Understanding transcriptional regulation quantitatively is a crucial step towards uncovering and ultimately utilizing the regulatory semantics encoded in the genome. Transcription of a gene is induced by the binding of site-specific transcription factors (TFs) to so-called cis-regulatory-modules (CRMs). The frequency and duration of the binding events are influenced by the concentrations of the TFs, the binding affinities and location of the transcription factor binding sites (TFBSs) in the CRM as well as the properties of the TFs themselves (e.g. effectiveness, competitive interaction with other TFs). Modeling these interactions using a mathematical approach, based on sound biochemical and thermodynamic foundations, enables the understanding and quantitative prediction of transcriptional output of a target gene. In the thesis I introduce the developed framework for modeling, visualizing, and predicting the regulation of the transcription rate of a target gene. Given the concentrations of a set of TFs, the TFBSs in a regulatory DNA region, and the transcription rate of the target gene, the method will optimize its parameters to generate a predictive model that incorporates the regulatory mechanism of the observed gene. I demonstrate the generalization ability of the model by subjecting it to standard machine learning and hypothesis testing procedures. Furthermore, I demonstrate the potential of the approach by training the method on a gene in D. melanogaster and predicting the output of the homologous genes in 12 other Drosophila species where the regulatory sequence has evolved substantially but the regulatory mechanism was conserved. Finally, I investigate the proposed role-switching behaviour of TFs regulating the development of D. melanogaster, which suggests that SUMOylation is the biological mechanism facilitating the switch.

Understanding transcriptional regulation quantitatively is a crucial step towards uncovering and ultimately utilizing the regulatory semantics encoded in the genome. Transcription of a gene is induced by the binding of site-specific transcription factors (TFs) to so-called cis-regulatory-modules (CRMs). The frequency and duration of the binding events are influenced by the concentrations of the TFs, the binding affinities and location of the transcription factor binding sites (TFBSs) in the CRM as well as the properties of the TFs themselves (e.g. effectiveness, competitive interaction with other TFs). Modeling these interactions using a mathematical approach, based on sound biochemical and thermodynamic foundations, enables the understanding and quantitative prediction of transcriptional output of a target gene. In the thesis I introduce the developed framework for modeling, visualizing, and predicting the regulation of the transcription rate of a target gene. Given the concentrations of a set of TFs, the TFBSs in a regulatory DNA region, and the transcription rate of the target gene, the method will optimize its parameters to generate a predictive model that incorporates the regulatory mechanism of the observed gene. I demonstrate the generalization ability of the model by subjecting it to standard machine learning and hypothesis testing procedures. Furthermore, I demonstrate the potential of the approach by training the method on a gene in D. melanogaster and predicting the output of the homologous genes in 12 other Drosophila species where the regulatory sequence has evolved substantially but the regulatory mechanism was conserved. Finally, I investigate the proposed role-switching behaviour of TFs regulating the development of D. melanogaster, which suggests that SUMOylation is the biological mechanism facilitating the switch.

Genetic associations have been discovered for many human complex traits, and yet for most associated loci the causal variants and molecular mechanisms remain unknown. Studies mapping quantitative trait loci (QTLs) for molecular phenotypes, such as gene expression, RNA splicing, and chromatin accessibility, provide rich data that can link variant effects in specific cell types with complex traits. These genetic effects can also now be modeled in vitro by differentiating human induced pluripotent stem cells (iPSCs) into specific cell types, including inaccessible cell types such as those of the brain. In this thesis, I explore a range of approaches for using QTLs to identify causal variants and to link these with molecular functions and complex traits. In Chapter 2, I describe QTL mapping in 123 sensory neuronal cell lines differentiated from human iPSCs. I observed that gene expression was highly variable across iPSC-derived neuronal cultures in specific gene categories, and that a portion of this variability was explained by commonly used iPSC culture conditions, which influenced differentiation efficiency. A number of QTLs overlapped with common disease associations; however, using simulations I showed that identifying causal regulatory variants with a recall-by- genotype approach in iPSC-derived neurons is likely to require large sample sizes, even for variants with moderately large effect sizes. In Chapter 3, I developed a computational model that uses publicly available gene expression QTL data, along with molecular annotations, to generate cell type-specific probability of regulatory function (PRF) scores for each variant. I found that predictive power was improved when the model was modified to use the quantitative value of annotations. PRF scores outperformed other genome-wide scores, including CADD and GWAVA, in identifying likely causal eQTL variants. In Chapter 4, I used PRF scores to identify relevant cell types and to fine map potential causal variants using summary association statistics in six complex traits. By examining individual loci in detail, I showed how the enrichments contributing to a high PRF score are transparent, which can help to distinguish plausible causal variant predictions from model misspecification.

