des ARN Xist et Tsix, nous avons inséré différents motifs d’étiquetage au locus Xist/Tsix endogène. Incorporés dans l’ARN sens ou antisens, ces étiquettes sont reconnues spécifiquement par des molécules fluorescentes, permettant ainsi la visualisation de ces transcrits dans les cellules vivantesIn female Mammals, the transcriptional silencing of one of the two X chromosomes during early embryogenesis compensates the dosage disequilibrium of X-linked genes between sexes. Random X chromosome inactivation occurs in the inner cell mass of the blastocyst and is maintained through adult life in the soma. In some Eutherian species including mice, extraembryonic tissues (trophectoderm and primitive endoderm) exhibit imprinted inactivation of the paternal X. The inactive state of the Xp can be extensively studied ex vivo in Trophoblast Stem (TS) cells derived from the trophectoderm. We were able to select from the general cell population, TS cells exhibiting partial reactivation of the Xp or showing a complete switch of imprinted X-inactivation pattern. This reveals an accrued epigenetic plasticity of imprinted X-inactivation in the trophectoderm as compared to random X-inactivation in the soma.Random X-chromosome inactivation is recapitulated during the differentiation of female Embryonic Stem (ES) cells – which serves as cellular model. This process is triggered by the cis-accumulation of Xist long non coding RNA molecules which create a nuclear repressive domain around the future inactive X chromosome. Before differentiation, the accumulation of Xist is repressed by another lncRNA, Tsix, that is transcribed antisense to Xist. In order to address the functional dynamics of Xist and Tsix RNAs, we inserted different types of tag sequences in the endogenous Xist/Tsix locus. Incorporated in the sense or antisense RNA, these tags are specifically recognized by fluorescent molecules, thereby allowing live cell imaging of these transcripts
41
Ciaudo, Constance. "Caractérisation fonctionnelle de nouveaux facteurs trans impliqués dans le processus d'inactivation du chromosome X murin." Paris 7, 2006. http://www.theses.fr/2006PA077084.
Full textAbstract:
Chez les mammifères, la compensation de dose du produit des gènes liés au chromosome X entre les sexes est assurée par l'extinction transcriptionnelle de la plupart des gènes de l'un des deux chromosomes X, au hasard, chez la femelle. Le gène Xist (X-inactive specific transcript), localisé dans le Xic (X-inactivation center) et essentiel à l'initiation de cette inactivation en c/s, produit un grand ARN non codant couvrant entièrement le chromosome X inactif dans les tissus somatiques femelles. La recherche systématique de nouveaux gènes impliqués dans le processus d'inactivation du chromosome X par SAGE, en comparant les transcriptomes d'embryons murins mâles et femelles de 6,5 jpc (jours post-coïtum), a permis de mettre en évidence 214 gènes surexprimés dans les embryons femelles. L'inactivation est établie lors de l'embryogenèse précoce, dans les cellules de la masse cellulaire interne. Les cellules embryonnaires souches (ES) qui en sont dérivées récapitulent, lors de leur différenciation in vitro, toutes les étapes de ce processus. Dans ce travail de thèse, nous avons validé ex vivo une soixantaine de gènes, surexprimés dans les embryons femelles, dans des cellules ES mâles et femelles. La mise en place de la technique d'ARN interférence dans notre système modèle, a permis l'étude fonctionnelle de certains de ces candidats. La génération de clones de cellules ES stablement interfères, a mis en évidence qu'une ou plusieurs voies de dégradation (NMD, exosome) des ARN, via les gènes Eif1, Rent1 et Exosc1O, sont impliquées dans la régulation du gène Xist et dans la mise en place du processus d'inactivation du chromosome XIn mammals, each cell of the female contains two X chromosomes and hence, potentially a double dose of ail X-linked genes when compared to XY males, who carry a single X chromosome. X-inactivation is the mechanism that ensures the dosage-compensation of X-linked gene products between the two sexes. X-inactivation is under the control of a specific region of the X chromosome, the X inactivation center (Xic), which contains the Xist gene encoding a large noncoding RNA transcript whose upregulation is critical to the initiation of X-inactivation. As an approach to the identification of some of the potential molecular players in this process we have performed comparative transcriptional profiling of mouse 6. 