Les amplificateurs (aussi appelés par le terme anglais enhancers) ont été initialement identifiés comme des séquences d'ADN agissant en cis qui augmentent la transcription d'une manière qui est indépendante de leur orientation et de leur distance par rapport au site d’initiation de la transcription. En outre, les gènes d'identité cellulaire sont souvent associés à des regroupements ou clusters d’enhancers, structures également appelées super-enhancers, censés assurer une régulation correcte de l'expression des gènes tout au long du développement et de la différenciation des cellules. Pour mieux comprendre la régulation des gènes à partir de ces réseaux régulateurs complexes, nous avons étudié la régulation du gène Ikzf1 qui code pour un facteur de transcription essentiel à la différenciation lymphoïde et également impliqué dans la leucémogenèse. En combinant différents types de données épigénomiques, nous avons privilégié l’étude d’un élément enhancer situé à 120 kb en amont du gène Ikzf1. Nous avons trouvé que la délétion de l'enhancer IkE120 entraine une réduction significative de l'ARNm d’Ikzf1. Cependant, nous avons observé que la transcription immature ainsi que l’usage des promoteurs et exons alternatifs d’Ikzf1 sont différemment affectée dans les cellules délitées par IKE120. Ces résultats semblent indiquer que l'élément IkE120 pourrait avoir des fonctions supplémentaires au-delà de la seule régulation de l'initiation de la transcription. / Enhancers were originally identified as cis-acting DNA sequences that increase transcription in a manner that is independent of their orientation and distance relative to the RNA start site. In addition, cell identity genes are often associated with cluster of enhancers, also termed super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. To better understand gene regulation based on these complex regulatory networks, we studied the regulation of the Ikzf1 gene which encoded for a lymphoid-specific transcription factor essential for lymphoid differentiation and also involved in leukemogenesis. By combining different epigenomics data sets we prioritize an enhancer element located 120 kb upstream the IKZF1 gene. We found that deletion of the E120 enhancer resulted in significant reduction of Ikzf1 mRNA. However, we observed that immature transcription, promoter and exon usage were differentially affected in the IKE120-deleted cells. The results indicated that E120 element might have additional functions over solely regulating transcription initiation. We suggest that expression of some tissue-specific and cell identity genes might, at least partially, be regulated at the level of mRNA maturation and that components of enhancer’s clusters are directly involved in this process.

Many developmental genes are located in gene-poor genomic regions and are activated by long-range enhancers located up to 1Mb away. Modification and reorganisation of chromatin structure is pivotal to such long-range gene regulation. A prerequisite for enhancer activity is the binding of transcription factors and co-factors with the interplay between activating and repressive factors determining tissue, spatial and temporal specificity. Spatiotemporal control of sonic hedgehog (Shh) and the 5′ Hoxd genes (especially Hoxd13) is crucial for vertebrate limb anterior-posterior (A-P) axis and autopod patterning. Shh tissue specificity is controlled by multiple enhancers throughout an adjacent gene desert. The ~0.8Mb-distant limb enhancer (ZRS) bypasses nearby genes to activate only Shh. In contrast, limb-specific HoxD expression is regulated by multiple enhancers, with the ~200kb-distant global control region (GCR) regulatory element the most characterised. In this thesis I investigated the mechanisms of ZRS and GCR regulation of Shh and Hoxd13 respectively. The model system used was immortalised cell lines derived from the anterior and posterior distal forelimb buds of E10.5 and E11.5 mouse embryos. Cell line data were confirmed in dissected limb tissue. Increased expression of the 5′ Hoxd genes, particularly Hoxd13, correlated with the loss of the repressive, polycomb catalysed, histone modification H3K27me3 and decompaction of chromatin structure over the HoxD locus at the distal posterior forelimb bud at stage E10.5. Moreover, I show that the GCR spatially co-localises with the 5′ HoxD locus at the distal posterior region of E10.5-11 embryos. These data are consistent with the formation of a chromatin loop between Hoxd13 and the GCR at the time and place of distal limb bud development when the GCR is required to initiate 5′ Hoxd gene expression. This is the first example of A-P differences in chromatin compaction and local folding in the limb. Point mutations within the ZRS cause ectopic (anterior) Shh expression, which results in preaxial polydactyly (PPD). The ZRS contains multiple canonical ETS transcription factor binding motifs, and point mutations in two families with PPD results in the formation of additional ETS binding sites. The point mutations cause the loss or reduction of ETV4/5 transcription factor