When a multicellular organism suffers damages to tissues/organs it heals itself by either substituting the lost cellular matrix by scar formation or by regenerating the lost tissue. Regeneration likely occurs by a recapitulation of the developmental process that formed the organ. Many processes regulating organ development are based on epithelial-mesenchymal interactions and a strict control of organ specific stem/progenitor cells. Elucidation of the molecular basis of these processes is therefore vital in order to develop novel therapies in regenerative medicine. The LIM homebox gene Lhx2 is interesting in this context since Lhx2 has been shown to be important for the formation of several organs by regulating epithelial-mesenchymal interactions and progenitor cell function. Targeted inactivation of Lhx2 leads to a lethal anemia due to malformed liver and severe neural abnormalities such as hypoplasia of the forebrain and anophtalmia. Thus, elucidation of the mechanisms of the function of Lhx2 in different organ systems would give important insights into the molecular mechanisms regulating epithelial-mesenchymal interactions and stem/progenitor cell function. To elucidate the function of Lhx2 in the hematopoietic system Lhx2 was initially expressed in hematopoietic progenitor cells derived from ES cells differentiated in vitro using retroviral vectors. This approach led to the generation of hematopoietic stem cell (HSC)-like cell lines suggesting that Lhx2 could impact HSC function. However neither the specificity nor the efficiency of the Lhx2-induced phenotype could be determined using this approach. To be able to elucidate the function of Lhx2 in the hematopoietic system, an ES cell line with inducible Lhx2 expression was generated. Lhx2 expression induces self-renewal of a distinct hematopoietic progenitor cell from which HSC-like cell lines were established. Down-regulation of Lhx2 in these HSC-like cell lines leads to a rapid loss of stem cell character, providing a good model to study the molecular function of Lhx2 in hematopoietic stem/progenitor cells. A global gene expression analysis was performed comparing the Lhx2+ stem cell population to the Lhx2- differentiated progeny. This approach identified genes putatively linked to self-renewal/differentiation of HSCs. A considerable proportion of the genes showed an overlapping gene expression pattern with Lhx2 expression in tissue of non-hematopoietic origin suggesting that Lhx2 function in stem/progenitor cells partly overlap with Lhx2 function during organ development. In order to define other Lhx2-dependent progenitor cell populations and to generate a tool to analyze the function of Lhx2 in organ development a new transgenic mouse model was generated. By using a specific part of the Lhx2 promoter to drive expression of Cre recombinase in vivo (Lhx2-Cre mice) we have been able to define the first eye committed progenitor cells in the forebrain. By using the Lhx2-Cre mice it will be possible to distinguish the function of genes during eye development from their function in the patterning of the forebrain e.g. the eye field transcription factors. Conditional inactivation of Lhx2 in these eye specific progenitor cells causes an immediate developmental arrest. The transgene is also active in Lhx2-/- embryonic forebrain, but re-expression of Lhx2 in Lhx2-/- progenitor cells only promote formation of retinal pigment epithelium cells. Analysis of genes expressed by the Lhx2+ stem cell population allowed us to define novel genes putatively linked to Lhx2 function in eye development. Thus, we have defined the progenitor cells in the forebrain committed to eye development and the expansion and patterning of these progenitors are dependent on Lhx2. Although commitment to eye development is Lhx2-independent, Lhx2 might be important for the acquisition of the oligopotent fate of these progenitor cells.