Apicomplexan parasites are leading causes of human and livestock diseases such as toxoplasmosis and malaria caused by Toxoplasma gondii and Plasmodium falciparum respectively. These organisms are varied in their morphologies and astoundingly complex on their life cycles that include infections of more than one host organism, differentiation through several morphologically distinct forms, and both sexual and asexual replication. What we and others have initially proposed was that the control of gene expression and cellular differentiation are particularly interesting in these organisms, as the apparent lack of large families of recognizable transcription factors typically found in other eukaryotic organisms suggests that they may be unusually reliant on epigenetic mechanisms. The initial hypothesis had to be re-assessed in light of the discovery in Apicomplexa of an expanded family of plant-like transcription factors (TFs) harbouring APETALA2 (AP2)-like domains. Yet, a growing body of evidence tends to favor epigenetic as one of the main contributor to parasite developmental programs and adjustments to fluctuant environment. One way to examine dynamic changes in post-translations modifications (PTMs) patterns is to alter the histone code writing. We therefore took advantage of HDAC inhibitors and showed that specific inhibition of TgHDAC3 by the cyclopeptide FR235222 disrupts the genome wide steady-state level of histone H4 acetylation inducing derepression of stage-specific genes. Yet, many questions about TgHDAC3 modus operandi remain unanswered. During my thesis, I uncovered the TgHDAC3-regulated proteome-wide acetylome typified by the presence of non-histone proteins including AP2 TFs and novel PTMs, e.g. the acetylation at Lys31 within the globular domain of histone H4. H4K31ac promotes a relaxed chromatin state at the promoter of active genes through nucleosome disassembly in both parasites. We identified TgGCN5B and TgHDAC3 as two antagonist enzymes regulating H4K31 acetylation in T. gondii. In contrast, H4K31monomethylation is enriched throughout the gene body of T. gondii active genes and contributes to transcription, whereas it is enriched at transcriptionally inactive pericentromeric heterochromatin regions in P. falciparum, a region that is lacking H3K9me3 and heterochromatin protein 1 in this parasite. We also showed that treating T. gondii cystogenic strains with a low dose of FR235222 induces the levels of proteins known to be expressed exclusively in cat (sporozoite and merozoite) or in murine chronic stage (bradyzoite). Lastly, we determined the specific interactome of TgHDAC3 and found as partners a MORC protein (CR230), several AP2 TFs, and ELM2 domain-containing scaffolding proteins. Collectively, these data established TgHDAC3 family as a central regulator of gene expression and stage conversion in T. gondii and, likely, other Apicomplexa. / Apicomplexan genome architecture is typified by a binary chromatin structure, with a major fraction of the bulk genome packaged as transcriptionally permissive euchromatin while few loci are embedded in silenced heterochromatin. There is evidence that histone modifications occurring at the lateral surface of the nucleosome play a substantial role in shaping chromatin structure, yet our understanding of the exact mechanism of action is poor. Here, we address how versatile modifications at Lys31 within the globular domain of histone H4 contribute to genome organization and expression in Apicomplexa. H4K31 acetylation was found at the promoter of active genes. The residue lies where the DNA wraps around the histone and its acetylation may enhance nucleosome disassembly, thereby favoring a more relaxed, open chromatin state. This residue tends also to be monomethylated and depending of the parasite examined different patterns were found. H4K31me1 was enriched in the core body of Toxoplasma active genes, yet its occupancy was inversely correlated with transcripts levels likely because the mark by reducing histone turnover impedes RNA polymerase progression across transcribed units. In contrast to the methylation of H3, it is the first time that a methylated residue of H4 has been clearly associated with transcriptional regulation. In Plasmodium, H4K31me1 was exclusively enriched at transcriptionally inactive genomic regions and peculiarly at pericentromeric heterochromatin, likely to replace the missing H3K9me3 that commonly decorated pericentric nucleosomes in other species.

