Diabetic embryopathy is one of many serious complications associated with diabetes. It is known that maternal diabetes increases the frequency of congenital defects up to ten times. The most common defects are cardiovascular and neural tube defects. Molecular mechanisms of diabetic embryopathy are still not known. This work contributes to elucidation of molecular processes leading to development of cardiovascular defects in diabetic embryopathy. This study is based on observation that maternal diabetes affects transcriptional regulation of hypoxia-inducible factor 1 (HIF-1) in developing embryo. To study the influence of maternal diabetes on HIF-1 signaling pathway, we used mouse model heterozygous for "knock-out" of Hif1α gene. Our analyses showed the negative combinational effects of maternal diabetes and Hif1α+/- genotype on embryonic development and increased risk of diabetic embryopathy. Histological analysis demonstrated the increased incidence of cardiovascular defects, particularly defects of interventricular septum and hypoplastic compact left ventricular wall in embryonic day (E) 14.5 Hif1α+/- embryos compared to wt littermates from the diabetic pregnancy. Using qPCR, we analyzed gene expression changes in the embryonic hearts at E9.5 and E10.5. We selected genes important for the...

Embryonic stem (ES) cell pluripotency is sustained by a network of transcription factors centred on Oct4, Sox2 and Nanog. Whilst Oct4 and Sox2 expression is relatively uniform, ES cells fluctuate between states of high Nanog expression possessing high self-renewal efficiency, and low Nanog expression exhibiting increased differentiation propensity. Moreover, modulation in the level of Nanog expression determines the efficiency of ES cell self-renewal. To identify genes regulated by Nanog, genome-wide transcriptional profiling was performed on ES cells expressing different Nanog levels and Nanog-null ES cells expressing a Nanog-ERT2 fusion protein in which nuclear Nanog activity can be regulated by tamoxifen. Surprisingly, only a minor fraction of the genes to which Nanog binds showed significant changes in response to Nanog induction. Prominent amongst Nanog-responsive genes is Estrogen-related receptor b (Esrrb). Nanog binds directly to Esrrb, enhances binding and pause-release of RNAPolII from the Esrrb promoter and stimulates Esrrb transcription. Consistent with these findings, elevation of Nanog produces a cell population that expresses uniformly high Esrrb levels. Moreover, double fluorescent reporter lines show that Esrrb and Nanog levels are strongly correlated in individual cells. Loss of Nanog is required for downregulation of Esrrb, which coincides with commitment to differentiate. Esrrb overexpression results in LIF independent self-renewal, and blocks neural differentiation, even in the absence of Nanog. Cell fusion experiments between ES and neural stem (NS) cells show that elevated Esrrb levels allow the reprogramming of the NS cell genome in the absence of Nanog. Esrrb can rescue stalled reprogramming during the derivation of Nanog-/- induced pluripotent stem (iPS) cells. Moreover, targeted knock-in of Esrrb at the Nanog locus rescues the ability of Nanog null ES cells to maintain germ cell development beyond E12. Finally, Esrrb deletion abolishes the defining ability of Nanog to confer LIF-independent selfrenewal to ES cells. Together these data identify Esrrb as a critical downstream mediator of Nanog function.