Las patologías más importantes del páncreas exocrino, como la pancreatitis crónica (PC) o el cáncer de páncreas, representan un gran problema de salud pública en Europa. En la PC, el tejido acinar es substituido por complejos ductales. Además, es difícil mantener el fenotipo diferenciado de las células acinares en cultivo ya que sufren una transdiferenciación acinar-ductal.Las células madre embrionarias (ES) de ratón han sido utilizadas en la última década para generar in vitro células completamente diferenciadas de varios linajes celulares. No obstante, la capacidad de las células ES a diferenciarse a tipos celulares de origen endodérmico es muy limitada. El objetivo principal de este proyecto ha consistido en desarrollar estrategias para diferenciar células ES de ratón a células pancreáticas acinares con una elevada eficiencia mediante 1) la optimización de las condiciones de cultivo con tal de activar vías de señalización implicadas en el desarrollo/diferenciación pancreáticas; 2) la sobreexpresión de factores transcripcionales maestros utilizando vectores virales con el fin de recapitular específicamente un programa de diferenciación acinar; 3) la selección genética de las células comprometidas al linaje acinar con el objetivo de purificar las células acinares diferenciadas.Mediante la integración de estos abordajes, hemos conseguido aislar células que comparten características fenotípicas con células acinares inmaduras según la expresión de marcadores de diferenciación y la respuesta funcional a secretagogos. / Exocrine pancreatic diseases such as chronic pancreatitis (PC) or pancreatic cancer are major health issues in Europe. In CP, the acinar tissue is substituted by ductal complexes. In addition, it is difficult to maintain the differentiated phenotype of the acinar cells in culture as within few days an acinar-ductal transdifferentiation takes place.In the last decade, mouse embryonic stem cells (mES) have been used to generate differentiated cells of a variety of cellular lineages in vitro. However, the ability of ES cells to differentiate into endodermal lineages is limited. The main objective of this project has focused on the development of strategies to differentiate mES to pancreatic acinar cells with high efficiency by means of: 1) Optimization of cell culture conditions to activate signalling pathways involved in pancreatic differentiation/development; 2) the overexpression of master transcription factors involved in pancreas development using viral vectors in order to recapitulate specific acinar differentiation program; 3) the genetic selection of cells committed to the acinar linage in order to purify the differentiated cells.The integration of these different strategies allowed us to isolate cells that share phenotypic features with immature acinar cells according to the expression of differentiation markers and the functional response to acinar secretegogues.

Genesis of life begins with the fusion of female and male haploid gametes through a process of fertilization leading to the formation of a diploid cell, the zygote. This undergoes successive cleavage divisions forming 2-, 4- and 8- cell embryos and their individual cells (blastomeres) are totipotent. As development proceeds, there is a gradual restriction in their totipotency, resulting in the generation of two distinct cell lineages i.e., the differentiated trophectoderm (TE) cells and the undifferentiated, inner cell mass (ICM) during blastocyst morphogenesis (Rossant and Tam 2009). During the course of development, the ICM cells can give rise to all cell types of an organism and can also provide embryonic stem (ES)-cells when cultured in vitro (Evan and Kaufman 1981). ES-cells are pluripotent cells, having the ability to self-renew indefinitely and differentiate into all the three primary germ layers (ectoderm, mesoderm and endoderm) derived-cell types. ES-cells are an excellent developmental model system to understand basic mechanisms of self-renewal, cell differentiation and function of various genes in vitro and in vivo (Capecchi 2001). Importantly, their cell derivatives could potentially be used for experimental cell-based therapy for a number of diseases. Although, human ES-cell lines have been successfully derived and differentiated to various cell types (Thomson et al., 1998; Odorico et al., 2001), their cell-therapeutic potential is far from being tested, in view of the lack of our understanding of lineage-specific differentiation, homing and structural-functional integration of differentiated cell types in the host environment. To understand these mechanisms, it is desirable to have fluorescently-marked ES-cells and their differentiated cell-types, which could facilitate experimental cell transplantation studies. In this regard, our