No genoma de camundongo existem por volta de 1000 genes que codificam para receptores olfatórios (ORs) e 150 genes que codificam para receptores de feromônios do tipo 1 (V1Rs) distribuídos em vários cromossomos. Cada neurônio olfatório e vomeronasal seleciona um único alelo de um único gene de receptor OR ou de V1R, respectivamente, para expressar enquanto que o restante do repertório é mantido silenciado. Os mecanismos que regulam esse padrão de expressão não são conhecidos. As similaridades no padrão de expressão dos genes de ORs e de V1Rs sugerem que o mecanismo de regulação possa ser comum. Até então poucas regiões promotoras de genes de ORs e de genes de V1Rs haviam sido experimentalmente determinadas e pesquisadas. Realizamos uma análise na qual regiões a montante de um grande número de diferentes genes de ORs e de genes de V1Rs foram comparadas. Primeiro, utilizando a técnica de RLMRACE, combinada com o uso de oligonucleotídeos capazes de reconhecer regiões conservadas entre diversos membros das famílias de genes de ORs e de V1Rs, geramos centenas de cDNAs contendo a região 5UTR completa para um total de 198 genes de ORs e 39 genes de V1Rs diferentes. Então, alinhamos as sequências desses cDNAs contra o genoma de camundongo e localizamos a posição exata dos sítios de início da transcrição (TSSs) de cada gene. Extraímos seqüências a 5 dos TSSs dos 198 genes de ORs e dos 39 genes de V1Rs e buscamos por motivos de DNA comuns, presentes em várias dessas regiões promotoras, que pudessem ser 6 candidatos a elementos cis-atuantes envolvidos na regulação geral desses genes de receptores sensoriais. Identificamos, na grande maioria das regiões promotoras dos genes de ORs e dos genes de V1Rs analisadas, a presença de motivos semelhantes a sítios de ligação para os fatores de transcrição O/E que são fatores de transcrição já caracterizados e envolvidos com a expressão de genes específicos do sistema olfatório. Ensaios de EMSA mostraram que os motivos semelhantes aos sítios de ligação de O/E identificados interagem com proteínas nucleares de epitélio olfatório, mas não interagem com proteínas nucleares de cérebro e fígado. Identificamos também nas regiões promotoras de genes de V1Rs a presença de um sítio de ligação que não se assemelha a nenhum sítio de ligação de fatores de transcrição conhecido. Esse motivo de DNA, além de estar presente na maioria dos promotores de genes de V1Rs analisados (77% do total de 39 genes pesquisados), também aparece, com alta frequência, em promotores de genes de ORs (52% do total de 198 genes analisados), preferencialmente próximo aos TSSs. Ensaios de interação in vitro indicam que este novo motivo de DNA interage com proteínas nucleares extraídas de órgão vomeronasal e também de epitélio olfatório, mas não interage com proteínas nucleares de cérebro, fígado e pulmão. Nosso trabalho mostra que genes de ORs e de V1Rs compartilham elementos comuns em suas regiões promotoras os quais podem ser sítios de ligação de fatores de transcrição específicos do sistema olfatório envolvidos no mecanismo de regulação da expressão desses genes. / In the mouse genome there are approximately 1000 genes that encode olfactory receptors (ORs) and 150 genes that encode type 1 vomeronasal receptors (V1Rs) dispersed in various chromosomes. Each olfactory or vomeronasal neuron selects one single allele from one single receptor gene (OR or V1R) for expression while the rest of the repertoire remains silenced. The mechanisms underlying OR and V1R gene expression are still unknown. The similarities of the pattern of expression in both types of olfactory sensory neurons suggest that the regulation of OR and V1R gene expression may be under the control of a common mechanism. Until now, promoter regions of different OR and V1R genes had not been extensively analyzed. We carried out a comprehensive analysis in which the upstream regions of a large number of different OR and V1R genes were compared. First, using the RLM-RACE strategy, combined with degenerate PCR we generated hundreds of complete 5UTR cDNAs for a total of 198 OR genes and 39 V1R genes. Then, these cDNAs were aligned against the mouse genome sequence and the transcription start sites (TSSs) were precisely determined. Sequences upstream of the TSSs were retrieved and searched for common DNA motifs that may play a role as cis-acting elements involved in the general regulation of OR and V1R gene expression. The analysis revealed the presence of motifs that resemble O/E-like sites overrepresented in the OR and V1R promoter regions. These O/E-like motifs specifically interact with nuclear protein prepared from olfactory epithelium, but not from brain and liver. 