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Orientador: Ney Lemke / Resumo: MicroRNAs (miRNAs) são pequenas moléculas de RNA que regulam pós-transcricionalmente a expressão de genes, modelando o transcriptoma e a produção de proteínas. Em geral, os miRNAs são conservados no genoma de eucariotos, sendo considerados elementos vitais em diversos processos biológicos durante o desenvolvimento, tais como crescimento, diferenciação e morte celular. A grande diversidade de miRNAs identificados está restrita a poucas espécies e apenas uma parte do total de alvos de miRNAs preditos foi caracterizada funcionalmente. Nesse contexto, o uso da tecnologia de sequenciamento de alto rendimento (high throughput sequencing) atrelada à análise de nível transcricional por RT-qPCR possibilitam a identificação do microRNoma. A tilápia do Nilo, Oreochromis niloticus, é considerada um excelente modelo biológico para o estudo de miRNAs em vertebrados devido à sua importância econômica e evolutiva. O presente trabalho teve como objetivos: organizar os dados do sequenciamento dos miRNAs da tilapia do Nilo; disponibilizá-los em forma de uma base de dados para a comunidade científica; integrar as informações dos miRNAs identificados com outros bancos de dados de miRNAs; analisar os dados através de análises de bioinformática para determinação de agrupamentos definidos pelo nível de expressão de cada miRNA em seis tipos de tecido (músculo branco, músculo vermelho, testículo, ovário, fígado, olho, cérebro e coração) com distinção entre os gêneros e nas fases do desenvolvimento (2,... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Os hormônios tireoidianos (HTs) promovem suas ações através de mecanismos genômicos, porém, há inúmeras evidências de que o HT também promove efeitos que ocorrem em curto espaço de tempo (poucos minutos), e que independem de, as quais são conhecidas como ações não genômicas ou extranucleares. É sabido que, na insuficiência cardíaca ocorre uma menor expressão dos receptores nucleares de T3, o que reduz em muito os efeitos cardioestimulantes deste hormônio, sendo muito vantajoso numa situação de contenção energética. Assim, o presente estudo visa avaliar o efeito agudo (não genômico) da administração de T3 sobre a translocação e expressão do GLUT4, e de proteínas-chave da atividade cardíaca, como GLUT1, Mb, SERCa2a, <font face=\"Symbol\">&#945; e <font face=\"Symbol\">b miosina, em: (1) ratos submetidos ou não à insuficiência cardíaca através de cirurgia de estenose aórtica, bem como em (2) cultura primária de cardiomiócitos neonatos e adultos. Nos modelos in vivo, observamos que, após 30 min da administração do T3 no grupo portador de ICC, há um aumento da expressão do mRNA do GLUT1, GLUT4 e Mb e da proteina GLUT1 e GLUT4. Quanto aos genes relacionados à função cardíaca, Atp2a2, Myh6 e Myh7, o tratamento com T3 por 30 min nos ratos portadores de ICC promoveu redução do conteúdo de mRNA dos três genes, bem como da proteína da beta MHC. O conteúdo de SERCa2a e da alfa MHC não se alterou em 30 min, mas aumentou após o tratamento com T3 por 60 min. No modelo in vitro de cardiomiócitos de neonatos, tivemos evidências de modulação do conteúdo de mRNA e proteínas, após 30 e 45 min, após a adição de T3 em diferentes doses (10-9 a 10-6 M). Quando avaliamos o efeito do T3 sobre o conteúdo de mRNA nos cardiomiócitos de adultos em cultura, também observamos uma resposta aleatória, não dependente de dose. O conjunto desses resultados aponta para a existência de um controle pós-transcricional do T3 sobre a expressão dos genes alvo desse estudo, podendo induzir uma melhora na função cardíaca na vigência de uma ICC, uma vez que essas ações são rapidamente desencadeadas e são fugazes, impedindo que os efeitos cardioestimulantes persistam, o que poderia ser deletério. / Through nuclear actions, thyroid hormones (TH) control the expression of several cardiac genes, but there are several evidences that TH also promotes effects that occur in a short time (few minutes), and which are independent of its interaction