laboratory has earlier generated enhanced green fluorescent protein (EGFP)-expressing FVB/N transgenic ‘green’ mouse, under the control of ubiquitous chicken -actin promoter (Devgan et al., 2003). This transgenic mouse has been an excellent source of intrinsically green fluorescent cell types. We have been attempting to derive ES-cell line from this transgenic mouse. Because the derivation of ES-cell line is genetic strain-dependent, with some strains being relatively permissible for ES-cell derivation while others are quite resistant (non permissive), it has been extremely difficult to derive ES-cell line from the FVB/N mouse strain. There is a need to evolve experimental strategies to derive ES-cell line from FVB/N mouse, a strain extensively used for transgenesis. Thus, the aims of the study described in the thesis are to: (1) develop an experimental system to derive EGFP-expressing fluorescently-marked ES-cell line from a non-permissive FVB/N mouse strain; (2) characterize the established ES-cell line; (3) achieve differentiation of various cell types from EGFP-expressing ES-cell line and (4) understand role of FGF signaling in cardiac differentiation from the established ES-cell line. In order to have an appropriate and relevant literature background, the 1st chapter in this thesis describes a comprehensive up-to-date review of literature, pertaining to the early mammalian development and differentiation of blastocyst, followed by origin and properties of ES-cells. Various ES-cell derivation strategies from genetically permissive and non-permissive mouse strains are described and also the ES-cell differentiation potential to various progenitors and differentiated cell types. Subsequently, details on molecular basis of cardiac differentiation and the therapeutic potential of ES-cell derived differentiated cell types to treat disease(s) are described. This chapter is followed by three data chapters (II-IV). Chapter-II describes the issues related to non-permissiveness of FVB/N strain for ES-cell derivation and strategies to overcome this hurdle. This is followed by detailed results pertaining to generation of homozygous EGFP-expressing transgenic mice and development of a two-pronged ES-cell derivation approach to successfully establish a permanent ES-cell line (named ‘GS-2’ ES-cell line) from the EGFP-transgenic ‘green’ mouse. This chapter also provides results pertaining to detailed characterization of the ‘GS-2’ ES-cell line which includes colony morphology, expansion efficiency, alkaline phosphatase staining, expression analysis of pluripotent markers by RT-PCR and immunostaining approaches and karyotyping. Following this, the outcome of results and significance in the context of reported information are discussed in detail. Having successfully derived the ‘GS-2’ ES-cell line, it is necessary to thoroughly assess the differentiation competence of the ‘GS-2’ ES-cell line. Therefore, the Chapter-III describes detailed assessment of the in vitro and in vivo differentiation potential of the ‘GS-2’ ES-cell line. For in vitro differentiation, results pertaining to ES-cell derived embryoid body (EB) formation and their differentiation to ectodermal, mesodermal and endodermal cell types, expressing nestin, BMP-4 and α-fetoprotein, respectively, are described. Besides, the robustness of adaptability of ‘GS-2’ ES-cells to various culture conditions for their maintenance and differentiation are described. Also shown in the chapter is the relatively greater propensity of this cell line to cardiac differentiation. For in vivo differentiation, the ‘GS-2’ ES-cell derived teratoma formation in nude mice and its detailed histological analysis showing three germ layer cell types and their derivatives are described. Last part of the data described in this chapter, pertains to generation of chimeric blastocysts by aggregation method. Because the ‘GS-2’ ES-cell line exhibited a robust differentiation potential, including an efficient cardiomyocyte differentiation, it is of interest to enhance the efficiency of cardiomyocyte differentiation by exogenous addition of one of the key growth factors i.e., FGF8b since this has been implicated to be critical for cardiogenesis in non-mammalian verterbrate species. Therefore, Chapter-IV is focused on assessing the ability of ‘GS-2’ ES-cell line for its cardiomyocyte differentiation property with particular emphasis on the FGF-induced cardiac differentiation. Results pertaining to the expressions of various FGF ligands and their receptors during differentiation of ES-cells are described. Besides, increases in the cardiac efficiency, following FGF8b treatment and the associated up-regulation of cardiac-specific markers such as GATA-4, ISL-1 and α-MHC are shown. At the end of data chapters, separate sections are devoted for ‘Summary and Conclusion’ and for ‘Bibliography’.