DNA methylation is a major form of epigenetic modification and involves the addition of a methyl group covalently to the 5-position of the cytosine pyrimidine ring, mostly within the context of CpG dinucleotides in vertebrate somatic cells. Methylation of CpG dinucleotides at promoter regions is generally associated with transcriptional repression. In this context, the methyl-CpG binding proteins (MeCPs) that are capable of recognition of methylated CpG dinucleotides are proposed to play a central role in DNA methylation associated transcriptional repression. Methyl-CpG binding domain protein 4 (MBD4) is an MeCP that possesses a glycosylase domain at its C-terminal, which can excise and repair both G:T and G:U mutations derived from DNA deamination at CpG dinucleotides, in addition to its Nterminal MBD binding domain. MBD4 has been associated with a number of pathways including DNA repair, apoptosis, transcriptional repression, and possibly DNA demethylation processes. However, the precise contribution of MBD4 to these processes remains unclear. To explore the functional repertoire of MBD4 I decided to undertake multiple protein interaction studies to identify potential partner proteins. I performed yeast 2-hybrid screens with an 11.5 day mouse embryonic cDNA library and multiple mass spectrometry of immunoprecipitates of tagged versions of MBD4 that were over-expressed in human cell lines. I detected ~380 potential interacting candidates with these assays. A significant number of candidates were detected in both assay systems. Chosen candidates were further validated by reciprocal co-IP of expressed partners and by immunofluorescence (IF) microscopy to determine their potential co-localisation in mouse and human cell lines. Subsequently, I identified the intervening domain of MBD4 as a novel protein interaction region for tested candidates. My analysis suggests that MBD4 can have a role in regulation of post-replication methyl-error repair/methylation machinery through its direct interaction with DNMT1 (previously shown), UHRF1 (novel) and USP7 (novel), as well as possible cross-talk to histone modification and chromatin remodelling pathways, through partners such as PRMT5 and ACF1. Interestingly the transcription regulatory components KAP1 and CFP1 not only interact with but also dramatically influence the stability of exogenously expressed MBD4 in human cells. In general positive validation by IP and IF demonstrates the robustness of the initial screens, and implies that MBD4 may impact upon several transcriptional and epigenetic networks along with a number of nuclear pathways that include transcriptional repression, DNA repair and RNA processing. To test for transcriptional aberration in the absence of Mbd4 function I profiled two independent mouse cell lines that lack MBD4 activity using Illumina MouseWG-6 v2.0 Expression BeadChip arrays. A number of genes were identified that are significantly up- or down- regulated in both Mbd4-/- MEFs. This included mis-expression of insulin-like growth factor-binding proteins and two paternally imprinted genes Dio3 and H19. The cohort of genes that were mis-expressed in the Mbd4-/- MEFs overlap with genes that responsed to tamoxifen exposure in an ER-positive ZR-75-1 xenograft model. In response to this observation I identified a potential interaction between MBD4 and estrogen receptor α (ERα) by co-IP and IF co-localisation. This suggests that MBD4 might potentiate transcription of estrogen regulated genes via a direct interaction with ERα, supporting a possible link between replication repair remodelling and steroid/thyroid hormone receptor transcriptional regulation. Additionally I performed a pathway analysis by which several developmental genes including Sox9, Klf2 and Klf4, were prioritised as possible MBD4 targets. On this basis I propose a role for MBD4 in acquired diseases such as cancers and autoimmune diseases via transcriptional regulation. I also performed a comparison of MBD4 DNA binding activity with MBD4 homologues from the Medaka fish (Oryzias latipes) and the amphibian, Xenopus laevis. I could show that DNA binding specificity to a series of methylated and mismatched probes is conserved regardless of the poor sequence conservation of the MBD domain of MBD4 between the species. I conclude that MBD4 is integrated in multiple pathways in the nucleus that includes DNA repair, chromatin remodelling, transcriptional regulation and genome stability.

Diabetes mellitus affects nearly 300 million people in the world. The development of diabetes is caused by dysfunction or by reduction of insulin-producing β-cells that are part of the endocrine pancreas. Therefore, the most critical step for understanding the pathophysiology of diabetes and for restoring lost β cells is the identification of molecular cues that specify the cellular phenotype in the pancreas. This work is based on the hypothesis that the transcription factor NEUROD1 is a key factor for the development of the pancreas and for the maintenance of endocrine tissue function. Neurod1 conditional KO mutants (Neurod1CKO) were generated using the Cre-loxP system by crossing floxed Neurod1 mice with Isl1-Cre line. Immunohistochemical analyses of the pancreas at embryonic day 17.5 and postnatal day 0 showed that the deletion of Neurod1 negatively affected the development, organization of endocrine tissue, and total mass of pancreatic endocrine cells. To better understand molecular changes, quantitative PCR was used to analyse mRNA expression in the developing pancreas at the age of embryonic day 14.5 and postnatal day 1. Genes important for the development and function of the pancreas have been selected for the study of expression changes. These analyses showed changes in expression of genes...