with specific nuclear receptors attached to the TH-responsive elements, known as non-genomic or extranuclear actions. In heart failure, there are a lower expression of nuclear T3 receptors, which reduce the cardiostimulating effects of the hormone, which is extremely advantageous in an energy contention. Thus, this study aims to evaluate the acute (nongenomic) administration of T3 on the expression and translocation of GLUT4, and key proteins of the cardiac activity, such as GLUT1, Mb, SERCa2a, <font face=\"Symbol\">&#945; and <font face=\"Symbol\">b myosin in: ( 1) rats with or without heart failure after aortic stenosis surgery, as well as (2) primary cultured cardiomyocytes neonates and adults. In the vivo model, after 30 min of the administration of T3 in the group with CHF, there is an increased in the mRNA expression in GLUT1, GLUT4 and Mb. Their proteins had an increase after 30 min (GLUT1 and GLUT4) and after 60 min (Mb). As for genes related to cardiac function, Atp2a2, Myh6 and MYH7, we observed that, the treatment with T3 for 30 min in rats with CHF promoted a decrease of the mRNA of three genes as well as the beta MHC protein. The content of alpha-MHC and SERCa2a did not change in 30 min, but increased after T3 treatment for 60 min. In the in vitro model of neonatal cardiomyocytes, we had evidence of modulation of mRNA and protein content after 30 and 45 min after the addition of T3 in different doses (from 10-9 to 10-6 M). When evaluating the effect of T3 on the mRNA content in adult cardiomyocytes in culture, we also observed a random response, not dependent on dose. All the data obtained so far points to the existence of a post-transcriptional control of T3 on the expression of target genes of this study, which could induce an improvement in cardiac function in the presence of an CHF, since these actions are elicited and fleeting, preventing cardiostimulating effects persist, which could be deleterious.

Pendrina é um transportador de ânions inserido na membrana apical de células foliculares. Estudos subseqüentes demonstraram que a proteína pode mediar o efluxo apical do iodeto nos tirócitos. Sendo o iodo fundamental para a síntese de hormônios tiroidianos foi objetivo deste estudo avaliar o efeito da administração aguda de iodo na expressão do mRNA da proteína pendrina, em curtos períodos de tempo (30min à 24h).Ratos Wistar foram divididos em: controle e iodo, que receberam injeção de salina ou NaI, sendo decapitados após 30, 1 e 24h dessa administração.O RNA da tiróide foi extraído para a análise da expressão do mRNA da Pendrina por Real Time PCR e Northern Blot. Para o estudo in vitro utilizou-se a linhagem celular de tiróide de rato PCCl3, que foi tratada ou não com 10-3M de NaI. As células permaneceram sob tratamento por 30´, 1 e 24h, quando então o RNA foi extraído para análise da expressão por Real Time PCR.Houve aumento significativo do mRNA da Pendrina em todos os grupos, indicando que mecanismos foram desencadeados visando o efluxo do iodeto da célula. / Pendrin is a chloride/iodide exchange located at the apical membrane of thyrocytes. Mutations in its gene lead to a defect in iodide organification. This suggested that pendrin could function as an apical iodide transporter in this cells. Since iodine is essential for thyroid hormone synthesis, this study attempted to investigate that possibility by evaluating whether the acute iodide administration, from 30min up to 24h, could regulate the Pendrin mRNA expression. Rats received NaI or saline, and were sacrificed 30´, 1 and 24h later.Thyroid total RNA was extracted and Pendrin mRNA content was evaluated by Northern Blotting and Real-Time PCR. For in vitro study,PCCl3 rat thyroid cells were cultured and treated or no with 103M NaI. After 30´, 1 and 24h, the cells were harvested and total RNA was extracted. The mRNA content was evaluated by Real-Time PCR. The mRNA increased in all groups of study, indicating that excess of iodide leads to an activation of Pendrin gene transcription and as consequence increased efflux of this element.