binding at a non-canonical ETS binding site and enable additional binding instead of ETS1. I show that ETV4/5, ETS1 and another ETS protein GABPα all bind to the ZRS. This work has revealed the differential effect on Shh expression of two groups of ETS factors mediated through the ZRS. The binding of ETS1/ GABPα determines the posterior Shh expression domain while ETV4/5 restricts anterior Shh expression. Two point mutations alter the ETS-binding profile, creating an additional ETS1/ GABPα site that is sufficient to drive ectopic Shh expression. DNA FISH on E11.5 forelimb and floorplate tissue sections revealed that the Shh-ZRS genomic locus is in a compact chromatin conformation in both Shhexpressing and non-expressing cells. However, I show that the ZRS co-localises with Shh to a significantly greater extent in the distal posterior limb bud and the floorplate compared with cells where Shh is not expressed. This thesis presents novel research into long-range gene regulation during limb development, elucidating the role of chromatin re-organisation and how spatial-specific enhancer activity is determined by opposing sets of binding factors.

No description available.

Transdermal drug delivery system is in the centre of attention in recent years. For efficient dermal drug delivery the drug has to overcome the barrier of the outermost layer of the skin, the stratum corneum. For facilitating dermal drug transport, the barrier properties of the stratum corneum can be varied by applying chemical penetration enhancers. The aim of this work was to characterize various penetration enhancers and investigate their mechanism of action. We combined well established techniques like differential scanning calorimetry (DSC) and infrared spectroscopy (IR) with confocal Raman microscopy (CRM) as an upcoming technique in skin research. CRM offers the possibility of label-free and non- destructive, chemically selective analysis of stratum corneum lipids and proteins. We used isolated human stratum corneum for incubation with the penetration enhancers. As a novel approach, the samples of treated stratum corneum were freeze dried to avoid any discrepancies which might come up with differences in the hydratation state of stratum corneum (SC). Furthermore, the structure of lipids and proteins in the stratum corneum was analyzed. In our study, stratum corneum was treated with dimethyle sulphoxide, propylene glycol, ethylene glycol, ethylene glycol-d4 and oleic acid. We observed that...

The vertebrate nervous system arises during embryogenesis from an epithelial sheet of cells called the neural plate that subsequently folds to become a rod of cells called the neural tube. Several signaling pathways act on the neural progenitors of the neural tube to give rise to the diverse set of neurons and glia that will make up the spinal cord and brain in adulthood. In vertebrates, Muscle segment homeobox (Msx) genes are expressed in the dorsal neural tube during development, and pattern dorsal neural progenitors to give rise to dorsal neuronal subtypes. Additionally, Msx genes are involved in the regulation of neurogenesis and proliferation in the neural tube. In zebrafish, three msx genes are expressed in the neural tube: msx1a, msx1b, and msx3. The Akimenko lab has identified a potential enhancer of msx3 called Fragment C that drives expression in the dorsal neural tube. We hypothesized that Fragment C is a bona fide enhancer of msx3 specifically in the neural tube, and that this enhancer contributes toward proper patterning and neurogenesis/proliferation in the developing neural tube of zebrafish. To test this hypothesis, I have generated zebrafish mutants with a deletion of the Fragment C enhancer using CRISPR/Cas9 that also have a transgenic Fragment C enhancer driving reporter expression of enhanced green fluorescent protein (Egfp). The deletion of Fragment C abolishes msx3 expression in the neural tube excluding the dorsal-most cells likely corresponding to the roof plate. The spatial domain in which msx3 is lost corresponds to where Fragment C drives expression in the neural tube, suggesting that Fragment C contains an enhancer of msx3. This domain of expression corresponds to where dorsal neural progenitors reside. Analysis of markers for the cells with Fragment C-driven Egfp expression shows that at least some of these cells are indeed neural progenitors, many of which give rise to neurons during embryonic and larval development. The deletion of Fragment C and loss of msx3 expression in neural progenitors did not affect the numbers of neurons or neural progenitors amongst cells with Fragment C-driven expression, nor did it affect the dorsoventral location of cells in the neural tube. Taken together, we conclude that Fragment C-driven msx3 expression does not contribute to the dorso-ventral position of neural progenitors nor the balance of proliferation and neurogenesis in the developing neural tube. However, a role for msx3 in regulating neural progenitor identity along the dorso-ventral axis without affecting progenitor position cannot be ruled out.