Thesis advisor: Jeffrey H. Chuang / Gene regulation is perhaps least understood among vertebrate species, where cell differentiation, tissue-types and body-plans indicate a complexity in need of careful coordination to achieve such hierarchical design. Recent studies reveal the intricacy of vertebrate gene regulation through diverse events including transcriptional regulatory histone modifications and non-coding DNA [1-5]. Almost 98% of the human genome is noncoding DNA, much of which may be actively involved in regulating healthy and disease-state gene expression and environmental response [6]. Conserved noncoding elements (CNEs) are sequences of noncoding DNA that are known to regulate gene expression [7-9]. The CNEs identified thus far are a small percentage of the total noncoding DNA in the human genome, and many identified CNEs still lack experimental characterization [10]. Thus, there is a need for functional characterization and streamlined identification of CNEs in order to more fully annotate vertebrate genomes and understand gene expression. The work in this thesis identified over 6000 CNEs and experimentally characterized over 150 CNEs conserved between zebrafish and human (> 60% DNA sequence conservation), using the experimental model Danio rerio (zebrafish). Functional, tissue and time-specific CNEs were identified through analysis of conservation, accelerated evolution, distance, GC content, motifs, transcription factors and gene function. In addition, a searchable database and website was created to host data and facilitate collaborative research between experimental and computational labs. While non-coding DNA is an important area of discovery for gene regulation, protein-coding DNA also has the potential to contain non-coding transcriptional information. DNA is typically conceptualized as either noncoding or protein coding. An underlying assumption to this framework assumes that the function of noncoding DNA is "regulatory" and coding DNA is "protein coding." Consequently, the potential for DNA to harbor both types of information in one sequence has been minimally researched. For the second-half of this thesis, I identified and experimentally tested 31 conserved coding exons ( > 60% zebrafish and human DNA sequence conservation) in zebrafish. To improve annotation of live embryonic expression, a novel voice-recognition expression analysis system was developed that allows quick comparison and annotation of embryonic expression at the microscope. In addition, a website and webtool to calculate significant expression was created as a resource for experimental research on anatomical analysis in whole organisms. The experimental results show that a large number of protein-coding DNA sequences can act as non-coding enhancers. This knowledge may impact methods to identify noncoding signals and, further, the scientific conceptualizations of coding and noncoding DNA in the genome. / Thesis (PhD) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

A ampliação do conhecimento sobre as formas de comunicação, controle e regulação existentes em bactérias traz luz aos avanços no combate das infecções hospitalares que são responsáveis por inúmeros prejuízos relacionados à saúde pública em todo planeta. DUMOULIN et al (2013), descreveram o regulador transcricional (RT) ElrR, que regula positivamente a transcrição do gene elrA, um fator de virulência de Enterococcus faecalis. ElrA apresenta grande similaridade com as internalinas de Listeria monocytogenes, que facilitam a invasão da bactéria ao hospedeiro. ElrR é considerada como pertencente à família Rgg-like de RT exclusivo de bactérias Gram positivas. Por vários motivos a família Rgg foi inserida à superfamília RNPP, gerando a superfamília RRNPP de RT. Os RRNPP fazem parte de um sistema de regulação por quorum sensing (QS), um sistema de comunicação célula-célula dependente de densidade celular, com função associada na ativação ou inibição da expressão de proteínas relacionadas, dentre outros, à virulência, formação de biofilme e esporulação. Para a melhor compreensão do mecanismo de como ocorre a ativação da transcrição do fator de virulência ElrA, este trabalho apresenta resultados de expressão heteróloga em E. coli e purificação das proteínas ElrR e ElrA, bem como resultados de experimentos biofísicos que caracterizam algumas propriedades estruturais e biológicas destas proteínas. Utilizando técnicas de cromatografia, espectroscopia de dicroísmo circular (CD), anisotropia de fluorescência, espalhamento dinâmico de luz (DLS), cristalografia de raios X e ressonância plasmônica de superfície (SPR), foi possível a obtenção da estrutura tridimensional de ElrR e de indícios da interação com uma região de 25bp do