Ο μεταγραφικός παράγοντας COUP-TF είναι ένας ορφανός πυρηνικός υποδοχέας, ο οποίος είναι πολύ σημαντικός κατά την εμβρυική ανάπτυξη. Στην παρούσα εργασία επιχειρήθηκε η μελέτη του φυσιολογικού ρόλου του COUP-TFII των θηλαστικών κατά την αναγέννηση του σκελετικού μυός, χρησιμοποιώντας ως μοντέλο διαφοροποίησης τη μυοβλαστική σειρά ποντικού C2C12, που προέρχεται από ενήλικα βλαστικά κύτταρα του ίδιου μυός. Ο mCOUP-TFII εμπλέκεται στη ρύθμιση της ανάπτυξης του καρδιαγγειακού συστήματος, της μυογένεσης και άλλων αναπτυξιακών διαδικασιών. Έχει δειχθεί ότι αναστέλλει τη διαφοροποίηση των μυοβλαστών C2C12 σε μυοσωλήνες, κυρίως μέσω καταστολής της έκφρασης των μεταγραφικών παραγόντων μυογένεσης MyoD και Myogenin. Επίσης, η έκφρασή του στους μυοβλάστες C2C12 καταστέλλεται με την έναρξη της διαφοροποίησης. Αδημοσίευτα αποτελέσματα του εργαστηρίου μας, έχουν δείξει ότι μέσω εναλλακτικού ματίσματος στο mRNA του PlCOUP-TF του αχινού προκύπτουν δύο ισομορφές του υποδοχέα που διαφέρουν ως προς ένα εξώνιο 21 αμινοξέων στην DBD. H μικρή ισομορφή είναι λειτουργικός μεταγραφικός παράγοντας και δρα ως ομοδιμερές, ενώ η μεγάλη ισομορφή και τα ετεροδιμερή των δυο ισομορφών εμφανίζουν αδυναμία πρόσδεσης στο DNA. Με αυτόν τον τρόπο, η μεγάλη ισομορφή ρυθμίζει την ποσότητα του λειτουργικού μεταγραφικού παράγοντα, δρώντας ως επικρατής κατασταλτική πρωτεΐνη. Αρχικά, μελετήθηκαν οι ιδιότητες πρόσδεσης του mCOUP-TFII και η δυνατότητα σχηματισμού ετεροδιμερών με τη μεγάλη ισομορφή του PlCOUP-TF (L.I.) μέσω δοκιμής in vitro πρόσδεσης (EMSA), δεδομένης της ικανότητας ετεροδιμερισμού του hCOUP-TFI με την ομόλογη πρωτεΐνη του αχινού. Βρέθηκε ότι ο mCOUP-TFII δύναται να προσδεθεί στο στοιχείο απόκρισης C1R με τη μορφή ομοδιμερών και έχει ικανότητα ετεροδιμερισμού με τη PlCOUP-TF L.I. Τα ομοδιμερή του mCOUP-TFII εμφάνιζαν μειούμενη πρόσδεση στο DNA, όσο αυξανόταν ο λόγος PlCOUP-TF L.I./mCOUP-TFII. Ο απώτερος στόχος της έρευνας ήταν η μελέτη του ρόλου του mCOUP-TFII στη μυϊκή διαφοροποίηση, μέσω της υπερέκφρασης της επικρατούς κατασταλτικής PlCOUP-TF L.I. σε καλλιέργειες κυττάρων C2C12. Η αρχική μας υπόθεση ήταν ότι η PlCOUP-TF L.I. δύναται να δράσει ως επικρατής κατασταλτική ισομορφή του mCOUP-TFII, μέσω σχηματισμού μη λειτουργικού ετεροδιμερούς μαζί του. Σε αυτή την περίπτωση, θα αναμενόταν η PlCOUP-TF L.I. να καταστείλει τη δράση του ενδογενούς mCOUP-TFII των κυττάρων C2C12, με αποτέλεσμα την επαγωγή της διαφοροποίησης των μυοβλαστών. Αντιθέτως, η υπερέκφραση του mCOUP-TFII, θα αναμενόταν να συντελέσει στη διατήρηση της αδιαφοροποίητης κατάστασης των μυοβλαστών. Δεν παρατηρήθηκε διαφορά στις δράσεις των δυο COUP-TFs, ωστόσο, από τα πειράματα αυτά δεν μπορεί να εξαχθεί κάποιο ασφαλές συμπέρασμα αναφορικά με το ρόλο του mCOUP-TFII στη διαφοροποίηση των μυοβλαστών και τη δυνατότητα in vivo αλληλεπίδρασης μεταξύ των δυο υποδοχέων. / The transcription factor COUP-TF is an orphan nuclear receptor, which is very important during embryonic development. In the present dissertation, we attempted to study the physiological role of mammalian COUP-TFII during skeletal muscle regeneration, by use of the myoblast cell line C2C12, which originates from adult stem cells of skeletal muscle, as a model system of cell differentiation. mCOUP-TFII is involved in the regulation of cardiovascular system development, myogenesis and other developmental processes. It has been shown to inhibit the differentiation of C2C12 myoblasts to myotubes, mainly through suppression of the myogenic regulatory factors MyoD and Myogenin gene expression. Moreover, its expression in C2C12 myoblasts is suppressed at the onset of differentiation. Alternative splicing of the sea urchin PlCOUP-TF mRNA results in two isoforms, which differ by a 21 aa insertion in the DBD (unpublished data). The small isoform is a functional transcription factor that acts as a homodimer, while the large isoform and the heterodimers of the two isoforms fail to bind DNA. In this way, the large isoform regulates quantitatively the functional transcription factor, acting as dominant negative protein. Initially, by using in vitro binding