5 dpc (days post-coïtum) female and male embryos using a modified SAGE (Serial analysis of gene expression) technique which allows the analysis of small quantifies of biological material. At 6. 5 dpc, a moment when random X-inactivation of embryonic tissues has just been achieved, some two hundred transcripts that were significantly enriched in the female gastrula compared to its male counterpart could be identified. The validation of an association with the X-inactivation process of a subset of these transcripts has been studied, ex vivo, in differentiating female and male ES cells and in female ES cells. We identified the Eif1 gene involved in translation initiation and RNA degradation. We show here that female embryonic stem cell lines, silenced by RNA interference for the Eif1 gene, are unable to form Xist RNA domains upon differentiation and fail to undergo X-inactivation. To probe further an effect involving RNA degradation pathways, the inhibition by RNA interference of Rent1, a factor essentiel for nonsense-mediated decay and Exosc1O, a specific nuclear component of the exosome, was analysed and shown to similarly impair Xist upregulation and XCI. Inhibition of the function of one or other of these genes leads to a failure of the female cells to undergo X inactivation, suggesting that post-transcriptional nuclear mRNA degradation pathway(s) are essential for the regulation of Xist RNA metabolism and X chromosome inactivation process
42
Seriola, Petit Anna. "Pluripotent stem cells as research models: the examples of trinucleotide repeat instability and X-chromosome inactivation." Doctoral thesis, Universitat Autònoma de Barcelona, 2015. http://hdl.handle.net/10803/325148.
Full textAbstract:
Els models de malalties són una eina bàsica per la comprensió de les malalties humanes. Actualment, la majoria de la informació de la que disposem de malalties humanes es basa en models animals. Tot i això, els models animals difereixen molecular i fenotípicament dels humans, i no sempre reprodueixen fidelment la malaltia humana. En les últimes dècades, les cèl·lules mare humanes s’han establert com una opció molt interessant en el camp de la modelització cel·lular. En aquest treball hem volgut caracteritzar les cèl·lules mare embrionàries com a models per a l’estudi de la inestabilitat de la repetició de trinucleotids a la distròfia miotonica tipus 1 (DM1) i la malaltia de Huntington (HD). Així mateix, hem volgut estudiar la inactivació del cromosoma X amb la intenció de fer servir linees cel·lulars com a models per l’estudi del desenvolupament embrionàri humà.
A la primera part d’aquest treball, hem observant una inestabilitat de repeticions de trinucleotids significativa al locus de la malaltia DM1 de les cèl·lules mare estudiades. La diferenciació d’aquestes cèl·lules va estabilitzar el número de repeticions. L’estabilització de les repeticions va ser concomitant amb la regulació a la baixa de l’expressió de gens involucrats en els mecanismes de reparació cel·lular. Posteriorment a la publicació del nostre article, altres grups varen reproduir els nostres resultats, però en aquest cas utilitzant cèl·lules mare induïdes. Els estudis recolzen la reproductibilitat dels nostres resultats, suggerint que poden ser extrapol·lats a altres linees de cèl·lules mare arreu del mon. Referent a la mutació de HD, varem trobar que era estable en totes les condicions estudiades, en cèl·lules indiferenciades, diferenciades a progenitors d’os, teratomes i progenitors neurals. Aquests resultats estan en concordancia amb els resultats obtinguts per altres grups que descriuen un baix nombre de repeticions al locus de HD. Per altra banda, varis grups han descrit la presencia de inestabilitat de les repeticions en cèl·lules diferenciades a la linea neural. La discrepància entre els nostres resultats i aquests últims podria ser deguda a la obtenció de cèl·lules neurals menys madures en el moment del nostre estudi.