Embryonic stem cells (ESC) are derived from the inner cell mass (ICM) of the blastocyst and have the capacity for unlimited proliferation while retaining their potential to differentiate into a wide variety of cell types when cultured in vitro. These properties have made of human embryonic stem cells (hESC) an excellent model on which to study the conditions required for differentiation into specific cell lineages, and consequently the possibility of transplanting specific cell types into damaged tissues. The continued turn over of ESC while maintaining an undifferentiated state is dependent on unusual cell cycle properties. These unusual proliferative properties are responsible for the generation of tumours when these cells are injected into adult animals. Thus, the study of the unusual proliferative properties of hESC needs to be addressed if their potential is to be realized. To date, most studies of the cell cycle in hESC have been descriptive, lacking functional studies that reveal the mechanisms of how the cell cycle maintains pluripotency and self- renewal of hESC. In this thesis we sought to understand the mechanisms of cell cycle control of hESC. We asked the question if a single cell cycle gene could regulate the self-renewal or pluripotency properties of hESC using a gain and loss of gene function strategy. We have identified that the protein expression of the p27Kip1 cell cycle inhibitor was low in human pluripotent cells, but its expression increased during differentiation together with changes in the cell cycle structure of pluripotent cells. By adopting a gain and loss of function strategy we increased or reduced its expression in undifferentiating conditions to define its functional role in self-renewal and pluripotency of Hesc, using undifferentiation conditions, overexpression of p27Kip1 in hESC lead to a G1 phase arrest with an enlarged and flattened hESC morphology and consequently loss of self-renewal ability. Loss of p27Kip1 caused an increase of self-renewal while maintaining an undifferentiated phenotype. Moreover, we have shown that a change in the balance of p27Kip1 levels in undifferentiated hESC affects expression of the mesoderm markers: BRACHYURY and TWIST. We have found that expression changes of TWIST are associated with the presence of p27Kip1 protein in the TWIST1 gene promoter. The results presented in this thesis have interesting implications in stem cell biology. Firstly, these results define that the maintenance of p27Kip1 protein levels at a certain level is essential for self-renewal and pluripotency of hESC. Secondly, p27Kip1 is involved in the regulation of TWIST which is upregulated in several types of tumours and induces an epithelial-mesenchymal transition to facilitate tumor metastasis. / Las células madre embrionarias humanas (conocidas como hESC por sus siglas en inglés de human embryonic stem cells) son derivadas de la masa celular interna de los blastocistos y poseen la capacidad para auto-renovarse ilimitadamente, reteniendo su potencial para diferenciarse hace una amplia variedad de tipos celulares (pluripotencia), cuando son cultivadas in vitro. Estas propiedades permiten el estudio de las condiciones requeridas para la diferenciación hacia linajes específicos y la posibilidad de trasplantar tipos celulares específicos en tejidos dañados. El continuo recambio de las hESC al mismo tiempo que mantienen un estado de indiferenciación es dependiente de sus inusuales propiedades proliferativas. El objetivo de esta tesis doctoral fue el estudio de los mecanismos de control del ciclo celular de las hESC. Nos preguntamos si una única proteína del ciclo celular podría regular las propiedades de auto-renovación o pluripotencia de las hESC. En esta tesis doctoral identificamos que la expresión proteica del inhibidor del ciclo celular p27Kip1 era baja en diversas líneas celulares humanas pluripotentes pero aumentó durante la diferenciación, al mismo tiempo que la estructura del ciclo celular cambió. Mediante una estrategia de ganancia y pérdida de función, aumentamos o reducimos la expresión de p27Kip1 a fin de definir su función en la auto-renovación y la pluripotencia de las hESC. En condiciones de indiferenciación, la sobreexpresión de p27Kip1 en las hESC resultó en un arresto del ciclo celular en fase G1 y un cambio hacia una morfología más grande y aplanada, y consiguiente pérdida de la propiedad de auto-renovación. La pérdida de p27Kip1 causó un aumento de la auto-renovación manteniendo un fenotipo indiferenciado. También, hemos demostrado que un cambio en la expresión de p27Kip1 en hESC indiferenciadas afecta la expresión de los reguladores de mesodermo: BRACHYURY y TWIST. Además, hemos descubierto que los cambios en la expresión de TWIST están asociados con la presencia de la proteína p27Kip1 en el promotor de TWIST1. Estos resultados definen que los niveles de expresión de p27Kip1 son críticos para la auto-renovación y la pluripotencia de las hESC y sugieren una función para p27Kip1 en el control de la transición de epitelio a mesénquima.

