The Drosophila hindsight (hnt) gene encodes a C2H2-type zinc-finger (ZNF) protein crucial for epithelial morphogenesis. The human HNT homologue, RREB1, functions as a transcriptional modulator and regulates several tumor suppressor genes. HNT’s functional motifs, target genes and its regulatory abilities have not been elucidated. Here I showed that the C-terminal region of HNT containing the last five of 14 ZNFs (ZNF 10-14) binds in vitro to DNA-elements similar to those identified for RREB-1. I then mapped HNT’s endogenous binding sites on polytene chromosomes and focus on two, at 4C and 60C, which are associated with the hnt and nervy (nvy) loci, respectively. Sequence analysis of the bound fragments shows conservation of motifs similar to those bound by HNT in vitro. Data from both hnt loss- and gain-of-function experiments show that HNT attenuates the transcription of the hnt and nvy genes in several tissues and developmental stages. I show that the identified HNT C-terminal DNA binding domain ZNF 10-14 is not required for these regulatory functions. I further delineate the minimal functional motifs of HNT in transcriptional regulation and show that its ninth ZNF in isolation has a repressive activity and is sufficient to confer many regulatory functions of HNT. On the other hand, mutation of ZNF 9 in the context of the full-length protein indicates that it is not necessary for HNT functions. Interestingly, ZNF 9 has been lost from HNT vertebrate homologues. I propose two redundant mechanisms of transcriptional regulation by HNT: one is mediated by the potential protein-interaction abilities of ZNF 9; another is through cooperation of other ZNF motifs of HNT; the DNA binding abilities conferred by the C-terminal five fingers may be essential for the latter mechanism.

The enzyme carbonic anhydrase (CA) contributes to multiple physiological processes by catalysing the reversible hydration of carbon dioxide. However, regulation of CA activity in response to homeostatic challenges remains poorly understood. The objectives of this thesis were to investigate whether CA is transcriptionally regulated by cortisol in fish and whether post-translational modification (PTM) of CA occurs in fish. The results of an in vivo reporter assay used to investigate potential transcriptional regulation of zebrafish, Danio rerio, cytoplasmic CA (CAc) were inconsistent, and it remains unclear whether zebrafish CAc is regulated transcriptionally by cortisol. Phosphorylation of rainbow trout, Oncorhynchus mykiss, CAc was predicted from in silico analysis of the putative amino acid sequence and confirmed by Western analysis of phosphoprotein levels following in vitro incubation of CA, purified from trout gill, under conditions designed to potentiate endogenous kinases. Again using in vitro incubations designed to potentiate endogenous kinases and phosphatases, changes to the phosphorylation state of CAc were found to modulate its enzymatic properties. These findings suggest that CA activity may be regulated by signalling pathways that activate cellular protein kinases, and future work should focus on identifying these pathways.

Mycoplasma hyopneumoniae é uma bactéria de tamanho diminuto, caracterizada por um genoma pequeno, com baixo conteúdo GC. Está associada com doenças respiratórias de suínos, resultando em prejuízos produtivos e econômicos na indústria animal. A presença de sequências de DNA repetitivas, que ocorrem em grandes quantidades em células eucarióticas, vem sendo cada vez mais identificadas em genomas de procariotos, sendo também associadas a um potencial papel regulador. Uma vez que a regulação da transcrição nesses organismos ainda é pouco entendida, o objetivo do presente estudo foi realizar uma busca in silico por elementos repetitivos nas regiões intergênicas do genoma de M. hyopneumoniae linhagem 7448. Dois tipos de repetições foram selecionados para a busca inicial: tandem e palindromes. Regiões intergênicas de até 500 pb a montante do sítio de início da tradução de todas as CDSs do genoma de M. hyopneumoniae linhagem 7448 foram utilizadas para a predição. Para cada tipo de elemento dois programas computacionais independentes foram utilizados. As predições in silico resultaram em 144 repetições em tandem e 1.171 palindromes. O DNA