A la segona part d’aquesta tesis hem estudiat la inactivació del cromosoma X en 23 línies femenines de cèl·lules mare pluripotents. Vàrem observar una ràpida progressió de les cèl·lules de dependència de XIST en la inactivació del cromosoma X cap a un estat d’adaptació al cultiu que es caracteritza per un estadi de inactivació independent de l’expressió de XIST i amb una erosió de la metilació. També describim un patró d’inactivació esbiaixat en la majoria de les línies estudiades, contrari al patró aleatori observat en cèl·lules femenines adultes. A més a més, aquest patró és independent de XIST, de l’origen del cromosoma X i d’aberracions cromosòmiques. Aquests resultats suggereixen que el patró esbiaixat observant esta dirigit provablement per l’activació o repressió d’al·lels específics que es troben en el cromosoma X i que li confereixen a la cèl·lula un avantatge respecte a les altres cèl·lules.
En conclusió, les cèl·lules mare pluripotents semblen ser un bon model in vitro per a l’estudi d’ambdues malalties, DM1 i HD, ja que presenten el mateix patró d’inestabilitat de la repetició del trinucleotid que s’observa in vivo. Cal remarcar també la depencia
Overall, hPSC appear to be a good in vitro model for the study of both DM1 and HD TNR instability, as the repeat follows in vitro the same patterns as found in vivo, including its dependency of the MMR machinery, particularly in the case of DM1. However, our results on the study of the X chromosome inactivation (XCI) state suggest caution when using hPSC as early human developmental research models. The eroded state of XCI found in many of the hPSC lines, and the frequency of skewed XCI patterns suggests that these cells are not a good proxy to early embryonic cells, at least what XCI is concerned. Conversely, they may still provide an interesting model to study gene function and mechanisms implicated.Disease modelling is an essential tool for the understanding of human disease. Currently, much of the information we have on human diseases is based on animal models. However, animal models differ molecularly and phenotypically from humans, and are not always suitable to reproduce with fidelity human diseases. In the past decades, human pluripotent stem cells (hPSC) have emerged as an interesting option in the field of cellular modelling, this development recently having taken up much momentum. In this work, we aimed at characterizing hPSC as models for the study of Myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD) trinucleotide repeat (TNR) instability and to investigate the status of the X-chromosome inactivation with an eye on using these cells as models for early human development. In the first part of our work, we observed a significant TNR instability for the DM1 locus in hESC, and that differentiation resulted in a stabilization of the repeat. This stabilization was concommitant with a downregulation of the mismatch repair (MMR). Our results were later replicated in hiPSC by other researchers, showing their reproducibility and suggesting they may be extrapolated to other hPSC lines worldwide. Regarding the HD repeat, we found it was very stable in all conditions studied, both in undifferentiated hESC and cells differentiated into osteogenic progenitor-like cells, teratoma cells and neural progenitors. This is in line with other studies showing that hESC show very limited TNR in the HD locus. On the other hand, some groups have now reported some instability of this locus in cells differentiated into the neuronal lineage. The instability seen in neuronal lineage in later studies, not in our study, is probably explained by the use of hPSC derived neurons more similar to the cells showing in vivo instability than the ones we were able to generate at the time of the study. In the second part of the thesis we studied the X-chromosome inactivation in 23 female hPSC lines. We found that hPSC rapidly progress from a XIST-dependent XCI state to a culture-adapted, XIST-independent XCI state with loss of repressive histone modifications and erosion of methylation. We also report a remarkably high incidence of non-random XCI patterns, and that this skewing of the methylation patterns is independent from the transition to the XIST-independent XCI state, the origin of the X chromosome or chromosomal aberrations. These results suggest that XCI skewing is possibly driven by the activation or repression of a specific allele on the X chromosome, conferring a growth or survival advantage to the cells. Overall, hPSC appear to be a good in vitro model for the study of both DM1 and HD TNR instability, as the repeat follows in vitro the same patterns as found in vivo, including its dependency of the MMR machinery, particularly in the case of DM1. However, our results on the study of the X chromosome inactivation (XCI) state suggest caution when using hPSC as early human developmental research models. The eroded state of XCI found in many of the hPSC lines, and the frequency of skewed XCI patterns suggests that these cells are not a good proxy to early embryonic cells, at least what XCI is concerned. Conversely, they may still provide an interesting model to study gene function and mechanisms implicated.