Made available in DSpace on 2014-06-11T19:35:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-02-05Bitstream added on 2014-06-13T20:26:13Z : No. of bitstreams: 1 goncalves_fs_dr_jabo.pdf: 3109118 bytes, checksum: 5a4b81536e1b9bd9d62a0e42796b675b (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O fator de transcrição Oct-4 é bem conservado entre as espécies e é conhecido por ser expresso em embriões e células-tronco embrionárias (CTE), sendo um importante marcador da pluripotência. Recentemente, foi relatado que a combinação de Oct-4 com três outros fatores de transcrição Klf-4, c-Myc e Sox2 foram capazes de reprogramar células somáticas a um estado indiferenciado pluripotente, chamadas células-tronco pluripotentes induzidas (“células iPS”), as quais apresentam várias das mesmas propriedades das CTE incluindo a pluripotência, auto-renovação e proliferação. O objetivo desse estudo foi avaliar a funcionalidade do promotor Oct-4 de eqüino em CTE de murinos. Três vetores plasmidiais expressando GFP (“green fluorescent protein”) sob o controle do promotor Oct-4 de equinos, camundongo e quatro vetores lentivirais, também contendo o gene reporter GFP e os promotores Oct-4 de equinos, camundongo e humanos, pLZ2-ecOCT-EGFP (meq) (sequência equivalente de camundongos), pLZ2-ecOCT-EGFP (heq) (sequência equivalente de humanos), pLZ2-mOCT-EGFP e pLZ2-hOCT-EGFP, respectivamente, foram construídos. Todos os vetores também contêm um sítio de resistência à blasticidina que permite a seleção das células estáveis e das células transduzidas. Essas construções plasmidiais foram verificadas se funcionavam eficientemente, bem como o efeito do promotor Oct-4 em transfectar transientes e estáveis CTE. As construções com promotor Oct-4 de camundongo, humano e eqüino (sequência análoga à de camundongo) produziram somente 6% de células GFP positivas com intensidade de fluorescência (IF) >1000 pela análise em citômetro de fluxo, enquanto que o plasmídeo contendo o promotor Oct-4 de eqüino (sequência equivalente à de humanos) produziu menos células GFP positivas (>3%) com IF >1000, quando... / The pluripotency transcription factor Oct-4 is well conserved among species and is known to be expressed in embryos and embryonic stem (ES) cells; it is being an important pluripotency marker. It was recently demonstrated that the combination of Oct-4 with three other factors Klf-4, c-myc and Sox2 were able to reprogram somatic cells to a pluripotent and undifferentiated state. These cells known as induced pluripotent stem (iPS) cells share several properties with ES cells including self-renewal, proliferation and pluripotency. The aim of this study was to assess the functionality of the horse Oct-4 promoter in mouse ES cells. Three plasmids vectors expressing GFP (green fluorescent protein) under the control of the horse, mouse and four lentivirus vectors also containing reporter gene GFP and horse, mouse and human promoters, pLZ2-ecOCT-EGFP (mouse sequence equivalent), pLZ2-ecOCT-EGFP (human sequence equivalent), pLZ2-mOCT-EGFP and pLZ2-hOCT-EGFP, respectively, were built. All these vectors also contain a blasticidin resistance cassette to allow selection of transfected stable cells and transduced cells. Afterwards, to assess the functionality of the Oct-4 promoter all plasmids were tranfected the into transient and stable mouse ES cells. Constructs with mouse, human and horse (mouse analog sequence) Oct-4 promoter produced only 6% GFP positive cells with fluorescence intensity (FI)>1000 by 20 FACs assay, while plasmid horse (human analog sequence) Oct-4 promoter produced less GFP positive cells (>3%) with FI>1000, when compared with the positive control and among groups. However, GFP expression was not present in stable cells, whereas there were Blasticidin-resistant colonies-forming from 6 days post-transfection. To optimize the system in mouse ES cells, pLZ2-mOCT-EGFP and pLZ2-hOCT-EGFP lentivectors, were tested as controls. It was used HIV-1-derived... (Complete abstract click electronic access below)