DNA. Realizou-se ainda, em colaboração com Dra. Pascale Serror, a tentativa de obtenção da molécula autoindutora (AI) de ElrR. São apresentados primeiros resultados da obtenção heteróloga de ElrA, sua purificação e cristalização, com importantes características que permitirão a continuação da investigação deste fator de virulência. ElrR é composta somente por alfa-hélices e apresenta-se dimérico em solução. Apesar da similaridade estrutural dos RRNPP, a identidade da sequência entre ElrR e os outros membros é extremamente baixa, o que motivou a resolução das fases cristalográficas experimentalmente. A estrutura de ElrR apresenta-se similar às homólogas, porém, com maior interface de interação entre os protômeros, que formam o dímero. O sítio de ligação do AI, em ElrR, apresenta-se mais amplo, com cavidade maior que as demais estruturas estudadas, conservando vários dos resíduos apresentados nos homólogos que realizam a estabilização do AI. Os altos fatores de temperatura dos cristais de ElrR, adicionado a anisotropia dos átomos, de uma das estruturas obtidas, apresenta a grande flexibilidade desse RT. Os indícios de interação entre ElrR e DNA aqui apresentados, obtidos por SPR e anisotropia de fluorescência, apresentam que ElrR liga especificamente ao fragmento proposto do DNA, ainda na ausência do AI. A não cristalização do complexo (ElrR-DNA), adicionada a alta flexibilidade apresentada na estrutura e a instabilidade observada na ligação ao DNA (por SPR) apontam para a obrigatoriedade da molécula de regulação (AI) para que o complexo ElrR-DNA seja estável. / The enhancing of the knowledge about communication, control and regulation in bacteria bring possibilities on the advance of hospital-acquired infections control responsible for various prejudices related to public health worldwide. DUMOULIN, et al (2013) described ElrR, a transcriptional regulator (TR), that positively regulates transcription of the elrA gene, which codifies a virulence factor of Enterococcus faecalis. ElrA shows high similarity with Listeria monocytogeneses internalins, which facilitates host invasion by these bacteria. ElrR are considered belonging to Rgg-like TR family exclusive of Gram positive bacteria. Several reasons include the Rgg family into the RNPP superfamily, generating the RRNPP superfamily of TR. The RRNPP are controlled by a quorum sensing (QS) regulation system, a cell-cell communication system based on cellular density that activates or inhibits the expression of proteins related with virulence, biofilm formation, sporulation, and others. For a better understanding of the transcription activation mechanism of ElrA, this work shows ElrR and ElrA heterologous expression in E. coli and purification of these proteins, as well as biophysics assays to characterize some structural and biological features of both proteins. Using chromatography, circular dichroism (CD), fluorescence anisotropy, dynamic light scattering (DLS), X-ray crystallography and surface plasmon resonance (SPR) technics, it was possible to obtain the tridimensional structure of ElrR, and evidences of ElrR-DNA complex formation, confirming DNA interaction site of ElrR with a 25 bp fragment. In collaboration with Dr. Pascale Serror, we attempted to achieve the ElrR auto-induction (AI) molecule. Also, results of the heterologous obtainment of ElrA are presented, as well as ElrA purification and crystallization, presenting important characteristics which will allow the further investigation of this virulence factor in near future. ElrR is composed by alpha-helices presenting dimeric fold in solution. Despite the similarity between the RRNPP members, the low identity of ElrR to the other members motivates the experimental crystallographic phases solution. ElrR structure is very similar to the homologous structures, presenting a higher interface between the protomers that compose the dimer. Its AI binding site is wider than the other structures studied, conserving several amino acid residues presented at the homologous proteins, that stabilizes the AI molecule. High temperature factors of the amino acid residues showed in all the obtained ElrR crystallographic structures plus the anisotropy of the atoms in one of those structures show the high flexibility of this TR. The evidence of the ElrR-DNA complex presented in this study, obtained by SPR and fluorescence anisotropy, indicates that ElrR binds at the proposed DNA site even in the absence of the AI molecule. The failure to obtain the ElrR-DNA complex crystals added to the high flexibility presented at some places of the structure and the observed instability at the formed complex (observed at SPR) suggest the mandatory need of the AI molecule to create a stable ElrR-DNA complex.