repetitivo se encontra distribuído a montante de 86% das unidades transcricionais de M. hyopneumoniae linhagem 7448. Análises comparativas entre genomas de micoplasmas demonstraram diferentes níveis de conservação dos elementos repetitivos entre linhagens patogênicas e não-patogênicas. Linhagens patogênicas revelaram uma conservação de 59%, enquanto que a não patogênica, somente de 46%. Através de ensaios de amplificação quantitativa de DNA, foi observado diferentes níveis de expressão em genes codificantes para importantes proteínas, como glicina hidroximetiltransferase, lipoproteína, adesinas e proteína ligadora de GTP. Os genes codificantes para essas proteínas divergiam no número de repetições palindromes e tandens na sua respectiva região intergênica. Além disso, repetições encontradas em 206 genes já descritos como regulados em diferentes condições em M. hyopneumoniae linhagem 232 mostraram aproximadamente 80% de conservação em relação à linhagem M. hyopneumoniae linhagem 7448. Todos esses resultados sugerem um potencial papel regulador das repetições de DNA em tandem e palindromes em Mycoplasma. / Mycoplasma hyopneumoniae is a diminutive bacterium, characterized by a small genome with a low GC content. It is commonly associated with swine respiratory diseases, resulting in productivity and economic losses in the animal industry. Repetitive DNA, which occurs in large quantities in eukaryotic cells, has been increasingly identified in prokaryotic genomes, and has been associated with a potential regulatory function. Once transcription regulation in these organisms is still poorly understood, the aim of the current study was to perform an in silico search of repeat elements in the genomic intergenic regions of M. hyopneumoniae strain 7448. Two types of repeats were selected for initial search: Tandem and Palindromic. Intergenic regions up to 500 bp upstream from start codon of M. hyopneumoniae strain 7448 CDSs were used as input for the software’s prediction. For each type of repeat sequence, two independent software packages were used. Computational analysis results in 144 tandem repeats and 1,171 palindrome elements. The repeats were distributed in the upstream region of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct mycoplasmas, demonstrate different indices of repeat conservation among pathogenic and non-pathogenic strains. Pathogenic strains revealed 59% conservation, while non-pathogenic only 46%. Through assays of quantitative amplification of DNA, different levels of expression in genes coding important proteins have been demonstrated, as glycine hydroxymethyltransferase, lipoprotein, adhesins and GTP-binding protein. These protein coding genes differ in number of palindromes or tandem repeats in respective upstream regions. In addition, repeats found in 206 genes already described to be regulated in different grow conditions in M. hyopneumoniae strain 232 showed almost 80% of conservation in relation to M. hyopneumoniae strain 7448. All these findings, suggests a potential regulatory role of tandem and palindrome DNA repeats.

Mycoplasma hyopneumoniae é uma bactéria de tamanho diminuto, caracterizada por um genoma pequeno, com baixo conteúdo GC. Está associada com doenças respiratórias de suínos, resultando em prejuízos produtivos e econômicos na indústria animal. A presença de sequências de DNA repetitivas, que ocorrem em grandes quantidades em células eucarióticas, vem sendo cada vez mais identificadas em genomas de procariotos, sendo também associadas a um potencial papel regulador. Uma vez que a regulação da transcrição nesses organismos ainda é pouco entendida, o objetivo do presente estudo foi realizar uma busca in silico por elementos repetitivos nas regiões intergênicas do genoma de M. hyopneumoniae linhagem 7448. Dois tipos de repetições foram selecionados para a busca inicial: tandem e palindromes. Regiões intergênicas de até 500 pb a montante do sítio de início da tradução de todas as CDSs do genoma de M. hyopneumoniae linhagem 7448 foram utilizadas para a predição. Para cada tipo de elemento dois programas computacionais independentes foram utilizados. As predições in silico resultaram em 144 repetições em tandem e 1.171 palindromes. O DNA repetitivo se encontra distribuído a montante de 86% das unidades