assays (EMSA), we studied the binding properties of mCOUP-TFII and the possibility of forming heterodimers with the large isoform of PlCOUP-TF (L.I.), provided that hCOUP-TFI has been reported to be able to heterodimerize with the sea urchin homologue. We found that mCOUP-TFII is capable of binding the C1R response element as a homodimer and of forming heterodimers with PlCOUP-TF L.I. The binding of mCOUP-TFII homodimers has been shown to reduce as the ratio PlCOUP-TF L.I./mCOUP-TFII increases. The ultimate goal of this research, was the study of the role of mCOUP-TFII in muscle differentiation via overexpression of the dominant negative PlCOUP-TF L.I. in C2C12 cell cultures. Our initial assumption was that PlCOUP-TF L.I. is capable of acting as a dominant negative isoform of mCOUP-TFII, by forming non functional heterodimers with it. In this case, PlCOUP-TF L.I. would be expected to suppress the action of endogenous mCOUP-TFII in C2C12 cells. In contrast, overexpression of mCOUP-TFII would be expected to contribute to the maintenance of myoblasts in an undifferentiated state. We did not observe any difference in the actions of the two COUP-TFs, however, we cannot report any result regarding either the role of mCOUP-TFII in myoblast differentiation or the ability of in vivo interaction between these receptors.

Un nouveau facteur de transcription, appartenant à la famille des protéines à domaine bHLH, a récemment été isolé dans notre laboratoire. Initialement appelé « clone bc8 » puis HRT1, ce facteur présentait des similitudes avec les protéines Hairy and Enhancer of split qui interviennent notamment dans le phénomène d’inhibition latérale lors de la formation du tissu neural. Des études d’hybridation in situ réalisées chez l'embryon de xénope ont suggéré un rôle important de XHRT1, la protéine HRT1 de xénope, dans le développement neural. Nous avons recherché les partenaires protéiques de XHRT1 par la technique du double-hybride afin de mieux comprendre son mécanisme d’action moléculaire dans la neurogenèse. Tout d’abord nous avons construit les outils appropriés pour l’élaboration du travail, à savoir, les clones de levures exprimant les appâts spécifiques des domaines de la protéine étudiée et la création d’une banque d’ADNc du xénope au stade de la neurulation. Ensuite, trois criblages ont été réalisés. Dans le premier cas, nous avons recherché les partenaires des domaines bHLH et Orange (bHLH-O). Le domaine bHLH est en effet responsable de la dimérisation de ce type de protéine. Le domaine Orange qui suit le domaine bHLH, pourrait participer dans le choix du partenaire d’hétérodimérisation. Nous avons isolé deux facteurs de type bHLH-Orange apparentés à HRT1, XHairy1 et XHairy2b et confirmé leur interaction avec XHRT1. Les domaines impliqués dans ces interactions sont les bHLH-O pour les trois facteurs. Ce même criblage nous a permis d’isoler un nouvel ADNc qui code une protéine sans domaine apparent connu actuellement. Nous avons montré que cette protéine reconnaissait spécifiquement le domaine Orange de HRT1 mais pas celui des autres facteurs de type bHLH-O. Elle a été baptisée BOIP pour Bc8 Orange Interacting Protein. Le rôle physiologique de cette interaction n’a pu être démontré. Nous avons établi que la protéine BOIP pouvait aussi s’homodimériser. Nous avons aussi déterminé son profil d’expression chez le xénope et la souris. Son transcrit est hautement présent dans les testicules adultes. La protéine pourrait donc jouer un rôle important dans la spermatogenèse. Les deux autres criblages, utilisant les domaines situés dans la partie C-terminale de XHRT1, ont apporté des nouveaux partenaires potentiels, mais ces interactions n’ont pu être confirmées dans un système indépendant. Enfin, en étudiant plus en détail les interactions entre XHRT1 et XHairy1 ou XHairy2b, nous avons mis à jour une possible fonction de spécificité dans le choix du partenaire dans la région C-terminale de HRT1. La formation de ces dimères pourrait jouer un rôle dans la formation du tube neural mais également dans d’autres différenciations tissulaires.