Les Facteurs de transcription du groupe PEA3 (Pea3, Erm et Er81) font partie de la famille d’oncogènes ETS. Leur expression est souvent observée lors de la mise en place des organes par morphogenèse de branchement tels que les poumons ou encore la glande mammaire. De plus une expression aberrante de ces facteurs de transcription est corrélée au caractère cancéreux de nombreux tissus tels que le côlon, les poumons ou encore le sein. Ainsi, l’expression d’Erm dans les tumeurs du sein est associée à un mauvais pronostic pour les patientes et celle de Pea3 constitue un marqueur de l’agressivité tumorale. Enfin, en qualité de facteur de transcription Pea3 module l’expression de gènes spécifiques alors appelés gènes cibles. Même si certains de ces gènes sont déjà bien caractérisés beaucoup de choses restent à faire pour comprendre les mécanismes moléculaires régulés par Pea3. Dans ce contexte lors de ma thèse je me suis intéressé à l’étude du rôle du facteur de transcription Pea3 dans les processus de morphogenèse et de tumorigenèse mammaires selon deux approches complémentaires : 1- l’étude des propriétés morphogénétiques modulées par Pea3 lors des étapes de morphogenèse et de tumorigenèse mammaires, 2- la recherche et la caractérisation de gènes régulés par Pea3 dans ce même contexte, par une analyse transcriptomique à grande échelle en utilisant des puces à ADN. Ces deux points sont développés grâce à l’utilisation de modèles cellulaires dans lesquelles nous modulons l’expression de Pea3. Les cellules épithéliales mammaires TAC 2.1 modèle de morphogenèse mammaire dans lesquelles nous surexprimons Pea3 et les cellules mammaires transformées MMT, modèle de tumorigenèse mammaire dans lesquelles nous inhibons l’expression du facteur de transcription Pea3. Au cours de ma thèse nous avons ainsi pu montrer l’importance du facteur de transcription Pea3 dans le contrôle des propriétés de migration, d’invasion et de prolifération des cellules cancéreuses TAC et MMT. En accord avec ces données, la recherche des gènes dont l’expression est régulée par Pea3 dans nos deux modèles cellulaires suite à la modulation de Pea3, a permis d’identifier de nombreux gènes capables de réguler la prolifération, la migration et l’invasion des cellules. Parmi ces gènes nous nous sommes intéressés au gène cycline d2 bien connu pour son implication dans le contrôle de la progression du cycle cellulaire. Nous avons pu montrer que le gène cycline d2 est un gène cible direct du facteur de transcription Pea3 qui module l’expression dans le modèle cellulaire TAC des deux transcrits (cycline d2 et cycline d2 trc) issus de ce gène et décrits à ce jour. L’étude de la fonction des protéines Cycline D2 et Cycline D2 Trc dans les cellules TAC a été entreprise. Tout d’abord la surexpression de l’une ou l’autre de ces isoformes dans les cellules TAC 2.1 modifie de façon opposée leur capacité à s’organiser dans un gel de collagène mimant l’environnement d’une glande mammaire, la Cycline D2 réprimant cette capacité et la Cycline D2 Trc l’augmentant. L’utilisation de petits ARN interférents permettant de réprimer l’expression de ces deux protéines a permis de montrer une relation fonctionnelle, toujours opposée, des deux isoformes avec le facteur de transcription Pea3 pour le contrôle de la progression du cycle cellulaire mais aussi pour l’induction d’une transition épithélio-mésenchymateuse étroitement reliée au pouvoir de migration des cellules épithéliales lors du développement des organes comme la glande mammaire mais aussi lors de la progression tumorale. Notre étude a ainsi permis de mieux définir l’implication du facteur de transcription Pea3 lors des événements de morphogenèse et de tumorigenèse de la glande mammaire. De plus elle ouvre la réflexion sur le rôle du gène cycline d2 lors de ces événements. / "Proteins of the PEA3 group (Pea3, Erm and Er81) belong to the ETS family of transcription factors. They are expressed in organs that undergo an epithelial branching morphogenesis process such as the lungs and the mammary gland. Moreover, in these organs, they are aberrantly expressed during cancer progression. Indeed, during breast cancer high Pea3 or Erm expression