43
Bartlett, Molly Harding. "X chromosome inactivation and the Pgk-1 gene methylation and mapping studies using female embryonal carcinoma cells." Thesis, University of Ottawa (Canada), 1989. http://hdl.handle.net/10393/5445.
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Penny, Graeme Douglas. "Analysis of the role of Xist in X chromosome inactivation using targeted mutagenesis in embryonic stem cells." Thesis, Imperial College London, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244103.
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Galupa, Rafael. "Exploring the structural and functional dynamics of the X-inactivation centre locus during development." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS305.
Full textAbstract:
La régulation de l’expression génique chez les mammifères dépend de l’organisation tridimensionnelle des chromosomes, en particulier à l’échelle des communications entre les séquences régulatrices et leurs promoteurs cibles. Ainsi, les chromosomes sont organisés en une nouvelle architecture consistant en domaines d’interactions topologiques (TADs, acronyme anglais). Mon projet de thèse avait pour but de caractériser les mécanismes moléculaires impliqués dans cette architecture et leurs importances au cours du développement embryonnaire, pour un locus bien particulier, le Xic (acronyme anglais pour X-inactivation centre). Le Xic contient les éléments régulateurs nécessaires pour initier l’inactivation du chromosome X (ICX), un phénomène épigénétique spécifique du développement des mammifères femelles, rendant l’un des deux chromosomes X inactif du point de vue transcriptionnelle. L’ICX permet d’égaliser l’expression des gènes liés au X entre les sexes chez les mammifères. Le Xic est organisé au moins en deux TADs mais une partie du locus reste encore non identifiée. Je présente ici une analyse fonctionnelle approfondie des différents éléments régulateurs au sein du Xic, comprenant des enhancers, des gènes d’ARNs non codants et des éléments structurels. Après avoir créé une série d’allèles mutés chez la souris et les cellules souches embryonnaires murines, j’ai caractérisé l’impact de ces réarrangements génomiques sur le paysage structurel et transcriptionnel du Xic. J’ai identifié des nouveaux acteurs dans la régulation de ce locus, en particulier des séquences régulatrices conservées chez les mammifères placentaires et des éléments structurels importants pour la formation d’une frontière entre les deux TADs du Xic, importante pour leur séparation et régulation. Je décris aussi la découverte de communication entre ces TADs, ce qui constitue un mécanisme inédit de régulation génique pendant le développement. Ce travail contribue à un nouveau niveau de compréhension des lois qui régissent l’organisation des TADs dans le contexte de la régulation génique chez les mammifèresMammalian gene regulatory landscapes rely on the folding of chromosomes in the recently discovered topologically associating domains (TADs), which ensure appropriate communication between cis-regulatory elements and their target promoters. The aim of my PhD project was to characterise the molecular mechanisms that govern this novel architecture and its functional importance in the context of a critical and developmentally regulated locus, the X-inactivation centre (Xic). The Xic contains the necessary elements to trigger X-chromosome inactivation, an epigenetic phenomenon that occurs during the development of female mammals to transcriptionally silence one of the X-chromosomes and equalise X-linked gene expression between sexes. The Xic is partitioned into at least two TADs, but its full extent is unknown. Here, I present a comprehensive functional analysis of different cis-regulatory elements within the Xic, including enhancer-like regions, long noncoding RNA loci and structural elements. Upon generating a series of mutant alleles in mice and murine embryonic stem cells, I characterised the impact of these genomic rearrangements in the structural and transcriptional landscape of the Xic and identified novel players in the regulation of this locus, including cis-acting elements conserved across placental mammals and structural elements critical for the insulation between the Xic TADs. I also found evidence for communication across TADs at this locus, which provides new insights into how regulatory landscapes can work during development. This study also extends our understanding of the rules governing the organisation of TADs and their chromatin loops in the context of mammalian gene regulation