8 We also identified a new motif that does not resemble any known transcription factor binding site. Besides, this new motif is present in 77% of the 39 V1R promoter regions and in 52% of the 198 OR promoter regions analyzed, preferentially concentrated near the TSSs. Interestingly, binding assays indicate that this new motif interacts with nuclear proteins prepared from the vomeronasal and the olfactory epithelia, but not from brain, liver and lung. Our results indicate that OR and V1R genes share common promoter elements that may be binding sites for specific olfactory transcription factors and may play a role in a common mechanism of olfactory and vomeronasal gene regulation

Chez les eucaryotes, l’ARN polymérase (RNAP) III transcrit les ARN de transferts, l’ARN ribosomique 5S, et plusieurs douzaines d’autres ARNs non traduits. Le génome des mammifères contient plusieurs milliers d’éléments répétés, les SINEs. In vitro, leur transcription dépend de la RNAP III. Le taux de transcription de la RNAP III détermine la croissance et la prolifération cellulaires, sa dérégulation a été associée à de nombreux cancers. Afin de caractériser la distribution sur l’ensemble du génome de la RNAP III et de ses facteurs de transcription TFIIIB et TFIIIC, nous avons développé un protocole très spécifique de ChIP-seq en tandem. Nous avons déterminé l’ensemble des gènes liés par la RNAP III dans les cellules souches embryonnaires de souris. Cet ensemble est bien inférieur au nombre de gènes prédits dans le génome. Nous avons également observé la RNAP III et ses facteurs de transcription liés à 30 régions non annotées, seule une d’entre elles est conservée chez l’humain. Un très faible nombre de SINEs sur un demi-million prédits est associé à la RNAP III. Notre étude révèle de nombreux sites liés uniquement par TFIIIC, nommés « extra-TFIIIC loci », ETC chez la levure. Ces sites sont associés à la protéine CTCF, et à la cohésine. La cohésine occupe les sites liés par CTCF, et contribue à la formation de boucles ADN, associées à la répression ou à l’activation de l’expression des gènes. Ces données suggèrent que TFIIIC peut jouer un rôle dans l’organisation de l’architecture chromosomique chez les souris. Nous avons également démontré que TCEA1, l’isoforme ubiquitaire de TFIIS, le facteur d’élongation de la RNAP II, est associée aux gènes actifs de classe III. Ceci suggére que TFIIS est un facteur de transcription de classe III. Finalement, la distribution de TFIIS aux gènes de classe II indique que le recrutement de TFIIS n’est pas suffisant pour contrôler la transition de la RNAP II pausée en 5’ des gènes en élongation. / In eukaryotes, RNA polymerase (RNAP) III transcribes the tRNAs, the 5S ribosomal RNA and a half a dozen known untranslated RNA. Mammalian genome contains several thousand of repeated elements, the Short interspersed repetitive elements (SINE). In vitro, they are transcribed by RNAP III. RNAP III transcription levels determine cell growth and proliferation and, importantly, its deregulation is associated with cancer. Looking at the genome-wide distribution of RNAP III and its transcription factors, TFIIIB and TFIIIC, we develop a highly specific tandem ChIP-sequencing method. We have determined the set of genes that are transcribed by RNAP III in mouse embryonic stem cells. We discovered that not all known class III genes were transcribed in ES cells. We also observed that RNAP III and its transcription factors were present at thirty unannotated sites on the mouse genome, only one of which was conserved in human. Only a couple of hundreds of SINEs out of more than half a million are associated with RNAP III in mouse ES cells. Our study reveals numerous ‘TFIIIC-only’ sites, called ETC for extra-TFIIIC loci in yeast. These sites are correlated with association of CTCF and the cohesin. Cohesin has been shown to occupy sites bound by CTCF and to contribute to DNA loop formation associated with gene repression or activation. This observation suggests that TFIIIC may play a role in chromosome organization in mouse. We also demonstrated that TCEA1, the ubiquitous isoform of TFIIS RNAP II elongation factor, is associated with active class III genes suggesting that TFIIS is a RNAP III transcription factor in mammals. Finally, the distribution of TFIIS on RNAP II-transcribed genes indicated that its recruitment does not control the transition of RNAP II paused at genes 5’ end into elongation.