transcricionais de M. hyopneumoniae linhagem 7448. Análises comparativas entre genomas de micoplasmas demonstraram diferentes níveis de conservação dos elementos repetitivos entre linhagens patogênicas e não-patogênicas. Linhagens patogênicas revelaram uma conservação de 59%, enquanto que a não patogênica, somente de 46%. Através de ensaios de amplificação quantitativa de DNA, foi observado diferentes níveis de expressão em genes codificantes para importantes proteínas, como glicina hidroximetiltransferase, lipoproteína, adesinas e proteína ligadora de GTP. Os genes codificantes para essas proteínas divergiam no número de repetições palindromes e tandens na sua respectiva região intergênica. Além disso, repetições encontradas em 206 genes já descritos como regulados em diferentes condições em M. hyopneumoniae linhagem 232 mostraram aproximadamente 80% de conservação em relação à linhagem M. hyopneumoniae linhagem 7448. Todos esses resultados sugerem um potencial papel regulador das repetições de DNA em tandem e palindromes em Mycoplasma. / Mycoplasma hyopneumoniae is a diminutive bacterium, characterized by a small genome with a low GC content. It is commonly associated with swine respiratory diseases, resulting in productivity and economic losses in the animal industry. Repetitive DNA, which occurs in large quantities in eukaryotic cells, has been increasingly identified in prokaryotic genomes, and has been associated with a potential regulatory function. Once transcription regulation in these organisms is still poorly understood, the aim of the current study was to perform an in silico search of repeat elements in the genomic intergenic regions of M. hyopneumoniae strain 7448. Two types of repeats were selected for initial search: Tandem and Palindromic. Intergenic regions up to 500 bp upstream from start codon of M. hyopneumoniae strain 7448 CDSs were used as input for the software’s prediction. For each type of repeat sequence, two independent software packages were used. Computational analysis results in 144 tandem repeats and 1,171 palindrome elements. The repeats were distributed in the upstream region of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct mycoplasmas, demonstrate different indices of repeat conservation among pathogenic and non-pathogenic strains. Pathogenic strains revealed 59% conservation, while non-pathogenic only 46%. Through assays of quantitative amplification of DNA, different levels of expression in genes coding important proteins have been demonstrated, as glycine hydroxymethyltransferase, lipoprotein, adhesins and GTP-binding protein. These protein coding genes differ in number of palindromes or tandem repeats in respective upstream regions. In addition, repeats found in 206 genes already described to be regulated in different grow conditions in M. hyopneumoniae strain 232 showed almost 80% of conservation in relation to M. hyopneumoniae strain 7448. All these findings, suggests a potential regulatory role of tandem and palindrome DNA repeats.

In nature, biofilm is a complex structure resulted of multicellular bacterial communities that provide important nutritional functions and the acquisition of protective traits such as antibiotics resistance and horizontal gene transfer. The development from the planktonic, lonely bacteria, to the mature multilayered biofilm structure consists of three main phases: motility, attachment and biofilm maturation. At cellular level, the process is controlled by several genes such as flhD, fliA, rpoS, csgD, adrA, cpxR all acting as master regulators. Additionally, the global regulators CRP, IHF, Fis, and others in less frequency, have been related to biofilm formation, although blurry information has been provided. In this thesis we used synthetic, molecular and cellular biology approaches to understand the effect of CRP, IHF and Fis in the transcriptional regulatory network in the bacterium Escherichia coli. In the first chapter, we employed network analysis to reconstruct and analyze part of the entire regulatory network described to modulate the flagella-biofilm program. With this analysis we identified some critical interactions responsible for the planktonic-biofilm transition. Next, we selected the top ten effectors nodes of the network and cloned the