Nos mamíferos, a regulação da expressão genética depende da organização tridimensional dos cromosomas, em particular ao nível da comunicação regulatória entre promotores e enhancers. A esta escala, descobriu-se recentemente que os cromossomas estão organizados em domínios de interações topológicas (conhecidos como TADs, no acrónimo inglês) que se pensa providenciarem uma base estrutural para as paisagens de regulação transcricional dos genes. O meu projecto de tese teve como objectivo caracterizar os mecanismos moleculares responsáveis por esta arquitectura e a sua importância funcional no contexto de um locus crítico para o desenvolvimento embrionário, o centro de inactivação do cromossoma X (Xic, acrónimo inglês). O Xic contém os elementos genéticos necessários e suficientes para iniciar a inactivação do cromossoma X, um fenómeno epigenético que ocorre durante o desenvolvimento das fêmeas de mamíferos para silenciar um dos cromosomas X e igualar a expressão dos genes do X entre indivíduos XX e XY. O Xic está organizado em pelo menos dois TADs, mas o seu intervalo genético completo permanece desconhecido. Apresento nesta tese uma análise funcional e detalhada de diferentes sequências reguladoras presentes no Xic, incluindo regiões do tipo enhancer, genes de ARNs não codificantes e elementos estruturais. Após a criação de diversos alelos mutantes (deleções, inserções, inversões) em ratinho e em células estaminais embrionárias, através das recentes técnicas de engenharia genética, TALENs e CRISPR/Cas9, caracterizei o impacto destes rearranjos genéticos na paisagem topológica e transcricional do Xic, o que permitiu a identificação de novos actores moleculares na regulação deste locus. Em particular, descobrimos sequências de regulação transcricional altamente conservadas em mamíferos placentários e elementos estruturais importantes para a formação da fronteira entre os dois TADs do Xic. Descrevo também evidência de que há comunicação entre os dois TADs neste locus, o que compromete os modelos actuais do modus operandis dos TADs, e por isso contribui para um novo nível de compreensão dos mecanismos que regulam a expressão genética durante o desenvolvimento
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Studer, Tania [Verfasser], and Henrik [Akademischer Betreuer] Kaessmann. "The developmental sex-biased expression of genes escaping X chromosome inactivation across mammals / Tania Studer ; Betreuer: Henrik Kaessmann." Heidelberg : Universitätsbibliothek Heidelberg, 2018. http://d-nb.info/1177044978/34.
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Nora, Elphege-Pierre. "Architecture chromosique du locus Xic : implications pour la régulation de l'inactivation du chromosome X." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00635540.
Full textAbstract:
Le développement embryonnaire précoce des mammifères femelles s'accompagne de l'inactivation transcriptionnelle d'un de leurs deux chromosomes X. Cet évènement est initié suite à l'expression mono-allélique de l'ARN non codant Xist, qui est contrôlée par de nombreux éléments cis-régulateurs présents dans le centre d'inactivation du chromosome X (Xic) - tel son anti-sens répresseur Tsix. Mon travail de thèse a consisté à développer des approches permettant d'appréhender le paysage structural dans lequel s'exerce cette régulation. La caractérisation de l'architecture tridimensionnelle du Xic, par des techniques basées sur la capture de conformation chromosomique (3C) et l'hybridation in situ en fluorescence (FISH), m'a permis de mettre en évidence que les promoteurs respectifs de Xist et Tsix sont engagés dans des interactions physiques intimes avec des loci distaux, localisés au sein du Xic, et de montrer qu'au moins certaines de ces régions exercent un effets régulateurs à longue-distance. Les éléments du Xic contactés par les régions promotrices de Xist et de Tsix sont en outre fondamentalement différents, chacune engageant des associations chromosomiques sur plusieurs centaines de kilobases dans leur direction 5' respective.Ce travail a également permis de révéler des propriétés insoupçonnées de l'architecture chromosomiques. En effet, le Xic apparaît scindé en plusieurs sous-régions, couvrant chacune entre 200kb et 1Mb, à l'intérieur desquelles les interactions chromosomiques sont préférentiellement établies. L'existence de ces domaines d'interaction s'intègre avec d'autres propriétés structurales du génome, tels la composition de la chromatine sous-jacente et l'association à la lamine nucléaire, mais n'apparaît pas en dépendre directement. En étudiant la dynamique de la conformation chromosomique du Xic au cours de la différenciation cellulaire, j'ai pu constater la robustesse de cette organisation, sauf sur le chromosome X inactif, qui se distingue par la perte des contacts chromosomiques préférentiels détectables sur son homologue actif.Enfin, j'ai pu mettre en évidence que la variabilité du repliement général du chromosome X amène à un instant donné chaque allèle de Tsix à contacter physiquement des jeux de séquences distales différents, suggérant que l'environnement structural instantané de chacun de ces allèles à l'orée de l'activation mono-allélique de Xist est différent. Ce travail, combinant des approches à l'échelle de la population cellulaire d'une part et de la fibre de chromatine unique d'autre part, apporte une nouvelle vision du paysage structural et régulateur dans lequel s'inscrit le contrôle de l'activité transcriptionnelle de Xist, et fourni de nouvelles perspectives concernant les principes fondamentaux de l'organisation topologique des chromosomes chez les mammifères.