Die vorliegende Studie präsentiert eine Analyse der Integration der AhR und Wnt/beta-catenin Signalwege in den CYP1A1 Promotor sowie den regulatorischen Einfluss der Promotorlogik auf die Genexpression. Experimentell wurde diese Analyse mithilfe 29 mutagener Reporterkonstrukte des humanen CYP1A1 Promotors durchgeführt. Ein mathematisches Modell, welches eine Repräsentation des Crosstalks der Signaltransduktionswege mit einer statistisch mechanischen Beschreibung der kombinatorischen Promotorbelegung kombiniert, komplementierte den experimentellen Ansatz. Unter zusätzlicher Zuhilfenahme von gut kontrollierbaren synthetischen Promotorkonstrukten fand ich heraus, dass nur jenes Dioxin-responsive Element das sich am nächsten am Transkriptionsstartpunkt befindet, die Promotorbelegung an die RNA Polymerase kommuniziert. Außerdem beobachtete ich, dass Transkriptionsfaktoren alleine mit Transkriptionsfaktoren interagieren die mit benachbarten Bindestellen assoziieren, d.h. Interaktionen überbrücken keine größeren Entfernungen. Der Modellierungsansatz ermöglichte zudem die erfolgreiche Vorhersage einer UND-Gatter-ähnlichen Integration der beiden Signalwege in den Promotor. Für die genomische Architektur des CYP1A1 Promotors konnte ich die Signifikanz der Zielbindestelle des Wnt/beta-catenin Signalwegs innerhalb des cis-regulatorischen Region demonstrieren. Mithilfe des Modells fand ich heraus, dass diese Bindestelle am stärksten und vielfältigsten mit den restlichen Transkriptionsfaktoren interagiert. Zusätzliche konnte, im Vergleich zu dem alles-oder-nichts UND-Gatter der synthetischen Konstrukte, eine sehr viel graduellere Antwort auf die Integration der beiden Signalwege aufgezeigt werden. Abschließend wurde das physiologisch zu beobachtende Expressionsmuster von dem Modell vorhergesagt und experimentell validiert. / The study at hand presents an analysis of the integration of the AhR and the Wnt/beta-catenin signaling pathways into the CYP1A1 promoter as well as the regulatory influence of the promoter logic on gene expression. Experimentally, this analysis was conducted with the help of 29 mutant constructs of the human CYP1A1 promoter. I complemented this experimental approach with a set of mathematical models that combined a representation of the signaling crosstalk with a statistical mechanics description of the combinatorial promoter occupancy. With the help of well controllable synthetic promoter constructs I found that only the dioxin responsive element closest to the transcription start site communicates the promoter occupancy to the RNA polymerase. Furthermore, transcription factors only interact with transcription factors that associate with nearby binding sites, i.e., no long-distance binding was observed. The modeling approach subsequently enabled the successful prediction of an AND-gate-like integration of the two signaling pathways into the promoter. For the genomic architecture of the CYP1A1 promoter, I could demonstrate the importance of the Wnt/beta-catenin pathway target binding site within the cis-regulatory region. The model uncovered that this binding site is the strongest and most promiscuous interaction partner of the remaining transcription factors. In addition, a less switch-like response to the integration of the two signaling pathways as compared to the all-or-none AND-gate within the synthetic constructs could be demonstrated. And lastly, the physiological expression pattern in liver lobules could be successfully predicted by the model and experimentally verified.