O estresse oxidativo, causado por níveis aumentados de espécies reativas de oxigênio (ROS), pode causar danos celulares. Várias enzimas, como as subunidades da alquil-hidroperóxido redutase (AhpC e AhpF) e as superóxido dismutases (SOD), são responsáveis por remover as ROS. Os mecanismos de regulação da expressão gênica de C. crescentus para os genes ahpC, sodA, sodB e sodC, foram analisados com fusões de transcrição ao gene repórter lacZ, permitindo a quantificação da expressão por ensaios da atividade de b-galactosidase, e RT-PCR quantitativo. As culturas foram cultivadas em meio PYE ou M2 e a expressão de cada gene foi avaliada na presença de peróxido de hidrogênio (H2O2), tert-butil hidroperóxido (tBOOH), paraquat, menadiona, pirogalol, FeSO4 ou DDPi. Em C. crescentus ahpC é induzido por peróxidos e regulado por OxyR. As SODs são induzidas principalmente por superóxidos, sodB e sodC possuem indução de fase na fase estacionária e possivelmente estão sob o controle do sigma J, enquanto o gene sodA é regulado por sigma F e sigma J. / Oxidative stress, caused by increased levels of reactive oxygen species, can lead to damage in all cellular components. Several enzymes, as subunit of alkyl hydroperoxide reductase (AhpC and AhpF) and superoxide dismutases (SOD), are responsible for removing ROS. Mechanisms of gene expression of C. crescentus for genes ahpC, sodA, sodB and sodC, were evaluated with transcription fusions with the lacZ reporter gene were constructed, allowing the quantification of expression by b-galactosidase activity assays, furthermore we analyze of the gene expression by qRT-PCR assay. The cultures were grown in PYE and M2 media, and gene expression was evaluated in the presence of hydrogen peroxide (H2O2), tert-butyl hydroperoxide (tBOOH), paraquat, menadione, pyrogallol, FeSO4 or DPPi. In C. crescentus ahpC is induced by peroxides and is under the control of OxyR. The SODs are mainly induced by superoxide, sodB and sodC are induction in stationary phase and are possibly under the control of sigma J, while the sodA gene is regulated by sigma F and sigma J.

Caulobacter crescentus pertence ao grupo das proteobactérias e apresenta a característica distinta de diferenciação celular a cada divisão. Este trabalho visou desvendar os mecanismos de reparo de DNA em C. crescentus. Identificamos 44 genes pertecentes ao regulon SOS através da construção de um mutante para o repressor deste, LexA. Caracterizamos funcionalmente alguns dos genes do regulon, como CC_2272 (que codifica uma proteína da família das endonucleases III) e CC_2433. A cepa deficiente em LexA apresentou morfologia filamentosa, e por esse motivo, buscamos também desvendar quais seriam os fatores genéticos responsáveis por esta morfologia. Investigamos também os processos de controle do ciclo celular após a introdução de danos na molécula de DNA pela luz UVC, em mutantes deficientes para diferentes vias de reparo. Estes experimentos nos mostraram que as células procariontes possuem mecanismos para acoplar a progressão do ciclo celular a integridade do material genético. Este trabalho abre novas e excitantes possibilidades no campo da biologia bacteriana. / Caulobacter crescentus belongs to the proteobacteria group and exhibts the distinctive feature of cellular differentiation after each division. This work aimed to reveal the DNA repair mechanisms in C. crescentus. We have identified 44 genes belonging to the SOS regulon through the construction of a mutant strain to its repressor. We have functionally characterized some of its genes, like CC_2272 (that encodes an endonuclease III family protein) and CC_2433. The lexA strain showed filamentous morphology, e because of that, we have tried to discover which the genetic factors responsible for this morphology were. We have also investigated the cell cycle control processes after the introduction of damages in the DNA by the UVC light, in mutant strains deficient in different repair pathways. These experiments showed us that prokaryotic cells possess mechanisms to couple the cell cycle progression to the integrity of the genetic material. This work opens new and exciting possibilities in the field of bacterial biology.