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Castagné, Raphaële. "Expression des gènes du chromosome X : approche intégrée par génomique et transcriptomique à haut-débit chez l'homme." Paris 6, 2011. http://www.theses.fr/2011PA066463.
Full textAbstract:
Le chromosome X présente par rapport aux autosomes des spécificités à la fois de régulation, de composition génétique et de fonction. Mon travail de thèse a porté sur l'analyse de l'expression des gènes du chromosome X en fonction du sexe et de la variabilité génétique à partir de données d'expression mesurées dans les monocytes circulants de 1467 sujets. Dans une première partie, nous avons montré qu'il y avait un excès de transcrits plus exprimés chez les femmes sur le chromosome X par rapport aux autosomes, ces transcrits pouvant correspondre à des gènes échappant à l'inactivation du chromosome X chez la femme. Même si l'impact de la variabilité génétique sur l'expression est globalement similaire chez les hommes et les femmes, nous avons identifié quelques gènes différentiellement régulés qui constituent des gènes candidats potentiels pour expliquer les différences entre sexes de susceptibilité génétique aux maladies complexes. Dans une seconde partie, nous nous sommes intéressés aux différences entre les niveaux d'expression des gènes du chromosome X et des gènes autosomaux. L'hypothèse de compensation de dose du chromosome X étayée par des données de microarray a été remise en cause par les résultats obtenus par séquençage à haut débit de l'ARN. Nous avons cherché à comprendre et expliquer cette différence de résultats entre les deux technologies. Pour tester cette hypothèse, nous avons analysé l'ensemble des transcrits du chromosome X et des autosomes en appliquant différentes méthodes de filtrage. Cette étude a montré que les conclusions concernant la compensation des gènes du chromosome X différaient en fonction de la méthode de filtrage utilisée.
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Bouazzi, Habib. "Contribution à l'identification de nouveaux gènes impliqués dans la Déficience intellectuelle liée au Sexe(X-LID) par séquençage à haut débit de l’exome du chromosome X avec la technologie SOLiD." Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCB009/document.