promoter region of those genes in a reporter system. As extensively explained in chapter II, this system allowed us to validate as well as suggest new interactions in the network. Additionally, the measurement of the promoter activity during bacterial development show that CRP, IHF and Fis differentially modulate most of the surveyed genes suggesting that those Global Regulators participate to modulate gene expression in different phases of the planktonic-biofilm development. At chapter three, to get a better overview of the entire process, we performed motility, adherence/early biofilm and mature biofilm assays. We describe the intrinsic ability of E. coli to perform motility, adherence and mature biofilm at 37?C. In contrast, the absence of ihf, fis as well as Carbon Catabolite Repression (CCR), lead to altered phenotypes at both motility and biofilm development. At the end, we discussed how the changes of promoter activity of target genes, together with our network analysis, could explain part of the altered phenotypes observed. For instance, we observed changes at the main stress responders rpoS and rpoE that, in combination with alterations at specific genes such as fliA, can explain the enhanced motility in the E. coli ?ihf strain. Altogether, in this thesis, we provided evidence that CRP, IHF and Fis control the activity of the promoter regions of genes involved in the planktonic-biofilm development. / Na natureza, o biofilme é uma estrutura complexa resultante de comunidades bacterianas multicelulares que fornece importantes funções nutricionais e a aquisição de traços de proteção como resistência a antibióticos e transferência horizontal de genes. O desenvolvimento das bactérias planctônicas solitárias para uma estrutura de biofilme maduro consiste em três fases principais: motilidade, fixação e maturação do biofilme. Ao nível celular, o processo é controlado por vários genes tais como flhD, fliA, rpoS, csgD, adrA, cpxR, todos agindo como reguladores mestre. Além disso, os reguladores globais CRP, IHF, Fis e outros em menor freqüência, têm sido relacionados à formação de biofilme, embora tenham sido fornecidas informações nao conclusivas sobre esse processo. Nesta tese foram utilizadas abordagens de bioinformática, assim como de biologia molecular e celular para entender o efeito de CRP, IHF e Fis na rede reguladora da transição de motilidade para biofilme na bactéria Escherichia coli. No primeiro capítulo, utilizamos a análise de rede para reconstruir e analisar parte da rede regulatória descrita para modular o programa flagelo-biofilme. Com esta análise identificamos algumas interações críticas responsáveis pela transição planctônica-biofilme. Em seguida, selecionamos os dez principais nós efetores da rede e clonamos a região promotora desses genes em um sistema repórter. Conforme explicado amplamente no capítulo II, este sistema nos permitiu validar e sugerir novas interações na rede. Adicionalmente, a medição da atividade do promotor durante o desenvolvimento bacteriano mostra que a CRP, a IHF e a Fis modulam diferencialmente a maioria dos genes analisados sugerindo que estes Reguladores Globais participam para modular a expressão génica em diferentes fases do desenvolvimento de estado planctónico para biofilme. No capítulo três, para obter uma melhor visão geral de todo o processo, realizamos ensaios de motilidade, aderência / biofilme precoce e biofilmes maduros. Descrevemos a capacidade intrínseca de E. coli para realizar motilidade, adesão e biofilme maduro a 37 °C. Em contraste, a ausência de ihf, fis, bem como o fenômeno de Repressão de Catabolite de Carbono (CCR), levam a fenótipos alterados, tanto na motilidade como no desenvolvimento do biofilme. No final, discutimos como as mudanças da atividade do promotor de genes alvo, juntamente com a nossa análise de rede, poderia !xi explicar parte dos fenótipos alterados observados. Por exemplo, observamos mudanças nos principais respondedores de estresse rpoS e rpoE que, em combinação com alterações em genes específicos como fliA, podem explicar a motilidade aumentada na estirpe de E. coli ?ihf. Em conjunto, nesta tese, apresentamos evidências de que CRP, IHF e Fis controlam a atividade das regiões promotoras de genes envolvidos no desenvolvimento planctônico-biofilme.