In this study, full coding sequences of Atlantic salmon (Salmo salar L.) muscle genes were cloned, including myogenic regulatory factors (MRFs) (myod1c, myog, mrf4, myf5), inhibitors of Myostatin (fst, decorin), markers of myogenic progenitor cell (MPC) proliferation (sox8) and fusion (calpastatin), a marker of slow muscle fibre differentiation (smlc1) and a novel eukaryotic gene involved in regulating growth (cee). Several of these genes were then characterised using a range of experimental and computational analyses with the aim to better understand their role in myogenesis and their evolution in teleosts. A series of experiments supported previous findings that teleosts have extra copies of many genes relative to tetrapods as a result of a whole genome duplication (WGD) event that occurred some 320-350 Mya. For example, it was shown that genes for myod and fst have duplicated in a common teleost ancestor, but were then specifically lost or retained in different lineages. Furthermore, several characterised Atlantic salmon genes were conserved as paralogues, likely from a later WGD event specific to the salmonid lineage. Phylogenetic reconstruction and comparative genomic approaches were used to characterise the evolution of teleost paralogues within a framework of vertebrate evolution. As a consequence of one experiment, a revised nomenclature for myod genes was proposed that is relevant to all diploid and polyploid vertebrates. The expression patterns of multiple myogenic genes were also established in Atlantic salmon embryos using specific complementary RNA probes and in situ hybridization. For example, co-ordinated embryonic expression patterns were revealed for six salmon MRFs (myod1a, myod1b, myod1c, myog, mrf4, myf5), as well as markers of distinct MPC populations (pax7, smlc1), providing insight into the regulatory networks governing myogenesis in a tetraploid teleost. Furthermore, it was shown that Atlantic salmon fst1 was expressed concurrently to pax7 in a recently characterised MPC population originating from the anterior domain of the epithelial somite, which is functionally analogous to the amniote dermomyotome. In another experiment, the individual expression domains of three Atlantic salmon myod1 paralogues were shown to together recapitulate the expression of the single myod1 gene in zebrafish, consistent with the partitioning of ancestral cis-acting regulatory elements among salmonid myod1 duplicates. Additionally, the in situ expression of cee a novel and highly conserved eukaryotic gene was revealed for the first time in a vertebrate and was consistent with an important role in development including myogenesis. Additionally, Atlantic salmon were reared at 2, 5, 8 or 10 ºC solely to a defined embryonic stage, which was just subsequent to the complete pigmentation of the eye. After this time, animals were provided an equal growth opportunity. Remarkably, changing temperature during this short developmental window programmed the growth trajectory throughout larval and adult stages. While 10 and 8 ºC fish were larger than those reared at 2 and 5 ºC at the point of smoltification, strong compensatory growth was subsequently observed. Consequently, after 18 months of on growing, size differences among 5, 8 and 10 ºC fish were not significant, although each group was heavier than 2 ºC fish. Furthermore, significant embryonic-temperature induced differences were observed in the final muscle fibre phenotype, including the number, size distribution and myonuclear density of muscle fibres. A clear optimum for the final muscle fibre number was observed in 5 ºC fish, which was up to 17% greater than other treatments. In a sub-sample of embryos, temperature induced heterochonies were recorded in the expression of some MRFs (myf5, mrf4) but not others (myod1a, myog). These results allowed the proposition of a potential mechanism explaining how temperature can program the muscle phenotype of adult teleosts through modification of the somitic external cell layer, a source of MPCs throughout teleost ontogeny.