Células tronco embrionárias (CTE) são capazes de proliferar indefinidamente mantendo a sua pluripotência, isto é, a capacidade de se diferenciar em diversos tipos celulares perante estímulos adequados. Esse potencial tem sido intensamente estudado, de modo a permitir a utilização dessas células em terapias de reposição celular. Trabalhos anteriores demonstraram que as proteínas kinases C (PKC) são importantes moduladores moleculares de cascatas de sinalização que levam ao processo de proliferação e auto-renovação das CTE. Porém o papel exato das diferentes isoenzimas das PKCs ainda não foi elucidado. Isso ocorre porque a família das PKCs é composta por pelo menos dez isoenzimas e apenas, recentemente, desenvolveram-se moduladores específicos para as diferentes isoenzimas, o que permitirá estudar o papel específico dessas quinases. No presente trabalho verificamos que a ativação da PKCδ induziu a proliferação de CTE indiferenciadas sem induzir a diferenciação das mesmas. Para tentar elucidar as vias de sinalização mediadas pela PKC&#948 que levam à proliferação das CTE indiferenciadas realizamos estudos de fosfoproteômica o que possibilitou a identificação de potenciais alvos diretos e indiretos da PKC&#948. Dentre os alvos identificados foram encontradas diversas proteínas relacionadas com proliferação, transcrição, tradução e resposta ao stress (chaperonas), contribuindo para a hipótese de que a ativação da PKCδ leva à proliferação das CTE indiferenciadas. Em diversos sistemas, a ativação da PKCδ leva à ativação da MAPK, em particular das ERK1/ 2, sendo essa via capaz de induzir a proliferação de diversas linhagens celulares. Identificamos diversas proteínas alvos da PKC&#948, que interagem também com componentes da via das MAPKs. Desta forma, verificamos a influência da ativação da PKC&#948 na via das MAPKs. De fato, a ativação da PKC&#948 na linhagem de CTE murinas indiferenciadas, E14TG2a, ativou a MEK, ERK1/ 2 e o fator de transcrição ELK-1. Como estudos anteriores demonstraram que a inibição da ERK1/ 2 mantém CTE indiferenciadas e que a ativação desta via poderia levar à diferenciação de CTE, investigamos a cinética de ativação da ERK pela PKC&#948. Demonstramos que a ativação da ERK pela PKC&#948 se da de modo transiente e que apesar da PKC&#948 não translocar para o núcleo, sua ativação induz a fosforilação e translocação nuclear da ERK, que atuará na fosforilação do fator de transcrição ELK-1. Desta forma, concluímos que a PKC&#948 induz a proliferação das CTE murinas indiferenciadas ativando transitoriamente a via das ERK1/ 2, que translocam para o núcleo fosforilando fatores de transcrição como a ELK1 e levando possivelmente ao aumento de proliferação dessas células. A ativação transiente das ERK1/ 2 pela PKC&#948 é importante para a auto-renovação das CTE. / Embryonic stem cells (ESC) are able of proliferating indefinitely maintaining their pluripotency, which is the capability to differentiate in different cell types upon appropriate stimuli. Pluripotency has been intensely investigated in order to allow the use of these cells in cellular replacement therapies. Previous work has demonstrated that the serine/ threonine kinases, such as, Protein kinases C (PKC) are important modulators of signaling cascades that lead to the process of proliferation and self-renewal of ESC. However, the exact role of the different PKC isoenzymes still remains to be elucidated. Due to the fact that the PKC family is composed of at least ten different isoenzymes and only recently isoenzyme specific modulators have been developed, which now allows the elucidation of these kinases roles. In the present work we verified that activation of PKC&#948 induced undifferentiated ESC have their proliferation rate increased. Trying to elucidate the signaling pathways mediated by PKC&#948 that lead to the proliferation increase we performed phosphoproteomic studies to identify potential PKC&#948 targets. Between the targets identified we found several proteins related with proliferation, protein transcription, translation and stress response (chaperones). These targets contributed to the hypothesis that PKC&#948 activation leads to undifferentiated ESC proliferation. In different cell lines, PKC&#948 activation leads to MAPK activation, through ERK1/ 2 activation, which are frequently involved with cellular proliferation. We also identified several targets of PKC&#948 that Interact with several components of MAPK`s signaling cascade. PKC&#948 activation in murine undifferentiated ESC line, E14TG2a, led to MEK, ERK1/ 2 and the transcription factor Elk-1 activation. Some articles demonstrate that the inhibition of ERK1/2 are responsible to maintains ESC undifferentiated and that it`s activation could lead to ESC differentiation. Analysing the kinetics of ERK activation in the ESC by PKC&#948, we show that ERK activation was transient and despite the fact that PKC&#948 does not translocated to the nucleus upon activation, but induces ERK activation and it`s nuclear translocation, where ERK could phosphorylate the transcription factor Elk-1. In conclusion PKC&#948 induces undifferentiated murine ESC proliferation increase by a transient ERK activation and it`s nuclear translocation.