Au cours de ma thèse, je me suis intéressée au développement du système cardio-vasculaire chez la drosophile afin de mieux comprendre la logique de régulation de ce processus. Au cours de l'embryogenèse, la cardiogenèse est réalisée grâce à un réseau de régulation génique (GRN) qui conduit à la formation d'un simple tube cardiaque linéaire. Ensuite, lors de la métamorphose, le tube cardiaque larvaire est remodelé pour former l'organe adulte.J'ai d'abord participé à l'évaluation et à l'amélioration d'une nouvelle méthode, cisTargetX, qui permet prédire des modules cis-régulateurs (CRM) présentant des caractéristiques communes à un groupe de gènes co-exprimés.En utilisant cette méthode, j'ai analysé le transcriptome du remodelage du cœur afin de prédire des motifs pouvant être liés par des TF impliqués dans le contrôle temporel de l'expression des gènes, ainsi que les CRM associés. Grâce aux validations in-vivo des CRM prédits, j'ai démontré qu'ils étaient capables de reproduire le patron d'expression temporel attendu. J'ai également démontré que la mutation du motif en question au sein de deux des CRM testés permet de supprimer son patron d'expression sauvage. Ce motif est reconnu par des facteurs de transcription (TF) de la famille des récepteurs nucléaires (NR). Dhr3, un NR fortement exprimé au début de l'induction des gènes analysés, est montré comme étant essentiel au patron d'expression temporel. Nos résultats suggèrent une architecture du GRN, dans lequel les régulations temporelle et spatiale sont distinctes.Par la suite, j'ai participé à la caractérisation du GRN impliqué dans la cardiogenèse. En combinant un transcriptome issu de la différenciation des cellules cardiaques avec des expériences ChIP-on-Chip sur le TF MEF2, j'ai prédit que certains TF appartenant aux familles bZIP et REL sont susceptibles de participer au GRN responsable de la différenciation cardiaque. La validation in-vivo de ces prédictions est en cours. / During my thesis, I focused on the development of the cardiovascular system in Drosophila in order to investigate the regulatory logic of this process. During embryogenesis, cardiogenesis is mediated by a gene regulatory network which includes conserved signaling pathways and transcription factors, and leads to the formation of a linear cardiac tube. Then, during metamorphosis, the larval cardiac tube is remodeled to form the adult organ.I first participated in the evaluation and the improvement of a new method, cisTargetX, that uses a comprehensive library of motifs, combined with phylogenetic conservation, to identify potential cis-regulatory modules (CRM) presenting common features in a cluster of co-expressed genes.Using this method among other tools, I analysed cardiac remodeling during metamorphosis to predict motifs for transcription factors (TF) involved in the temporal control of gene expression, and also their associated CRM. I performed in-vivo validations of predicted CRM, and demonstrated that they reproduce the expected temporal expression pattern. In addition, I demonstrated that motifs mutation within selected CRM abrogate this expression pattern. This motif is predicted to be recognized by a TF that belong to the nuclear receptor (NR) family. Dhr3, a NR highly expressed at the onset of the induction of the analysed gene set, is demonstrated to be essential for CRM temporal pattern. Our results suggest a modular architecture of the regulatory machinery, in which the temporal and spatial regulations are distinct.Next, I participated in the characterization of the Gene Regulatory Network (GRN) involved in cardiac differentiation during embryogenesis. Combining transcriptome profiling of differentiating cardiac cells with Mef2 Chip-on-Chip experiments allowed me to predict that TF belonging to bZIP and REL family are likely to participate in the GRN driving cardiac differentiation. In-vivo validation of these predictions is in progress.

Adult skeletal muscles can regenerate after injury due to the presence of satellite cells, a quiescent population of myogenic progenitor cells characterized by expressing the transcription factor Pax7. Once activated, satellite cells repair the muscle damage and replenish the stem cell niche due to the coordinated function of several transcription factors including Pax7 and the myogenic regulatory factors (MRFs). MRFs are skeletal muscle-specific transcription factors that can convert non-muscle cells into the myogenic lineage. MRFs are known to cooperate with other transcription factors in regulating the complex transcriptional network driving myogenic differentiation of muscle progenitors. The Six4 transcription factor emerges as a strong candidate for cooperating with MRFs. Six4 is expressed in skeletal muscles; the lack of a muscle development phenotype in Six4-null mice has been attributed to compensation by other Six family members. However, this did not exclude a critical role for Six4 during muscle development as Six1;Six4 double mutant mice show a more severe muscle phenotype than Six1 mutant mice. Nevertheless, the role of Six4 during adult muscle regeneration has never been addressed. I combined a partial loss-of-function of Six4 with high-throughput approaches to address the role of Six4 during adult skeletal muscle regeneration. I observed an important function of Six4 during muscle regeneration in vivo and in in vitro cell models. Using RNA interference assays against Six4 in tibialis anterior muscle regeneration after cardiotoxin-induced muscle damage, I observed for the first time that Six4 plays a role in proper muscle regeneration. The ability of the MRF MyoD, a central regulator of skeletal myogenesis, to convert a non-muscle cell model into the myogenic lineage was impaired with attenuated Six4 expression. I employed genome-wide approaches by combining ChIP-sequencing with gene expression profiling and identified a set of muscle genes coordinately regulated by both Six4 and MyoD. Throughout the genome, the cooperation between Six4 and MyoD was associated with binding of the H3K27me3 demethylase Utx and depletion of the H3K27me3 repressive chromatin mark. Together, these results reveal an important role for Six4 during adult muscle regeneration, and suggest a widespread mechanism of cooperation between Six4 and MyoD that correlates with modifying the epigenetic landscape of the regulatory regions of a large set of genes needed for efficient myogenesis.