Nesta dissertação consideramos um o modelo para um gene como sendo um sistema de dois estados, tipo spin, e apresentamos um modelo estocástico para a expressão gênica. As soluções estacionárias e, também, as dependentes do tempo, para o processo de transcrição, são obtidas e as distribuições de probabilidade, que descrevem o estado funcional do gene, são calculadas analiticamente. O valor médio e o ruído transcricional na população de mRNA são analisados. O efeito do ruído transcricional na síntese proteica é contemplado acoplando-se os processo de transcrição e tradução. / In this dissertation we present a two state stochastic model, spin-like, for gene expression. The steady-state solutions and also the time-dependente solutions for the transcription are probed and the probability distribution functions, which describe the functional state of the gene, are exactly calculated. The mean value and the transcriptional noise in the mRNA population are analyzed. The effects of the transcriptional noise in the protein synthesis are contemplated by coupling the transcription and the translation.

The human proteom diversity is caused by the ability of a single gene locus to encode more protein isoforms. The TCF/LEF genes produce a broad spectrum of protein variants, which consequently leads to a great functional diversity of the TCF/LEF proteins. The TCF/LEF transcriptional factors regulate the canonical Wnt signaling target genes. In this diploma project we focused on the Caenorhabditis elegans gene pop-1, the ortholog of the TCF/LEF genes. Using the Northern blot analysis we tried to identify alternative isoforms of the pop-1 mRNA in C. elegans. Using quantitative RT-PCR we also analyzed the pop-1 mRNA levels. Key words: canonical Wnt signaling pathway, TCF/LEF transcription factors, Caenorhabditis elegans, pop-1

La famille des protéines IMPs (IGF2 mRNA binding proteins) compte trois membres IMP1, 2 et 3. Les IMPs participent au développement embryonnaire. IMP1 et IMP3 sont considérées comme des protéines oncofoetales. En effet, malgré leur faible expression dans les tissus adultes, elles se retrouvent fortement surexprimées dans des cellules tumorales. Malgré la forte homologie entre les membres de la famille, les IMPs présentent des différences fonctionnelles qui restent très mal comprises jusqu’à présent. De nombreuses études montrent que la protéine IMP3 est très abondante dans de nombreux cancers tels que les carcinomes utérin, rénal, pulmonaire, les hépatocarcinomes et les rhabdomyosarcomes. Ces dernières années, IMP3 est devenu un marqueur de mauvais pronostique pour les patients atteins de cancer. Au cours de ma thèse j’ai principalement travaillé sur une lignée cellulaire de rhabdomyosarcomes (RMS). Les RMS sont des tumeurs principalement pédiatriques mais qui peuvent survenir à tout âge. En outre, la moitié des patients atteints des RMS meurent dans l'année suivant leur rechute et 90% des patients meurent dans les cinq ans suivant leur rechute. De nouvelles approches thérapeutiques sont absolument nécessaires. Mon sujet de thèse consiste à comprendre par quels mécanismes moléculaires les IMPs participent au processus oncogénique des RMS embryonnaires (eRMS). Pour cela, je me suis intéressée à la régulation des cyclines par les IMPs. Dans le cadre de mon projet, j’ai étudié l’effet des IMPs sur trois cyclines différentes : D1, D3 et G1. J’ai montré qu’IMP3, à la différence des deux autres, est capable de contrôler l’expression des cyclines D1, D3 et G1 dans les eRMS, ainsi que dans huit autres lignées de cancer humain différentes. Cette régulation a également des effets sur le cycle cellulaire des eRMS, expliquant l’importance d’IMP3 dans les cancers. Par diverses approches biochimiques, j’ai démontré que, sur les trois IMPs, seule IMP3 est très enrichie dans le noyau des eRMS, dans lequel elle forme des complexes avec les ARNm des CCND1, D3 et G1. Les différents résultats obtenus suggèrent un modèle selon lequel ces interactions au sein du noyau semblent indispensables à la régulation de la traduction des trois cyclines en protégeant leurs ARNm du complexe de silencing RISC (RNA induced silencing complex) et constituent donc la clé du mécanisme par lequel IMP3 contrôle la prolifération des cellules cancéreuses. / RNA-binding proteins of the IMP family (IGF2 mRNA-binding proteins 1-3) are key post-transcriptional regulatory factors of gene expression. They are known to control cell motility, adhesion, and proliferation. In our previous work, we show that all three IMP proteins can directly bind the mRNAs of cyclins D1, D3, and G1 (CCND1, D3, and G1) in vitro. Nevertheless, only IMP-3 regulates their expression in a significant manner in vivo, thus controlling proliferation of a number of human cancer cell lines. Importantly, the nuclear localization of IMP-3 is essential for the post-transcriptional regulation of the expression of CCND1, CCND3, and CCNG1 (CCNs). To elucidate the molecular mechanisms of IMP-3- specific regulation, we have identified its protein partners in human embryonic rhabdomyosarcoma (RMS) cells. We now show that in the nucleus and in the cytoplasm, IMP-3 interacts with a number or RNA-binding nucleocytoplasmic proteins, including DHX9, PTBP1, NF90, NF110, HNRNPA1, HNRNPA2/B1 and HuR. These IMP-3 partners have a dramatic impact on the protein levels of the cyclins. Interestingly, the decrease of CCNs protein synthesis in IMP-3 depleted cells can be fully reversed by down-regulating the key proteins of RNAi machinery, such as AGO2 and GW182. These findings suggest that IMP-3- dependent RNP complexes pre-assembled in the nucleus can protect their target mRNAs from cytoplasmic RNAi-dependent repression in human cancer cells.