Full textAbstract:
La Déficience Intellectuelle liée au chromosome X (X-LID), anciennement appelée RMLX (retard mental lié au chromosome X) est une pathologie fréquente (3 % de la population) et handicapante. Cette déficience se manifeste par la réduction de la capacité à comprendre les informations nouvelles ou complexes, des difficultés d’acquisition de nouvelles compétences et l’échec dans la gestion de sa vie en toute autonomie ; celle-ci est souvent accompagnée par un dysmorphisme corporel. Cette pathologie s’installe dès l’enfance (avant l'âge de 18 ans) et a des répercussions sur le développement de l’individu (QI<70). La pathogénie de la déficience intellectuelle reste obscure et dans 50 % des cas, la cause n’est pas connue. Dix pour-cent (10 %) des cas de la déficience intellectuelle seraient liés à des gènes localisés sur le chromosome X, avec une mutation transmise par les mères et affectant principalement les garçons. Parmi les 931 gènes du chromosome X, seulement 114 gènes ont été identifiés comme gènes de déficience intellectuelle. Le dernier (le gène SSR4) fut caractérisé en mars 2014. À l’heure des technologies du séquençage de haut débit, le laboratoire de génétique moléculaire de l’hôpital Necker de Paris s'est doté d’une plateforme d’identification de mutation génétique humaine par séquençage à haut débit permettant le diagnostic des maladies rares. L’objectif de mon travail de thèse était d’appliquer l’approche du séquençage à très haut débit (technique SOLiD) dans l’identification de nouveaux gènes de la déficience intellectuelle liée au chromosome X chez des familles ayant des garçons atteints de déficience intellectuelle non-syndromique, d’identifier les mutations des gènes qui sont déjà connus et d’en discuter la corrélation génotype-phénotype. L’approche que j’ai utilisée dans cette étude est le diagnostic génétique par séquençage à haut débit de l’exome du chromosome X de vingt sujets appartenant à dix familles (X-LID) françaises. La procédure consiste à capturer l’exome du chromosome X des patients atteints, à l’enrichir par la technologie Rain-Dance, puis à le séquencer dans notre plateforme avec un séquenceur à haut débit de la technologie SOLiD5500 afin d’analyser les résultats et pour ne retenir que les nouvelles mutations et commenter leur pouvoir pathogène. Cette étude a mis en évidence de nouvelles mutations dans 21 gènes, dont neuf gènes ne sont pas encore décrits parmi les gènes X-LID et a révélé l’importance de l’hétérogénéité génétique tout en relevant la possibilité de l’effet des charges mutationnelles et le rôle gènes modificateurs. Certaines nouvelles mutations, nous les avons identifiées dans des gènes connus pour leur implication dans la déficience intellectuelle et les avons publiées durant les études doctorales. Pour confirmer la causalité des nouveaux gènes ayant muté chez les familles atteintes, des études fonctionnelles supplémentaires in vivo doivent être appliquées tout en suivant les publications sur le même sujet afin de comparer avec des cas similairesX linked Intellectual deficiency (X - LID); formerly X-LMR (X Linked Mental Retardation) is a common pathology (3 % of the population). Intellectual Deficiency (ID) is the most frequent cause of serious handicap in children and young adults. Defining features of ID include an overall intelligence quotient (IQ) of less than 70 together with associated functional deficits in adaptive behavior (such as daily living, social and communication skills), which manifest before18 years of age. ID pathogenesis remains obscure and 50% of cases have no known cause. Ten percent of the intellectual intellectual deficiency would be related to genes located on the X chromosome, and subsequently inherited by affected boys. Among the 931 genes of the X chromosome, only 114 genes have been identified as X-LID genes. The last (SSR4 gene) was characterized in March 2014. At the time of the Next Generation Sequencing (NGS), the laboratory of molecular genetics of Necker hospital in Paris is equipped with a platform for the identification of human genetic mutation by high-throughput sequencing for the diagnosis of rare diseases. The objective of my thesis work was to seek new genes for X linked intellectual deficiency in families with non-syndromes cognitive disorder affected boys and to identify mutations in the genes that are already known and to discuss the genotype, phenotype correlation. The approach that I have used in this study is genetic diagnosis by high-throughput sequencing of chromosome X exomes of 20 subjects belonging to ten X-LID French families. The procedure is to capture and enrich the exome of the X chromosome of patients, then to sequence it in our platform with a high throughput sequencer of SOLid technology then analyze the results and retain that new mutations to discuss their pathogenity. This study has highlighted new mutations in 21 genes, including nine that are not yet described among the X-LID genes. Some new mutations, we identified in genes known through their involvement in cognitive impairment were published during my doctoral studies. To confirm causality of new genes that were found mutated in families, additional studies in vivo must be applied while following the literature to make comparisons with similar cases
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Barros, de Andrade e. Sousa Lisa [Verfasser]. "Using interpretable machine learning to understand gene silencing dynamics during X-Chromosome inactivation / Lisa Barros de Andrade e Sousa." Berlin : Freie Universität Berlin, 2021. http://d-nb.info/1239115164/34.
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