The enzyme carbonic anhydrase (CA) contributes to multiple physiological processes by catalysing the reversible hydration of carbon dioxide. However, regulation of CA activity in response to homeostatic challenges remains poorly understood. The objectives of this thesis were to investigate whether CA is transcriptionally regulated by cortisol in fish and whether post-translational modification (PTM) of CA occurs in fish. The results of an in vivo reporter assay used to investigate potential transcriptional regulation of zebrafish, Danio rerio, cytoplasmic CA (CAc) were inconsistent, and it remains unclear whether zebrafish CAc is regulated transcriptionally by cortisol. Phosphorylation of rainbow trout, Oncorhynchus mykiss, CAc was predicted from in silico analysis of the putative amino acid sequence and confirmed by Western analysis of phosphoprotein levels following in vitro incubation of CA, purified from trout gill, under conditions designed to potentiate endogenous kinases. Again using in vitro incubations designed to potentiate endogenous kinases and phosphatases, changes to the phosphorylation state of CAc were found to modulate its enzymatic properties. These findings suggest that CA activity may be regulated by signalling pathways that activate cellular protein kinases, and future work should focus on identifying these pathways.

La génération de la diversité morphologique n’implique pas seulement l’émergence de nouveaux caractères morphologiques, mais aussi la modification de caractères pre-existants. Des changements dans l'expression génique sous-tendent l’apparition et la divergence de morphologies au cours de l'évolution. Les variations de l'expression d'un gène peuvent résulter des modifications dans la séquence nucléotidique de ses éléments cis-régulateurs (ECRs) et/ou dans la séquence codante des facteurs de transcription (FTs) qui le régulent. En conséquence, la compréhension de l'évolution d'un nouveau trait exige l'élucidation des modifications en cis et en trans expliquant les différences d'expression des gènes. Les études sur la pigmentation des drosophiles ont considérablement contribué à notre compréhension du rôle joué par la modification des ECRs dans la diversification morphologique. Pour comprendre les mécanismes génétiques et moléculaires qui sous-tendent l’émergence et la diversification des traits morphologiques, nous avons décidé d’étudier l'évolution des motifs de pigmentation de l’aile chez les mouches du groupe d'espèces Drosophila melanogaster. Nous constatons que la diversification des modes de pigmentation de l’aile dans ce groupe est en corrélation avec la divergence d'expression d'un gène de pigmentation, yellow. Nous avons choisi de disséquer la régulation transcriptionnelle de yellow dans l’une des espèces tachetées, Drosophila biarmipes, avec pour objectif d'élucider les mécanismes responsables de la diversification de l'expression de yellow.Drosophila biarmipes, une espèce proche de Drosophila melanogaster, a développé une nouvelle tache de pigmentation sur aile qui est absente chez D. melanogaster. L'évolution de ce caractère est corrélée au changement d’expression de yellow. Une précédente étude a identifié, dans la région 5' du promoteur de yellow de D. biarmipes, un ECR qui suffit à reproduire une partie de l'expression de yellow lorsqu’il est transformé chez D. melanogaster. Avec un crible RNAi, j’ai identifié cinq FTs qui peuvent réguler l’ECR de yellow. Un de ces candidats, Distal-less, est exprimé d’une façon qui correspond à celle de l'expression de yellow et au profil de la pigmentation de l’aile chez D. biarmipes. Une analyse comparative de Distal-less et yellow a mis en évidence que les profils d'expression de ces gènes sont également corrélés avec les différents patrons de pigmentation dans les ailes d’autres espèces de drosophiles. J’ai aussi pu montrer que la surexpression de Distal-less dans l’aile de D. biarmipes est suffisante pour induire de la pigmentation ectopique. Ceci suggère que Distal-less ne régule pas seulement yellow, mais l’ensemble des gènes de pigmentation nécessaires à l’apparition de tache chez D. biarmipes. Mon travail montre que l'évolution de nouveaux motifs de pigmentation a commencé par le recrutement de Distal-less sur une batterie de gènes