Chez les cellules eucaryotes, la transcription est réalisée par les ARN polymérases I, II et III. L’ARN polymérase III (Pol III) transcrit des petits ARNs non codants tels que les ARNt, l’ARN U6, l’ARNr 5S et certains microARN. Il a été montré précédemment que l’augmentation de l’activité transcriptionnelle de la Pol III était associée à la transformation tumorale. Au sein du laboratoire, nous avons décrit une nouvelle sous–unité de la Pol III, RPC32α, qui met en évidence l’existence de deux isoformes de la Pol III humaine : la Pol IIIα et la Pol IIIβ. La sous-unité RPC32β, présente dans la Pol III, est exprimée de façon ubiquitaire et parait comme essentielle pour la croissance cellulaire. La sous-unité RPC32α n’est pas essentielle pour la survie cellulaire et son expression est limitée aux cellules souches non différenciées et aux cellules tumorales. De plus, l’expression ectopique de RPC32α induit la transformation tumorale des cellules fibroblastes IMR90 et change totalement l’expression de nombreux transcrits Pol III mais aussi d’autres ARNm impliqués dans la tumorogenèse (Haurie et al., 2010). Les travaux décrits dans ce manuscrit ont eu pour but de mieux caractériser et comprendre les deux isoformes de la Pol III humaine. Nous avons purifié les Pol IIIα et Pol IIIβ afin d’identifier tous les composants protéiques des deux isoformes du complexe. Au cours de cette étude nous avons observé que des modifications post-traductionnelles de RPC32α semblaient jouer un rôle déterminant dans la capacité oncogénique de la Pol IIIα. Pour comprendre par quel mécanisme moléculaire les Pol IIIα et Pol III pouvaient influencer l’expression de transcrits Pol II, notamment lors de la transformation cellulaire induite par l’expression de RPC32α, nous avons étudié cette régulation lors de la surexpression des deux sous unités paralogues. Ainsi, nous avons mené des analyses ciblées révélant la régulation de certains gènes impliqués dans le développement, la différenciation et la tumorogenèse. Nous avons également essayé de décrire les changements d'expression des gènes au niveau globale en utilisant la technologie des puces à ADN. Cette approche innovante et puissante nous a permis d’obtenir une vision d’ensemble des transcrits Pol II différentiellement régulés lors de la surexpression de RPC32α et RPC32β Nous avons pu apprécier l’impact de la Pol III pour le développement embryonnaire, la différenciation cellulaire, la survie de la cellule, la prolifération tumorale ou encore à la réponse immunitaire innée. Les résultats de cette étude qui demandent à être confirmés ouvrent des voies de recherches particulièrement intéressantes qui mériteront d’être approfondies dans le futur / Transcription in eukaryotic nuclei is carried out by DNA-dependent RNA polymerases I, II, and III. Human RNA polymerase III (Pol III) transcribes small untranslated RNAs that include tRNAs, 5S RNA, U6 RNA, and some microRNAs. Increased Pol III transcription has been reported to accompany or cause cell transformation. In the laboratory, we described a Pol III subunit (RPC32β) that led to the demonstration of two human Pol III isoforms (Pol IIIα and Pol IIIβ). RPC32β-containing Pol IIIβ is ubiquitously expressed and essential for growth of human cells. RPC32α-containing Pol IIIα is dispensable for cell survival, with expression being restricted to undifferentiated ES cells and to tumor cells. In this regard, and most importantly, ectopic expression of RPC32α in fibroblast IMR90 enhances cell transformation and dramatically changes the expression of several tumor-related mRNAs and that of a subset of Pol III RNAs. These results identify a human Pol III isoform and isoform-specific functions in the regulation of cell growth, the differentiation and transformation. (Haurie et al., 2010).The work described in this manuscript enables identification and understanding the function of the two human Pol III isoforms. Pol IIIα and Pol IIIβ are purified in order to describe all the protein components of the two Pol III complex. During this study, we observed that post-translated modifications of RPC32α seem to have a crucial function in oncogenic capacity of Pol IIIα. To understand how Pol IIIα and Pol IIIβ can affect Pol II RNA expression, in particular during cell transformation induced by RPC32α, we studied this regulation during the overexpression of the two paralogue subunits. We performed focused analysis, this study revealed the regulation of certain genes involved in the development, the differentiation and the tumorigenesis. We also tried to describe global gene expression modification using microarray technology. This new and powerful approach enables to obtain a global view on mRNA regulation by overexpression of RPC32α and RPC32β. We observed the effect of Pol III on embryo development, cell differentiation, cell survival, tumor proliferation and on innate immune response. The results of this study need further confirmation pave the way for interesting projects which are worth going into detail for the future.