<p>The growing complexity of scientific research demands further development of advanced gene regulation systems. For instance, the ultimate goal of tissue engineering is to develop constructs that functionally and morphologically resemble the native tissue they are expected to replace. This requires patterning of gene expression and control of cellular phenotype within the tissue engineered construct. In the field of synthetic biology, gene circuits are engineered to elucidate mechanisms of gene regulation and predict the behavior of more complex systems. Such systems require robust gene switches that can quickly turn gene expression on or off. Similarly, basic science requires precise genetic control to perturb genetic pathways or understand gene function. Additionally, gene therapy strives to replace or repair genes that are responsible for disease. The safety and efficacy of such therapies require control of when and where the delivered gene is expressed in vivo.</p><p>Unfortunately, these fields are limited by the lack of gene regulation systems that enable both robust and flexible cellular control. Most current gene regulation systems do not allow for the manipulation of gene expression that is spatially defined, temporally controlled, reversible, and repeatable. Rather, they provide incomplete control that forces the user to choose to control gene expression in either space or time, and whether the system will be reversible or irreversible.</p><p>The recent emergence of the field of optogenetics--the ability to control gene expression using light--has made it possible to regulate gene expression with spatial, temporal, and dynamic control. Light-inducible systems provide the tools necessary to overcome the limitations of other gene regulation systems, which can be slow, imprecise, or cumbersome to work with. However, emerging light-inducible systems require further optimization to increase their efficiency, reliability, and ease of use.</p><p>Initially, we engineered a light-inducible gene regulation system that combines zinc finger protein technology and the light-inducible interaction between Arabidopsis thaliana plant proteins GIGANTEA (GI) and the light oxygen voltage (LOV) domain of FKF1. Zinc finger proteins (ZFPs) can be engineered to target almost any DNA sequence through tandem assembly of individual zinc finger domains that recognize a specific three base-pair DNA sequence. Fusion of three different ZFPs to GI (GI-ZFP) successfully targeted the fusion protein to the specific DNA target sequence of the ZFP. Due to the interaction between GI and LOV, co-expression of GI-ZFP with a fusion protein consisting of LOV fused to three copies of the VP16 transactivation domain (LOV-VP16) enabled blue-light dependent recruitment of LOV-VP16 to the ZFP target sequence. We showed that placement of three to nine copies of a ZFP target sequence upstream of a luciferase or eGFP transgene enabled expression of the transgene in response to blue-light. Gene activation was both reversible and tunable based on duration of light exposure, illumination intensity, and the number of ZFP binding sites upstream of the transgene. Gene expression could also be spatially patterned by illuminating the cell culture through photomasks containing various patterns.</p><p>Although this system was useful for controlling the expression of a transgene, for many applications it is useful to control the expression of a gene in its natural chromosomal position. Therefore we capitalized on recent advances in programmed gene activation to engineer an optogenetic tool that could easily be targeted to new, endogenous DNA sequences without re-engineering the light inducible proteins. This approach took advantage of CRISPR/Cas9 technology, which uses a gene-specific guide RNA (gRNA) to facilitate Cas9 targeting and binding to a desired sequence, and the light-inducible heterodimerizers CRY2 and CIB1 from Arabidopsis thaliana to engineer a light-activated CRISPR/Cas9 effector (LACE) system. We fused the full-length (FL) CRY2 to the transcriptional activator VP64 (CRY2FL-VP64) and the N-terminal fragment of CIB1 to the N-, C-, or N- and C- terminus of a catalytically inactive Cas9. When CRY2-VP64 and one of the CIBN/dCas9 fusion proteins are expressed with a gRNA, the CIBN/dCas9 fusion protein localizes to the gRNA target. In the presence of blue light, CRY2FL binds to CIBN, which translocates CRY2FL-VP64 to the gene target and activates transcription. Unlike other optogenetic systems, the LACE system can be targeted to new endogenous loci by solely manipulating the specificity of the gRNA without having to re-engineer the light-inducible proteins. We achieved light-dependent activation of the IL1RN, HBG1/2, or ASCL1 genes by delivery of the LACE system and four gene-specific gRNAs per promoter region. For some gene targets, we achieved equivalent activation levels to cells that were transfected with the same gRNAs and the synthetic transcription factor dCas9-VP64. Gene