pigmentation. A partir de ces constatations, nous proposons un modèle expliquant les mécanismes de régulation conduisant à l'émergence et la diversification des motifs de pigmentation de l'aile au sein du groupe d'espèces melanogaster. Nous suggérons que dans un ancêtre commun de ce groupe, Distal-less a été recruté par une batterie des gènes de pigmentation, qui conduisent à l'émergence d'un motif de pigmentation. Par ailleurs, nous faisons l’hypothèse qu’une fois un lien régulatoire a été formé entre Distal-less et les gènes de pigmentation, alors la divergence d'expression de Distal-less pourrait entraîner des changements dans la régulation spatiale de tous les gènes de pigmentation donnant lieu à la diversification des motifs de pigmentation. / The generation of morphological diversity involves not only the emergence of novel morphological traits but also the modification of pre-existing ones. To understand the genetic and molecular mechanisms underlying the gain and diversification of morphological traits, we chose to study the evolution of wing pigmentation patterns in a group of flies in the melanogaster species group. We find that the diversification of wing pigmentation patterns in this group is mirrored by the divergence of expression of a pigmentation gene, yellow. To decipher the regulatory mechanisms underlying the diversification of yellow expression, we chose to dissect the transcriptional regulation of yellow in one spotted species, D. biarmipes. A functional dissection of the yellow spot enhancer, situated at the 5’ of the D. biarmipes yellow promoter, shows that a homeobox transcription factor, Distal-less (Dll), is a direct activator of yellow. Moreover, we show that ectopic expression of Dll is sufficient to induce ectopic pigmentation in D. biarmipes, which suggests that Dll is regulating yellow and other pigmentation genes. Furthermore, we find that the divergence of Yellow expression pattern in the melanogaster species group is correlated with the divergence in expression of Dll. Based on our findings we propose a model to explain the regulatory mechanisms that lead to the emergence and diversification of wing pigmentation patterns within the melanogaster species group. We suggest that in a common ancestor of all spotted species within the Oriental lineage, there was a gain of regulatory links between Dll and terminal pigmentation genes, such as yellow, which lead to the emergence of an ancestral pigmentation pattern. We further propose that once a regulatory link was formed between Dll and terminal pigmentation genes, divergence of Dll expression could lead to changes in the spatial regulation of all downstream target genes, which would give rise to the diversification of pigmentation patterns. Our study illustrates how key regulators of terminal genes could be targets for mutations that are more likely to lead to morphological diversification.

Although pathological alterations in gene expression and mitochondria function in response to cardiac ischemia are well recognized, the mechanisms driving these changes are incompletely understood. Nuclear to mitochondrial communication regulating gene expression and mitochondrial function is a critical process following cardiac ischemic injury. Here we determine that cyclin C, a component of the transcriptional regulator, Mediator complex, directly regulates cardiac and mitochondrial function by modifying mitochondrial fission. We tested the hypothesis that cyclin C has a binary function as a transcriptional cofactor in the nucleus and acute regulation of cardiac energetics in ischemia by enhancing mitochondrial fission in the cytoplasm. In response to stress, cyclin C translocates to the cytoplasm enhancing mitochondria fission in part through interactions with Cdk1. Using cardiac specific cyclin C knockout and overexpression mouse models, we determined cyclin C regulates mitochondria morphology under basal and ischemic conditions in vivo. Furthermore, pretreatment with a Cdk1 inhibitor followed by ischemia in vivo results in reduced mitochondrial fission. Together, our study reveals that cyclin C regulates both hypertrophic gene expression and mitochondrial fission providing new insights into the regulation of cardiac energy metabolism following acute ischemic injury.