Nesta tese desenvolvemos um modelo estocástico para a transcrição do gene even-skipped de Drosophila melanogaster no qual a variável estocástica é o número de moléculas de mRNA transcritas. Nesse modelo, consideramos um gene com dois níveis de ativação sendo regulado externamente. As probabilidades de se encontrar o gene ligado ou desligado e com determinado número de moléculas de mRNA transcritas obedecem equações lineares dadas por processos markovianos de nascimento-e-morte (taxas de produção e degradação) e termos de chaveamento entre os níveis cujas dependências temporais são dadas por funções de Heaviside. Notamos que tal dependência é suficiente para garantir uma atividade transcricional inicial intensa seguida de uma súbita interrupção, conforme sugerem os dados experimentais. Desconsiderando efeitos difusivos e fenômenos de transporte, estendemos esse constructo às outras regiões do embrião, permitindo dependências espaciais apenas às termos de chaveamento, e o resultado gerado descreve os dados experimentais com boa concordância, indicando também que o aspecto binário do gene é suficiente para uma descrição semiquantitativa do fenômeno. Notavelmente, na região onde a listra se forma e concomitantemente a sua formação, o modelo prevê a redução do desvio quadrático (flutuação) e do ruído. Calculando a distribuição de probabilidade, verificamos que o regime estacionário é atingido antes da listra começar a desaparecer. Também estudamos uma conexão entre parâmetros do modelo e as proteínas envolvidas na regulação e, baseado em resultados da literatura, obtemos uma função com aproximadamente o mesmo efeito regulatório considerando gradientes de seis fatores de transcrição (Bcd, Hb, Gt, Kr, Kni e Tll) e apenas quatro sítios de ligação, o que sugere que a informação transcricional pode estar concentrada na regulação de poucos sítios. / In this thesis we develop a stochastic model to transcription of Drosophila melanogaster even-skipped gene in which the stochastic variable is the number of mRNA molecules transcribed. In this model we considered a gene with two activation levels being regulated externally. The probabilities of gene being on or off when there is a certain number of transcripts obey linear equations given by Markovian birth-and-death processes (production and degradation rates) and terms of switch between levels whose time-dependence is given by Heaviside functions. We note that is sufficient to ensure a strong transcriptional activity followed by a sudden disruption, as suggested by the experimental data. Disregarding diffusion effects and transport phenomena, we extend this construct to the others regions ot the embryo, allowing space-dependence only to terms of switch, and the results describe the experimental data with good agreement, indicating also that binary character of gene is sufficient to a semiquantitative description of the phenomenon. Notably, in the region where the stripe 2 is formed and simultaneously with its formation, the model predicts the reduction in standard deviation (fluctuation) and noise. By calculating the probability distribution, we find that stationary state is reached before stripe 2 starts to fade. We also study a connection between the parameters of the model and proteins involved in regulation and, based on results from the literature, we obtain a function with approximately the same regulatory effect considering six transcription factors (Bcd, Hb, Gt, Kr, Kni e Tll) and only four binding sites, suggesting that transcriptional information may be concentrated in regulation of few sites.