activation was also shown to be reversible and repeatable through modulation of the duration of blue light exposure, and spatial patterning of gene expression was achieved using an eGFP reporter and a photomask. </p><p>Finally, we engineered a light-activated genetic "on" switch (LAGOS) that provides permanent gene expression in response to an initial dose of blue light illumination. LAGOS is a lentiviral vector that expresses a transgene only upon Cre recombinase-mediated DNA recombination. We showed that this vector, when used in conjunction with a light-inducible Cre recombinase system,1 could be used to express MyoD or the synthetic transcription factor VP64-MyoD2 in response to light in multiple mammalian cell lines, including primary mouse embryonic fibroblasts. We achieved light-mediated upregulation of downstream myogenic markers myogenin, desmin, troponin T, and myosin heavy chains I and II as well as fusion of C3H10T½ cells into myotubes that resembled a skeletal muscle cell phenotype. We also demonstrated LAGOS functionality in vivo by engineering the vector to express human VEGF165 and human ANG1 in response to light. HEK 293T cells stably expressing the LAGOS vector and transiently expressing the light-inducible Cre recombinase proteins were implanted into mouse dorsal window chambers. Mice that were illuminated with blue light had increased microvessel density compared to mice that were not illuminated. Analysis of human VEGF and human ANG1 levels by enzyme-linked immunosorbent assay (ELISA) revealed statistically higher levels of VEGF and ANG1 in illuminated mice compared to non-illuminated mice.</p><p>In summary, the objective of this work was to engineer robust light-inducible gene regulation systems that can control genes and cellular fate in a spatial and temporal manner. These studies combine the rapid advances in gene targeting and activation technology with natural light-inducible plant protein interactions. Collectively, this thesis presents several optogenetic systems that are expected to facilitate the development of multicellular cell and tissue constructs for use in tissue engineering, synthetic biology, gene therapy, and basic science both in vitro and in vivo.</p> / Dissertation

Calpaïne 3 est une cystéine protéase retrouvée principalement au niveau du tissu musculaire. Cette enzyme joue un rôle clef dans le maintient de l’intégrité des fibres musculaires. En effet, des mutations au niveau du gène de calpaïne 3 ont été identifiées comme étant responsables d’une dystrophie musculaire autosomale récessive, la LGMD2A (Limb-girdle muscular dystrophy type 2A), caractérisée par une atrophie progressive des muscles des ceintures scapulaires et pelviennes. Nos travaux montrent que calpaïne 3 inhibe l’activité transcriptionnelle de MyoD. Ce facteur de transcription myogénique (MRF) joue un rôle central dans le contrôle de la myogenèse aussi bien au cours du développement embryonnaire que chez un individu adulte au cours du processus de régénération musculaire. Cette diminution d’activité transcriptionnelle a lieu aussi bien dans des cellules myoblastiques (C2C12) que fibroblastiques (C3H10T1/2). Par contre calpaïne 3 ne modifie pas l’activité transcriptionnelle des autres MRFs (Myf5, myogénine ou MRF4). Nous avons pu montrer que calpaïne 3 affecte spécifiquement l’activité transcriptionnelle de MyoD en entraînant une diminution de son niveau protéique (Western-blot, microscopie confocale), sans affecter son niveau d’ARNm (RT-QPCR). De plus, des expériences de détermination de la demi-vie protéique ont pu montrer que calpaïne 3 intervenait sur la dégradation protéique de MyoD. Des expériences sont en cours afin de déterminer si calpaïne 3 hydrolyse directement ou non le facteur MyoD. Nos travaux montrent que l’hydrolyse de MyoD induite par calpaïne 3 représente une voie parallèle à celle du système protéolytique protéasome ubiquitine-dépendant connu pour être impliqué dans sa dégradation. Nous avons également montré qu’une modification de l’expression de calpaïne 3, soit par surexpression soit par inhibition avec des siRNA spécifiques, entraîne une perturbation du processus de différenciation myogénique. Cet effet a été plus particulièrement étudié au sein d’une sous-population de cellules qui reste indifférenciée dans les cellules C2C12 induites en différenciation. Ces cellules, appelées cellules de réserve, s’apparentent aux cellules satellites intervenant dans la régénération musculaire. Nous avons montré que calpaïne 3 participe à la régulation du nombre des cellules de réserve au cours de la différenciation des cellules C2C12. Ce rôle de calpaïne 3 pourrait être lié à son intervention dans la dégradation du facteur MyoD. L’ensemble de ces résultats suggère ainsi que calpaïne 3 pourrait jouer un rôle in vivo dans le maintien d’un stock de cellules satellites au cours de la régénération musculaire. / Calpain 3 (CAPN3) is a calcium-dependent cysteine protease mainly expressed in skeletal muscle. This protease plays a key role in