is respectively associated with cancer metastatic potential and a lower patient survival rate. Finally, as transcription factors they control the expression of specific genes called target genes. Even though some of these genes are known, more work is needed to understand the molecular mechanism governed by the PEA3 transcription factors. The main topic of my PhD is the study of the role of the Pea3 transcription factor during mammary morphogenesis and tumorigenesis using two complementary approaches: 1- characterize the morphogenetic properties that are controlled by Pea3 during the mammary morphogenesis and tumorigenesis events 2- find and characterize the genes that are regulated by Pea3 using a large scale transcriptomic analysis based on a microarray technology. The strategy is based on the utilization of two main cell lines in which we modulate Pea3 expression: an epithelial cell line, model of mammary morphogenesis (TAC 2.1) in which we overexpress Pea3 and a cancer cell line, model of mammary tumorigenesis (MMT) in which Pea3 expression is knocked down by means of small interfering RNA sequences. During my PhD we showed that Pea3 controls the proliferation, invasion and migration properties of TAC 2.1 and MMT cells. In agreement with these data, the transcriptomic analysis after Pea3 expression modulation in these cells (overexpression or knockdown) demonstrate that a large proportion of the Pea3 regulated genes are already known players in the regulation of the proliferation, invasion and migration processes. Amongst these genes, we focused on the cyclin d2 gene which is a well characterized actor in cell cycle progression and cell proliferation. We showed that cyclin d2 is direct Pea3 target gene. The cyclin d2 gene gives rise to two different isoforms generated by a splicing event (Cyclin D2 and Cyclin D2 Trc) that are both regulated by Pea3 at the mRNA and protein levels. We then evaluated the function of these two isoforms in the mammary epithelial cell line TAC 2.1. Overexpression of these proteins in the TAC2.1 cells leads to a modification, in an opposite fashion, of their ability to grow and organize in 3D structures within a collagen envirronement. The Cyclin D2 and the Cyclin D2 Trc respectively repressing and enhancing these abilities. The use of small interfering RNA sequences targeting specifically one or the other isoform allowed us to show a functional link between both isoforms and the Pea3 transcription factor , again in an opposite way, especially during cell cycle progression and during epithelial to mesenchymal conversion, a hallmark of development and cancer progression. Thus, this study gives new clues to understand the involvement of the Pea3 transcription factor during mammary morphogenesis and tumorigenesis, events in which the cyclin d2 gene seems to be a major player. The characterization of the molecular events governed by Pea3 should help in defining new therapeutic strategies against breast cancer progression. "

Human cytomegalovirus infects approximately 50% of adults in the United States and in most cases is asymptomatic. However, in the case of immune compromised persons such as AIDS patients, transplant patients, and newborn babies, life threatening CMV disease can occur. The HCMV major immediate-early enhancer functions as a master regulatory switch, whose activation is essential for the expression of the major IE transactivating proteins, IE1 p72 and IE2 p86. While critical to the viral lifecycle, regulation of MIE enhancer activation is very complex and not yet fully understood. I characterized the role of cis-acting partners within the MIE enhancer that function to strengthen MIE gene expression and discovered a novel mode of post-IE enhancer regulation. These results add significantly to our understanding the inner workings of the HCMV MIE enhancer/promoter in lytically infected cells. The distal portion of the MIE enhancer is composed of two functionally redundant segments, which are necessary for MIE gene expression at low multiplicity of infection (MOI). Using an unbiased genetic approach I identified a previously unrecognized cis-acting TGGGCA/G repeat that is inextricably