Colorectal cancer (CRC) remains a significant burden in contemporary society due to an aging population, unhealthy dietary choices and an increasingly sedentary lifestyle. While the underlying defects for many hereditary forms of CRC have been determined, many genetic and epigenetic changes promoting common sporadic CRCs have yet to be identified. The Mutated in Colorectal Cancer (MCC) gene, identified in 1991, was initially thought to be responsible for the hereditary form of CRC, familial adenomatous polyposis, before the discovery of the susceptibility gene Adenomatous Polyposis Coli (APC), which then became the focus of intense research. Recent data, however, suggests that MCC may also be important in the development of CRC. I have investigated the mechanism of MCC gene silencing, the putative structure, and multiple functions of MCC. MCC was frequently silenced by promoter hypermethylation in CRC cell lines and primary tumours. MCC methylation showed strong molecular and clinicopathological associations with hallmarks of the serrated neoplasia pathway. Furthermore, MCC methylation was more frequent in serrated precursor lesions compared with adenomas, thus occurring early during carcinogenesis. MCC is highly conserved in complex multicellular organisms. Re-introduction of MCC in CRC cell lines resulted in partial G1 to S phase, and G2/M phase cell cycle blocks, potentially by upregulating cell cycle inhibitor gene transcription and interfering with the process of mitotic checkpoints and division, respectively. Changes in MCC levels also modulated NF?B pathway signalling, the pathway required for maintaining cell viability and proliferation in colonic epithelial cells. In particular, MCC overexpression suppressed both TNF? and LPS-induced NF?B activation, decreasing both the magnitude and rate of cellular responses. Overexpression also resulted in downregulation of proteins involved in canonical NF?B pathway signalling, while increasing the transcription of non-canonical NF?B genes. Therefore, MCC may direct activation of this pathway to a specific subset of NF?B-regulated genes. These data provide a molecular basis for the role of MCC as a tumour suppressor gene in CRC. MCC may have multiple functions, regulating cell cycle progression and modulating NF?B pathway signalling, either through direct involvement in pathway signalling cascades, or by providing a scaffold on which signalling events can occur.

&alpha / -Galactosidase is an exo-glycosidase that hydrolyses non-reducing, &alpha / -1,6-linked &alpha / -galactose units from oligosaccharides, galactomannans, and galactolipids. &alpha / -Galactosidase activity has biotechnological, industrial, and medical importance. &alpha / -Galactosidase from A. fumigatus IMI 385708, in particular, can catalyse unique hydrolysis and transgalactosylation reactions on polymeric substrates. In this study, &alpha / -galactosidase of the human pathogen A. fumigatus IMI 385708 was first produced in a GRAS organism, Aspergillus sojae. For this aim, &alpha / -galactosidase gene (aglB) of A. fumigatus IMI 385708 was ligated onto pAN52-4 vector (Acc. No: Z32699) and transformed into Aspergillus sojae ATCC11906, under the control of the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (gpdA) of A. nidulans and the signal sequence of glucoamylase gene (glaA) of A. niger. This allowed high level of &alpha / -galactosidase production on glucose instead of locust bean gum (2.45 U/mL), corresponding to a 3-fold increase in volumetric production. Next, using response surface methodology, carbon and nitrogen sources and agitation speed were optimized (10.5% molasses (w/v) / 1.3% NH4NO3 (w/v) / 276 rpm). Compared to non-optimized cultivation, a further 4-fold increase in &alpha / -galactosidase production (10.4 U/mL) was achieved. Recombinant &alpha / -galactosidase was purified 18.7-fold using Anion Exchange and Hydrophobic Interaction Chromatography with an overall yield of 56% and 64.7 U/mg protein. The Vmax and Km values for the hydrolysis of p-nitrophenyl &alpha / -D-galactopyranoside were 78 U/mg protein and 0.45 mM, respectively. Optimum pH and temperature for &alpha / -galactosidase activity were between pH 4&ndash / 6 and 50&ndash / 60 &deg / C, respectively. Among the tested chemical