maintaining the integrity of muscular fibers. Indeed, mutations in CAPN3 encoding gene cause limb-girdle muscular dystrophy type 2A, an autosomal recessive muscular dystrophy characterized by progressive atrophy and weakness of the proximal limb muscles. Our work reveals an inhibitory effect of CAPN3 directed against the myogenic regulatory factor (MRF), MyoD. We have shown that CAPN3 inhibits the transcriptional activity of MyoD either in myoblastic cells (C2C12 cells) or in fibroblastic ones (C3H10T1/2 cells). On the contrary, no variation in the transcriptional activity of the other members of the MRFs family (Myf5, myogenin, or MRF4) was observed. CAPN3 affects the transcriptional activity of MyoD by decreasing the quantity of the endogenous protein MyoD (Western-blots, confocal microscopy experiments), without affecting its mRNA level (RT-QPCR). Moreover, half-life determination experiments showed that CAPN3 induce MyoD degradation acts on MyoD by a proteic degradation. Experiments are in progress to determine whether CAPN3 acts directly or not on MyoD. Furthermore, the inhibitory effect of CAPN3 on MyoD is independent of the ubiquitin-proteasome proteolytic pathway that is known to play a role during MyoD degradation. Indeed, MyoD mutants resistant to proteolytic degradation by the proteasome are sensitive to CAPN3 action. Interestingly, we have shown that modifications in CAPN3 expression, induced by overexpression or downregulation (siRNA), cause perturbations in myogenic differentiation. CAPN3 appears as a regulator of myogenic differentiation by modulating the quantity of MyoD available for progressing in differentiation. In addition, we have highlighted a potential role of CAPN3 in maintaining a pool of reserve cells along C2C12 cells differentiation. These cells share numbers of similarities with satellite cells present in the adult muscles. In conclusion, we have shown that CAPN3 acts as a regulatory molecule on myogenic differentiation, and probably have implications in the area of regeneration.

L'acide ascorbic acid (AA) a été considéré, pendant longtempss, comme une molecule devantêtre absorbée dans la nutrition, et prévenant le scorbut. Notre hypothèse, fondé sur desrésulats de notre groupe, suggèrent de nouvelles fonctions.Parmi celles-ci, nous nous sommes posé la question de l'AA molècule de signalling, durantl'embryogenèse et chez l'adulte, commme l'acide rétinoique (principe actif de la vitamine A)l'est. A cet effet, nous avons utilisé deux modèles cellulaires : des cellules souchesembryonnaires murines et des lignées de cellules souches/progénétrices adultes. Nous avonsainsi montré que l'AA stimule la différentiation de ces cellules en cellules musculairessquelettiques et en osteoblastes et inhibe l'adipogenèse et la neurogenèse. Cet effet passe parle transporteur de l'AA SVCT2 et implique la voie p38/MAPK. D'autre part, nous avonsdemontré que l'AA agit en compétition avec le RA, sur la neurogenèse et la myogenèse.Enfin, dans des cellules mésenchymateuses adultes, nous avons montré que l'AA inhibel'adipogenèse et stimule l'ostéogenèse. Cette action, comme chez l'embryon implique SVCT2et une modulation du pool du cAMP.En conclusion, l'AA pousse les cellules à se différencier en cellule musculaire squelettique eten ostéoblste et inhibie l'adipogenèse et la neurogenèse. / AA has been considered for a long time as a molecule involved in nutrition, to prevent scurvy. Our hypothesis is that AA could also be involved in development during embryogenesis, as well as in cell differentiation in adults. The aim of this study is to evaluate the potential implication of AA in cell differentiation, especially of mesenchyme cells, and to propose potential pathways that could be involved in these processes. Using murine ESCs we observed that AA markedly enhance the differentiation of ESCs toward muscle cells. Furthermore, we demonstrated that induction of myocytes by AA involves p38MAPK pathway and p-CREB. Moreover, we demonstrated that AA acts in mirror with retinoic acid. ESCs treated with RA mainly differentiate into neuronal cells, but AA compete, in a dosage dependent way to this differentiation. AA induces differentiation of ESCs into cardiac myocytes and could probably acts through p38MAPK pathway. Regarding adipocyte we revealed that SVCT2 expression significantly decreased as preadipocytes cells differentiate to adipocytes. This data suggests that mature adipocytes could not receive signals from AA. In addition, our results show that the expression of SVCT2 is increased in cells treated with AA and without IBMX. Moreover, we demonstrated that AA evolves in decreasing of cells containing lipids. Finally, we demonstrated that AA is not only involved in muscle differentiation of mesenchyme but is also involved in adipose tissue as a negative inducer. In conclusion, AA drives differentiation of ESCs toward muscle cells and osteoblast, incompetition with RA, and has a negative effect on adipogenesis and neurogenesis differentiation.