linked to GC-box repeats, which together form an enhancer-spanning network. This network of elements (TG network) is conserved in nonhuman primate CMV MIE enhancers. HCMV constructs lacking the entire enhancer TG network inadequately sustain MIE gene expression at low MOI at post-immediate early (IE) times of infection (≥8 h pi). An MIE enhancer-specified mode of post-IE regulation has not been described before and suggests a cis-regulatory code specialization that has evolved to sustain rather than to initiate MIE gene expression. I hypothesized that another cis-acting element(s) function together with the TG network to form a multi-network system that senses and integrates a variety of cellular environmental signals to modulate efficiency in the initiation and/or maintenance of MIE enhancer-dependent gene expression. Using recombinant viruses with mutations in either the cyclic AMP response element (CRE) network, NFkB network, TG network, or a combination of these networks, I show that the TG-C and TG-K partnerships are the most important for conferring the greatest level of MIE enhancer-dependent MIE gene expression, frequency and size of viral plaques in HFF cells, while the TG-K partnership is most important to DNT-2 cells. Additionally, I conclude that the C-K partnership functions through an alternate mechanism than that of the TG network. Together these results suggest that the strength of enhancement by cis-acting network pair interactions forms a multi-network system that modulates efficiency of MIE enhancer-dependent gene expression and which differs in relation to cell type during lytic infection.

No description available.

Eukaryote DNA is organised into the more compact nucleosome by wrapping 147bp of DNA around a histone octamer core. The N-terminal tails of the histones protrude through the DNA and can be modified by a variety of enzymes. Acetylation of Histone 4 Lysine 16 (H4K16ac) is an important modification associated with an increase in transcription, and in flies is an important component of the doseage compensation system. It is also unique amongst histone modifications in that it has been directly associated with chromatin decompaction. H4K16ac has been linked to development through its Histone Acetyltransferase, MOF. Deletion of MOF in mice leads to mass chromatin defects, and embryonic lethality prior to the blastocyst stage. I set out to understand the role of H4K16ac in differentiating Embryonic Stem cells (ES cells) and chromatin compaction in vivo. I generated a ChIP-seq profile for H4K16ac in undifferentiated ES cells, and after 3 days of retinoic acid (RA) differentiation. This revealed an association of H4K16ac with the promoters of transcribed genes in pluripotent ES cells, followed by loss H4K16ac on ES cell specific genes and gain of the modification on differentiation specific genes. There were some silent genes in ES cells, however, which were acetylated on their promoters. Through this study I also found that H4K16ac and MOF mark active enhancers in ES cells, along with H3K4me1 and H3K27Ac and p300. H4K16ac did not mark a known regulatory region in limb cells, and it is possible that it marks active enhancers only of ES cells. Furthermore, I looked at the compaction state large regions (>100kb) which lost H4K16ac upon differentiation by FISH, to determine if loss of H4K16ac could predict compaction. The regions selected showed no change in compaction state between UD and D3 cells, meaning that loss of H4K16ac does not directly lead to chromatin compaction in vivo. However loss of H4K16ac may be necessary for any subsequent compaction, or the change in compaction may take place at nucleosomal level. Finally, I attempted both to overexpress and reduce the level of MOF in ES cells. I was unable to manipulate the level of MOF in this cell type in either direction; expression of endogenous MOF was silenced after very little time, and stable MOF shRNA cell lines showed no reduction in levels of MOF. Therefore, potentially, dosage of MOF/H4K16ac in this cell type is critical. This study may help to understand the significance of H4K16ac in ES cell differentiation and chromatin compaction.