agents, Ag+, Hg2+, and Fe2+ drastically decreased the activity, while biotin, I+1, Mn+2, Pb+2, Li+1, and Mg+2 enhanced between 12&ndash / 29%. To analyse the influence of osmotic stress as a means of further inducing &alpha / -galactosidase production, salt was added into the complete growth medium. In addition to enzyme production, fungal growth and morphology were analysed for both &lsquo / salt-adapted&rsquo / and &lsquo / salt non-adapted&rsquo / A. sojae Ta1 cells in the presence of KCl, MgCl2, MgSO4, NaCl, and Na2SO4 at 1 M and 2 M. Accordingly, 3-fold increase in &alpha / -galactosidase production was achieved by non-adapted cells in the presence of 1 M NaCl. Exposure of A. sojae Ta1 cells to salt resulted in predominantly mycelial form, rather than the pellet form observed under normal conditions. Finally, the transgalactosylation ability of &alpha / -galactosidase was studied. &alpha / -Galactosidase efficiently catalysed galactose transfer to different monosaccharides and disaccharides in the presence of pNP&alpha / Gal as monitored by TLC, ESI-MS, and HPLC.

Polymorphism in coding regions and regions controlling gene expression is the major determinant of adaptive differences in natural populations. Genes of the major histocompatibility complex (MHC) possess a high level of genetic variation, which is maintained by selection over long coalescence times. MHC genes encode antigen-presenting molecules in the adaptive immune system, which protects the host from infectious diseases. However, MHC molecules may also present self-peptides and for most autoimmune diseases there is a genetic factor associated with the MHC. MHC genes have been used to learn about the interplay of selection and historical population events. In domestic dogs and their progenitor, the wolf, I explored factors associated with domestication and breed formation and their influence not only on MHC coding regions but also on the haplotypic structure of the class II region. Polymorphism and strong selection was demonstrated in the proximal promoters of MHC genes in dogs and wolves. Hence, genetic variation associated with MHC gene expression may have at least equal importance for a well functioning immune system. Associations between promoter sequences and particular coding alleles suggested allele-specific expression patterns. SNP haplotypes of the MHC class II region revealed ancestral as well as convergent haplotypes, in which combinations of alleles are kept by selection. Interestingly, weaker allelic associations were found between different genes and between coding regions and promoters in dogs compared to wolves. Potentially, this could cause insufficient defense against infections and predispose dogs to autoimmune diseases. For example, I identified a site in the promoter region that showed a consistent difference between haplotypes conferring susceptibility and protection to diabetes in dogs, which should be investigated further. Furthermore, I investigated how selection and demographic changes associated with glacial and inter-glacial periods have affected MHC variation in European hedgehogs and extended the prevailing knowledge concerning their population history.

Previous studies suggest that the IGF-I stimulates the elastin gene transcription through the unique responsive sequence on the elastin promoter, which is a putative retinoblastoma control element (RCE). This site interacts with (Sp)-family transcription factors whose delivery is mediated by the retinoblastoma protein (Rb). Since Rb (phosphorylated on serine 780) has been implicated in the initiation of the cell cycle, we speculated that a different phosphorylation of Rb might determine Rb involvement in elastogenesis. Obtained results demonstrated that, IGF-I-induced elastogenic signaling pathway in human dermal fibroblasts includes activation of cyclinE/cdk2 causing a site specific phosphorylation of Rb on threonine 821. This permits the sequestration of Sp1 by Rb before it could bind the elastin promoter, thereby allowing the elastin gene transcription. We also found that blocking of H-Ras in Costello syndrome fibroblasts (characterized by heightened proliferation and impaired elastogenesis), selectively down-regulated Rb phosphorylation on serine 780 and normalized impaired elastogenesis.