Durant la régénération du muscle suite à une lésion, les cellules souches musculaires, aussi appelées les cellules satellites, quittent leur état de quiescence et s’activent. Elles pourront soit emprunter la voie de la myogenèse afin de former de nouvelles fibres musculaires, soit retourner à leur état de quiescence pour reformer la réserve de cellules souches mobilisable en cas de lésion ultérieure. La régulation du devenir de la cellule souche est modulée par de nombreuses voies de signalisation telles que la voie Wnt, la voie Notch ou la voie des TGFb. Cependant, rares sont les données concernant l’implication du métabolisme sur le devenir de la cellule souche. Pourtant il a été démontré que l’activation des cellules satellites est étroitement liée avec le métabolisme cellulaire, dont l’un des principaux acteurs est la protéine kinase AMPK. Ce complexe hétérotrimérique, composé de trois sous-unités a, b et g est responsable de l’équilibre entre consommation énergétique et production d’énergie au sein de la cellule. Grâce à la modulation de mTORC1, il a également été prouvé que l’AMPKa1 était responsable de la croissance cellulaire et de la prolifération des précurseurs myogéniques. A l’aide de différents modèles murins, de lignées primaires et de cellules satellites en sortie de tri, nous avons déterminé le rôle que pouvait jouer chacun des isoformes, AMPKa1 et AMPKa2 au sein de la cellule souche, sur le déroulement de la myogenèse adulte post- lésionnelle ainsi que sur l’homéostasie du muscle régénéré. Dans un premier temps nous avons démontré que la voie de signalisation AMPKa1-LDH permettait de réguler l’autorenouvellement des cellules satellites grâce au contrôle du métabolisme. En effet, au moment de l’entrée de la cellule dans la voie de la différenciation, la voie de l’AMPKa1 induit une diminution de l’activité de la LDH, permettant aux cellules d’adopter un métabolisme de phosphorylation oxydative répondant à leurs besoins énergétiques. Dans un second temps, nous avons démontré que l’isoforme AMPKa2, exprimé uniquement après l’entrée de la cellule dans la voie de la myogenèse, était responsable d’une modulation de la régénération musculaire et que son absence induisait un défaut de différenciation et un retard de maturation des fibres néoformées. Nos travaux nous ont ainsi permis de confirmer la place centrale de la protéine kinase AMPK dans la modulation via le métabolisme du devenir de la cellule souche musculaire dans un contexte de régénération du tissu musculaire squelettique dans un modèle murin / During muscle regeneration following injury, muscle stem cells, also called satellite cells,leave their quiescent state and activate. MuSCs are capable of both differentiating torepair muscle tissue after an injury and self-renewing to replenish the pool of stem cells.The regulation of their fate is modulated by several signaling pathways such as Wnt,Notch or TGFb pathway. However, there are few data concerning the involvement ofmetabolism in the fate of satellite cells. Yet it has been shown that the activation ofsatellite cells is closely related to cellular metabolism, which one of the main players isAMPK protein kinase. This heterotrimeric complex, composed of three subunits a, b andg, is responsible for the balance between energy consumption and energy productionwithin the cell. With the modulation of mTORC1, AMPKa1 has also been shown to be responsible for cell growth and proliferation of myogenic precursors. Using different mouse models, primary lines and sorted satellite cells, we determined the role that each isoform, AMPKa1 and AMPKa2, could play within the cell, on myogenesis and on the homeostasis of the regenerated muscle. First, we demonstrated that AMPKa1-LDH signaling pathway regulates the satellite cells self-renewal by controlling metabolism. Indeed, at the time of cell fate choice between commitment into terminal differentiation versus self-renewal, the AMPKa1 pathway induces a decrease in LDH activity, allowing cells to adopt an oxidative phosphorylation metabolism responding to their energy needs. In a second time, we demonstrated that the AMPKa2 isoform, expressed during myogenesis only after the induction of muscle cell differentiation, was responsible for a modulation of the muscular regeneration and that its absence induced a lack of differentiation and a delay in maturation of the new formed myofibers. Our work allowed us to confirm the central role of AMPK protein kinase in the regulation, by the modulation of metabolism, of muscle stem cell fate in a context of skeletal muscle regeneration in a mouse model

Gene positioning changes with respect to the nuclear periphery correlate with their activation in a number of tissues during development. However, the determination of the function this serves or the mechanism through which this was achieved has been remarkably difficult to resolve. It may now be possible to address these questions due to the recent identification of a number of tissue-specific nuclear envelope transmembrane proteins (NETs) which are capable of promoting the repositioning of specific subsets of chromosomes and concomitantly inducing changes to gene expression (Zuleger et al,. 2013). In this thesis I describe the role of NETs in the positioning of genes to the nuclear envelope (NE) during muscle differentiation and the role this activity plays in the optimisation of myogenic gene expression in as myoblasts (MTs) differentiate to myotubes (MTs). To do this I identified four NETs with the capacity to reposition a chromosome to the periphery that are present specifically in the NEs of skeletal muscle. Using a combination of genome-wide gene expression analysis and DamID I determined that depletion of these NETs disrupted myogenic gene expression and, more significantly, prevented the targeting to and silencing of normally repressed genes at the NE. I also investigated an analogous role for the blood-specific NET TAPBPL in the regulation of the critical T-cell regulator interleukin 2 (IL-2) at the NE in T-cells. Depletion of this NET caused release of the IL2 locus from the periphery and promoted its inappropriate and long-term activation. Interestingly, depletion of TAPBPL also prevented IL2 silencing following the end of T-cell activation, suggesting this genome organisation activity is critical for the maintenance of normal T-cell function. Collectively, the results discussed herein describe a new role for NETs in the regulation of gene expression through the manipulation of spatial genome organisation and may serve as an additional layer of higher order tissue-specific gene regulation in higher organisms.