Le séquençage du génome humain, il y a maintenant 12 ans, a mis en lumière la complexité des mécanismes des processus nucléaires tels que la transcription, la réplication ou l'organisation de la chromatine. Depuis, afin de mieux comprendre ces processus, un ensemble sans cesse croissant de données sur le noyau cellulaire a été produit et mis en ligne par un nombre important de laboratoires de par le monde. Ces données sont à la fois d'une richesse extraordinaire et d'une complexité embarrassante. Dans cette thèse, nous mettons à profit l'ensemble de ces données afin de mieux comprendre les déterminants nucléaires du programme spatio-temporel de réplication. Pour cela nous utilisons pas moins d'une centaine de profils épigénétiques ChiP-seq le long des chromosomes humains et dans diverses lignées cellulaires pour caractériser la structure primaire de la chromatine. Nous démontrons, à l'aide d'outils issus des statistiques multivariées, que l'immense complexité potentielle de ces jeux de données peut être réduite à quatre états chromatiniens principaux et ce dans toutes les lignées cellulaires somatiques étudiées. Cette classification simple, robuste et néanmoins complète est un excellent point d'appui pour l'étude de la réplication. Les quatre états principaux de chromatine sont répliqués à des moments distinct de la phase S (leur « timing » de réplication est différent) et ont un contenu en gènes drastiquement différents. Leur répartition spatiale le long du génome est structurée et est particulièrement visible dans les domaines où le « timing » de réplication dessine un U comme signature de l'existence d'un gradient de polarité des fourches de réplication. Ces U-domaines de la taille du Mpb recouvrent 50% du génome humain et les quatre états chromatiniens principaux se succèdent du bord au centre de ces U-domaines. Les mêmes techniques statistiques appliquées au cas d'une lignée embryonnaire révèlent aussi l'existence de quatre états principaux de chromatine mais de nature différente. La classification en quatre états s'avèrent alors très utile pour comparer l'épigénétique d'une lignée somatique à celle d'une lignée embryonnaire. Aussi, les spécificités du programme de réplication embryonnaire sont mises en rapport avec les spécificités de l'organisation de la chromatine dans cette lignée cellulaire. En particulier, notre étude révèle le rôle majeur de l'histone variant H2AZ dans la pluripotence. / The sequencing of the human genome, twelve years ago, revealed the complexity of the mechanisms underlying nuclear process such as transcription, replication and chromatin organization. In the past few years, to delineate better these processes, datasets on the cell nucleus were gathered and made available online by numerous laboratories around the world. These datasets are, at once, extraordinarily rich and daunting to handle. In this thesis, we take advantage of these datasets to understand better the nuclear determinants of the replication program. We analyze not less than a hundred ChiP-seq profiles along human chromosomes in several cell lines to characterize the primary structure of chromatin. We demonstrate, when using tools from multivariate statistics, that the immense potential complexity of these datasets can be reduced to four prevalent chromatin states in all studied somatic cell lines. This simple and comprehensive classification is an excellent starting point for the study of replication. The four prevalent chromatin states are replicated at different moments of the S-phase (they have a different replication “timing”) and have drasticaly different gene contents. Their spatial repartition along the genome is structured, especially in domains where the timing replication is U-shaped. These megabase sized U-domains cover 50% of the human genome and the four prevalent chromatin states succeed each other from their borders to their center. The same statistical techniques applied on an embryonic stem cell (ESC) also reduced the epigenetic complexity to four prevalent chromatin states which are qualitatively different from the ones in somatic cells. We further show that the specificities of embryonic replication program are link to the specificities of embryonic chromatin. Importantly, our study reveals that the histone variant H2AZ plays a major role in pluripotency.

No description available.

This thesis addresses the puzzle of variation in first-generation regulatory policies for controversial science and technology, as demonstrated in the cases of agricultural genetically modified organisms (GMOs) and human embryonic stem cell research in the United Kingdom and the United States. Why did policy outcomes vary in each technology case? This study answers this question by placing greater emphasis on institutional factors. Although works within institutional analysis, bureaucracy and regulation literatures make significant progress in revealing how existing institutions can shape outcomes, how far one can characterize bureaucratic behavior and whether interest groups capture regulation, they nevertheless create an opening for research that: describes a mechanism for path dependence to explain variation in policies; shows the degree to which bureaucratic behaviors can influence outcomes; and, highlights instances in which regulatory officials hold power. This thesis makes an original contribution by providing new historical details relating to these cases, and by providing an extensive elaboration of Pierson’s criteria for increasing returns and a so-called secondary test of path dependence to explain outcomes. The study recounts the biography of key policy documents in each case by tracing the process of decision-making through government and archival sources, secondary literature and more than 40 elite interviews. In doing so, it details the activities of key governmental bodies within the European Union, UK and US. Moreover, it shows how the Coordinated Framework (1986) and Human Fertilisation and Embryology Act 1990 framework represented decision-making structures which triggered changes in actors and interests and shaped permissive outcomes for GMOs and stem cell research in the US and UK, respectively. Furthermore, lack of comparable structures may help account for restrictive policies for GMOs in Europe and the UK, and for stem cell research in the US.