Previous studies suggest that the IGF-I stimulates the elastin gene transcription through the unique responsive sequence on the elastin promoter, which is a putative retinoblastoma control element (RCE). This site interacts with (Sp)-family transcription factors whose delivery is mediated by the retinoblastoma protein (Rb). Since Rb (phosphorylated on serine 780) has been implicated in the initiation of the cell cycle, we speculated that a different phosphorylation of Rb might determine Rb involvement in elastogenesis. Obtained results demonstrated that, IGF-I-induced elastogenic signaling pathway in human dermal fibroblasts includes activation of cyclinE/cdk2 causing a site specific phosphorylation of Rb on threonine 821. This permits the sequestration of Sp1 by Rb before it could bind the elastin promoter, thereby allowing the elastin gene transcription. We also found that blocking of H-Ras in Costello syndrome fibroblasts (characterized by heightened proliferation and impaired elastogenesis), selectively down-regulated Rb phosphorylation on serine 780 and normalized impaired elastogenesis.

Aspergillus fumigatus produces enzymes required for the hydrolysis of galactomannans like locust bean gum. Among these enzymes endo-beta-1,4 mannanase is also produced at high levels. However, the fungus is not safe for use in the food industry. Therefore, the gene encoding endo-beta-1,4-mannanase of A. fumigatus IMI 385708 was previously cloned in our laboratory into Aspergillus sojae ATCC11906 which is a safe microorganism for use in food applications. Altogether eight transformants were obtained. It was shown that some of these transformants overproduce the enzyme because of expression under the control of glyceraldehyde-3-phosphate dehydrogenase promoter and fusion to the glucoamylase signal and pro-peptide coding region of Aspergillus niger. In this study, mannanase production of these transformants was compared with A. fumigatus and A. sojae transformant AsT1 showed c. 12 fold increase with the maximum activity of 352 U/ml. The effects of initial medium pH and number of spores on activity were investigated and maximum activity was achieved at pH 7.0 and the number of spores was found as 3.6 &times / 106. Optimization of the growth conditions for maximum mannanase production in shake flasks by using the best mannanase producing transformant AsT1 was carried out by using Box-Behnken design under Response Surface Methodology. The highest beta-mannanase activity on the fourth day of cultivation at 30 &ordm / C was obtained as 363 U/ml in the optimized medium containing 7% sugar beet molasses, 0.43% NH4NO3, 0.1% K2HPO4, 0.05% MgSO4 as the weight/volume percentage at 207 rpm. On sixth day of cultivation under the optimized conditions, the highest mannanase activity was achieved as 482 U/ml which is 1.4 fold of 352 U/ml activity found on glucose medium previously. After 48 h of LBG hydrolysis by 40 U of mannanase, mannotriose, 61-galactosyl-beta-D-mannotriose and 63,64-di-alpha-galactosyl-beta-1,4-mannopentaose were found as the main products via HPLC analysis.

Promoter classification is the task of separating promoter from non promoter sequences. Determining promoter regions where the transcription initiation takes place is important for several reasons such as improving genome annotation and defining transcription start sites. In this study, various promoter prediction methods called ProK-means, ProSVM, and 3S1C are proposed. In ProSVM and ProK-means algorithms, structural features of DNA sequences are used to distinguish promoters from non promoters. Obtained results are compared with ProSOM which is an existing promoter prediction method. It is shown that ProSVM is able to achieve greater recall rate compared to ProSOM results. Another promoter prediction methods proposed in this study is 3S1C. The difference of the proposed technique from existing methods is using signal, similarity, structure, and context features of DNA sequences in an integrated way and a hierarchical manner. In addition to current methods related to promoter classification, the similarity feature, which compares the promoter regions between human and other species, is added to the proposed system. We show that the similarity feature improves the accuracy. To classify core promoter regions, firstly, signal, similarity, structure, and context features are extracted and then, these features are classified separately by using Support Vector Machines. Finally, output predictions are combined using multilayer perceptron. The result of 3S1C algorithm is very promising.