The spatial and temporal patterning of sequence specific transcription factors (SSTFs) contributes to cell type specification and organ formation during embryogenesis. Homeodomain transcription factors are evolutionally conserved among invertebrate and vertebrate animals. They are responsible for body segmentation and organogenesis. Lbx1 and Pitx2 both are homeodomain transcription factors contributing to SSTF pattern formation during multiple organ formations. We studied how homeodomain transcription factors regulate SSTF and non-SSTF genes in a population-specific manner using the Lbx1[superscript EGFP] and Pitx2[superscript LacZ] mouse models. We have studied the role of Lbx1 in dorsal horn interneuron specification and Pitx2 in forelimb muscle formation. The two top non-SSTF target genes, NPY and Chmp2b, of Lbx1 are studied for expression pattern and potential neuronal function in neural tube. The T box, Hox gene families and Pax genes were identified as Pitx2 target genes via microarray analysis and their expression pattern were analyzed in forelimb. The expression domains of signaling molecules were altered in absence of Pitx2, suggesting that Pitx2 played a general role in pattern formation in forelimb mesenchyme. / Graduation date: 2013

The Hedgehog (Hh) signalling pathway is one of the key signalling pathways orchestrating intricate organogenesis, including the development of neural tube, heart and skeletal muscle. Yet, insufficient mechanistic understanding of its diverse roles is available. Here, we show the molecular mechanisms regulating the neurogenic, cardiogenic and myogenic properties of Hh signalling, via effector protein Gli2, in embryonic and adult stem cells. In Chapter 2, we show that Gli2 induces neurogenesis, whereas a dominant-negative form of Gli2 delays neurogenesis in P19 embryonal carcinoma (EC) cells, a mouse embryonic stem (ES) cell model. Furthermore, we demonstrate that Gli2 associates with Ascl1/Mash1 gene elements in differentiating P19 cells and activates the Ascl1/Mash1 promoter in vitro. Thus, Gli2 mediates neurogenesis in P19 cells at least in part by directly regulating Ascl1/Mash1 expression. In Chapter 3, we demonstrate that Gli2 and MEF2C bind each other’s regulatory elements and regulate each other’s expression while enhancing cardiomyogenesis in P19 cells. Furthermore, dominant-negative Gli2 and MEF2C proteins downregulate each other’s expression while imparing cardiomyogenesis. Lastly, we show that Gli2 and MEF2C form a protein complex, which synergistically activates cardiac muscle related promoters. In Chapter 4, we illustrate that Gli2 associates with MyoD gene elements while enhancing skeletal myogenesis in P19 cells and activates the MyoD promoter in vitro. Furthermore, inhibition of Hh signalling in muscle satellite cells and in proliferating myoblasts leads to reduction in MyoD and MEF2C expression. Finally, we demonstrate that endogenous Hh signalling is important for MyoD transcriptional activity and that Gli2, MEF2C and MyoD form a protein complex capable of inducing skeletal muscle-specific gene expression. Thus, Gli2, MEF2C and MyoD participate in a regulatory loop and form a protein complex capable of inducing skeletal muscle-specific gene expression. Our results provide a link between the regulation of tissue-restricted factors like Mash1, MEF2C and MyoD, and a general signal-regulated Gli2 transcription factor. We therefore provide novel mechanistic insights into the neurogenic, cardiogenic and myogenic properties of Gli2 in vitro, and offer novel plausible explanations for its in vivo functions. These results may also be important for the development of stem cell therapy strategies.