L'identité et la réactivité cellulaires sont établies, maintenues et modulées grâce à l'orchestration de programmes transcriptionnels spécifiques. Les éléments régulateurs, des régions particulières de la chromatine responsables de l'activation ou de la répression des gènes, sont au coeur de cette opération. Ces dernières années, de nombreuses études ont révélé le rôle central des « enhancers » dans ce processus. En effet, des centaines de milliers « enhancers » seraient éparpillés dans le génome humain, majoritairement dans sa portion non-codante, et contrairement au promoteur, leur activation varierait selon le type ou l'état cellulaire ou en réponse à une stimulation physiologique, pathologique ou environnementale. Les « enhancers » sont, en quelque sorte, des carrefours où transitent une multitude de protéines régulées par les signaux intra- et extra-cellulaires et un dialogue s'établit entre ces diverses protéines et la chromatine. L'identification des « enhancers ainsi qu'une compréhension de leur mode de fonctionnement sont donc cruciales, tant au plan fondamental que clinique. La chromatine joue un rôle indéniable dans l'activité des éléments régulateurs, tant par sa composition que par sa structure, en régulant, entre autres, l'accessibilité de l'ADN. En effet, l'ADN des régions régulatrices est bien souvent masqué par un nucléosome occlusif, lequel doit être déplacé ou évincé afin de permettre la liaison des protéines régulatrices, notamment les facteurs de transcription (FTs). Toutefois, la contribution de la composition de la chromatine à ce processus reste incomprise. Le variant d'histone H2A.Z a été identifié comme une composante de la chromatine aux régions accessibles, dont des « enhancers » potentiels. Toutefois son rôle y est inconnu, bien que des études récentes suggèrent qu'il pourrait jouer un rôle important dans la structure de la chromatine à ces régions. Par ailleurs, un lien étroit existe entre H2A.Z et la voie de signalisation des oestrogènes (notamment la 17-[beta]-estradiol (E2)). Ainsi, H2A.Z est essentiel à l'expression de plusieurs gènes cibles de l'E2. Les effets de l'E2 sont en partie exercés par un FT, le récepteur alpha des oestrogènes (ER[alpha]), lequel se lie à l'ADN suite à son activation, et ce majoritairement à des « enhancers », et permet l'établissement d'un programme transcriptionnel spécifique. Cette thèse vise à définir le rôle d'H2A.Z aux « enhancers », et plus particulièrement son influence sur l'organisation des nucléosomes aux « enhancers » liés par ER[alpha]. D'abord, mes travaux effectués à l'échelle du génome ont démontré qu'H2A.Z n'est présent qu'à certains ER[alpha]-« enhancers » actifs. Cette particularité a fait en sorte que nous avons pu comparer directement les « enhancers » actifs occupés par H2A.Z à ceux non-occupés, afin de mettre en évidence sa relation à l'environnement chromatinien. Étonnamment, il est apparu qu'H2A.Z n'introduit pas une organisation unique ou particulière des nucléosomes aux « enhancers ». Par ailleurs, nos résultats montrent qu'H2A.Z joue un rôle crucial dans la régulation de l'activité des « enhancers ». En effet, nous avons observé que suite à leur activation par l'E2, les « enhancers » occupés par H2A.Z recrutent l'ARN polymérase II (ARNPII) et produisent un transcrit. Ils recrutent également RAD21, une composante du complexe cohésine impliqué, entre autres, dans des interactions chromosomiques entre « enhancers » et promoteurs. De façon intéressante, nous avons mis en évidence que ces trois évènements, connus pour leur importance dans l'activité des « enhancers », sont dépendants d'H2A.Z. Ainsi, la présence d'H2A.Z à l' « enhancer » pourrait permettre un environnement chromatinien favorable à trois aspects clés de l'activité des « enhancers » : la présence de l'ARNPII, la transcription et la formation d'une boucle d'interaction, et par la suite, de par la proximité « enhancer »-promoteur ainsi créée, augmenter la concentration d'ARNPII à proximité du promoteur favorisant l'expression du gène cible. Un tel rôle central d'H2A.Z dans l'activité d' « enhancers » spécifiques pourrait participer à un mécanisme épigénétique ciblé de la régulation de l'expression des gènes.