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.

Submitted by REGINALDO KELLER FERNANDES null (regiskeller@msn.com) on 2017-04-12T12:10:23Z No. of bitstreams: 1 Tese Dr definitiva.pdf: 5601863 bytes, checksum: 50eec58640e31a0c12ce54dde368d5a3 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-04-17T20:28:15Z (GMT) No. of bitstreams: 1 fernandes_rk_dr_bot.pdf: 5601863 bytes, checksum: 50eec58640e31a0c12ce54dde368d5a3 (MD5) / Made available in DSpace on 2017-04-17T20:28:15Z (GMT). No. of bitstreams: 1 fernandes_rk_dr_bot.pdf: 5601863 bytes, checksum: 50eec58640e31a0c12ce54dde368d5a3 (MD5) Previous issue date: 2017-02-24 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / A paracoccidioidomicose (PCM) é uma micose sistêmica endêmica na América Latina, principalmente no Brasil, Argentina e Venezuela, e que promove um importante impacto na saúde pública. Seu agente etiológico é um fungo termodimórfico pertencente ao gênero Paracoccidioides que compreende o Paracocidioides brasiliensis (Pb) e suas espécies crípticas S1, PS2, PS3 e Paracoccidioides lutzii. As consequências da interação do fungo com as células da resposta imune inata, tais como as células dendríticas (DC), destacando a capacidade destas células para instruir a resposta imune adaptativa, não são totalmente compreendidas. Em estudo anterior, descobrimos que DCs não maturam em resposta ao desafio com Pb. Esta falha foi associada à inibição de PGE2 nas DCs pelo fungo, uma vez que este eicosanóide é um fator importante para a maturação dessas células. Na tentativa de melhor entender este processo e suas conseqüências para a instrução da resposta adaptativa CD4, nós buscamos analisar o perfil transcricional de DCs em resposta ao Pb assim como o de linfócitos CD4+ cocultivados com DCs sensibilizados com o fungo. Para estas análises, nós utilizamos a metodologia de RNA-seq, que permitiu o sequenciamento de alto rendimento e a quantificação sistemática de expressão gênica. Após as análises, os genes que foram regulados positivamente ou negativamente em ambas as células (DCs e CD4) foram listados e as funções das proteínas codificadas por eles, identificadas. A análise geral das proteínas codificadas por esses genes, como diversas citocinas e quimiocinas, mediadores inflamatórios, bem como fatores de transcrição envolvidos na diferenciação de populações de linfócitos, permitiram determinar o perfil de resposta adaptativa que foi diferenciado após Interação de DCs com células CD4, bem como alguns mecanismos que levaram a este perfil. / FAPESP: 2013/14733-0

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.

Drosophila melanogaster is a widely used and efficient genetic model to study nervous system development. The conservation of many genes from Drosophila to vertebrates and a short reproduction cycle makes the fruitfly a great tool for providing insight into crucial events in nervous system formation. In studying the development of the sensory nervous system, Drosophila also provides a model for understanding the formation and function of structurally diverse cilia. Cilia are hairlike organelles present throughout our bodies and responsible for many processes such as chemo, mechano, and thermosensation, fluid movement, hearing and fertility. In Drosophila the only somatic ciliated cells are the Type I sensory neurons in which a cilium forms the sensory dendrite. There are more than two diverse subtypes of the ciliated sensory neurons and the mechanism by which this diversity is achieved remains unclear. The mechanism of ciliated sensory neuron differentiation was hereby studied on an example of a differentially expressed ciliary gene - CG6129 - a Drosophila orthologue of human Rootletin, a main protein components of ciliary rootlets. CG6129 expression is specific to the ciliated cells and exhibits so called chordotonal-enriched pattern - a strong and permanent expression in the chordotonal subtype of type I neurons and weaker and transient expression in the external sensory subtype. I have shown that CG6129 knock-down causes severe disruption of the chordotonal organs function without any obvious change in the structure of the cilium, other than the lack of ciliary rootlet. The function of the external sensory subtype was only slightly affected which further highlights the difference between the two types of ciliated sensory organs. The fact that CG6129 is differentially expressed in the two subtypes of the Drosophila ciliated sensory neurons suggests that the genes involved in the formation of various cilia are differentially regulated. I have shown that CG6129 is regulated by the two well known ciliary transcription factors - RFX and fd3F (distant homologue of Foxj1). Of the two enhancers found the early-to-late enhancer is almost entirely dependent on RFX and not on fd3F while the late enhancer is dependent on both fd3F and RFX. The fact that there is some residual CG6129 expression in the absence of both RFX and fd3F suggests involvement of another regulator that may contribute to the cilia diversity. Zmynd10 is a recently characterised ciliary gene that is involved in the axonemal dynein arms assembly. Mutations in human Zmynd10 cause primary ciliary dyskinesia (PCD) and Drosophila Zmynd10 mutants have immotile cilia that lack dynein arms. Due to the presence of specific protein domains Zmynd10 has been suggested to act as a transcriptional regulator. I have shown that the transcript levels of CG6129 and other ciliary genes are reduced in the Zmynd10 mutant. This implies that Zmynd10 may regulate ciliary genes on a transcriptional or post transcriptional level and may contribute to the regulatory network governing ciliogenesis.

Long terminal repeat (LTR) retrotransposons account for approximately 10% of mouse and 8% of human genomes and may play a role in modifying gene expression. Many species harbor retrotransposon families encompassing both autonomous and non-autonomous members. Specifically, the mouse Early Transposon (ETn) family members lack all retroviral genes but are transcriptionally and retrotranspositionally active, causing over 20 known insertional germline mutations. ETns owe their retrotransposition potential to proteins encoded by structurally intact MusD retrotransposons with whom they share LTRs. ETn elements are transcribed at a much higher level than MusD retrotransposons in embryos and undifferentiated cells, suggesting their evasion of host restriction mechanisms. However, mechanisms responsible for the replicative success of non-autonomous retrotransposon subfamilies over their coding-competent relatives are poorly understood. In the first stage of my research, I analyzed regulatory sequences in an ETn LTR responsible for its high promoter activity in the undifferentiated cell line P19. I found that three GC-boxes that may function as Sp1/Sp3 binding sites act synergistically and are indispensable for undifferentiated cell-specific promoter activity of the LTR. Sp1 binding partners may be responsible for the restricted ETn expression. Moreover, I have shown that unlike many retroviruses, ETn elements possess multiple transcription initiation sites and that they have amplified via intracellular retrotransposition in the P19 teratocarcinoma cell line. In the next step of my research, I performed analysis of epigenetic mechanisms as a means of ERV suppression. Specifically, I showed that in embryonic stem cells, autonomous MusD retrotransposons are epigenetically suppressed to a greater degree than non-autonomous ETn retrotransposons, illustrated by a higher level of DNA methylation and a lower level of active histone modifications. I hypothesize that MusD elements may be silenced by DNA methylation and repressive chromatin spreading into the LTR from the CpG-rich internal retroviral sequence absent in ETn elements. I propose that internal structure largely devoid of high CG content enables ETn elements to evade host-imposed transcriptional repression, contributing to their high mutagenic activity in the mouse germline. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Pax3 and Pax7 belong to a family of conserved transcription factors that play important and diverse roles in development. In the embryo, they carry out similar roles in neural and somite development, but Pax7 fails to compensate for critical functions of Pax3 in the development of limb musculature. Conversely, in the adult, Pax7 is necessary for the maintenance and survival of muscle satellite cells, whereas Pax3 cannot effectively fulfill these roles in the absence of Pax7. To identify the unique roles of Pax7 in adult muscle cells, we have analyzed global binding of Pax3 and Pax7 by ChIP-Seq. Here, we show that despite highly homologous DNA-binding domains, the majority of binding sites are uniquely recognized by Pax7 and are enriched for homeobox motifs. Genes proximal to conserved, unique Pax7 binding sites cluster into specific functional groups which may reflect the unique biological roles of Pax7. Combining Pax7 binding sites with gene expression data, we describe the regulatory networks directed by Pax7 and show that Pax7 binding is associated with positive gene regulation. Moreover, we show Myf5 is a direct target of Pax7 and identify a novel binding site in the satellite cell control region upstream of Myf5.

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.

With the increasing threat of multidrug resistant bacteria, there is a growing need to invent new drug classes that combat untreatable infections. Small molecule antibiotics have been successful in the past, but humanity is now losing the arms race against previously treatable pathogens. However, the number of clinically approved drugs targeting traditionally undruggable targets in bacteria remains low. New targets of complex protein-target interactions must be targeted for future pharmacological development. In an effort to create clinically viable biologics, the Verdine lab has developed a class of therapeutics called hydrocarbon stapled α-helical peptides; these peptides are known to affect protein-protein interactions by retaining secondary structure in vivo. Although this class of molecules has been extensively researched in cancer and viral therapies, there has been little work in bacteria due to the proposed endocytic method of entry. Moreover, DNA-binding stapled peptides have not been extensively investigated due the complexities in designing a peptide with gene selectivity. In an attempt to study peptides in bacteria, two stapled peptides based on the RpoN domain of σ54 and the FtsZ C-terminus have been synthesized. σ 54 is a DNA-binding co-factor of RNA polymerase (RNAP) and has been shown to regulate virulence and nitrogen and carbon metabolism. FtsZ is the structural unit of the contractile Z-ring that induces cell division. By designing stapled α-helical peptides to target these untraditional PPIs, we anticipate that these molecules may be used for future antimicrobial pharmacological development that treat multidrug resistant bacteria.