A quantitative view of the transcriptome of Schistosoma mansoni adult-worms using SAGE

Abstract Background Five species of the genus Schistosoma, a parasitic trematode flatworm, are causative agents of Schistosomiasis, a disease that is endemic in a large number of developing countries, affecting millions of patients around the world. By using SAGE (Serial Analysis of Gene Expression) we describe here the first large-scale quantitative analysis of the Schistosoma mansoni transcriptome, one of the most epidemiologically relevant species of this genus. Results After extracting mRNA from pooled male and female adult-worms, a SAGE library was constructed and sequenced, generating 68,238 tags that covered more than 6,000 genes expressed in this developmental stage. An analysis of the ordered tag-list shows the genes of F10 eggshell protein, pol-polyprotein, HSP86, 14-3-3 and a transcript yet to be identified to be the five top most abundant genes in pooled adult worms. Whereas only 8% of the 100 most abundant tags found in adult worms of S. mansoni could not be assigned to transcripts of this parasite, 46.9% of the total ditags could not be mapped, demonstrating that the 3 sequence of most of the rarest transcripts are still to be identified. Mapping of our SAGE tags to S. mansoni genes suggested the occurrence of alternative-polyadenylation in at least 13 gene transcripts. Most of these events seem to shorten the 3 UTR of the mRNAs, which may have consequences over their stability and regulation. Conclusion SAGE revealed the frequency of expression of the majority of the S. mansoni genes. Transcriptome data suggests that alternative polyadenylation is likely to be used in the control of mRNA stability in this organism. When transcriptome was compared with the proteomic data available, we observed a correlation of about 50%, suggesting that both transcriptional and post-transcriptional regulation are important for determining protein abundance in S. mansoni. The generation of SAGE tags from other life-cycle stages should contribute to reveal the dynamics of gene expression in this important parasite.

Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific genes

Abstract Background The prostate stroma is a key mediator of epithelial differentiation and development, and potentially plays a role in the initiation and progression of prostate cancer. The tumor-associated stroma is marked by increased expression of CD90/THY1. Isolation and characterization of these stromal cells could provide valuable insight into the biology of the tumor microenvironment. Methods Prostate CD90+ stromal fibromuscular cells from tumor specimens were isolated by cell-sorting and analyzed by DNA microarray. Dataset analysis was used to compare gene expression between histologically normal and tumor-associated stromal cells. For comparison, stromal cells were also isolated and analyzed from the urinary bladder. Results The tumor-associated stromal cells were found to have decreased expression of genes involved in smooth muscle differentiation, and those detected in prostate but not bladder. Other differential expression between the stromal cell types included that of the CXC-chemokine genes. Conclusion CD90+ prostate tumor-associated stromal cells differed from their normal counterpart in expression of multiple genes, some of which are potentially involved in organ development.

Transcriptional profiling of Saccharomyces cerevisiae exposed to propolis

Abstract Background Propolis is a natural product of plant resins collected by honeybees (Apis mellifera) from various plant sources. Our previous studies indicated that propolis sensitivity is dependent on the mitochondrial function and that vacuolar acidification and autophagy are important for yeast cell death caused by propolis. Here, we extended our understanding of propolis-mediated cell death in the yeast Saccharomyces cerevisiae by applying systems biology tools to analyze the transcriptional profiling of cells exposed to propolis. Methods We have used transcriptional profiling of S. cerevisiae exposed to propolis. We validated our findings by using real-time PCR of selected genes. Systems biology tools (physical protein-protein interaction [PPPI] network) were applied to analyse the propolis-induced transcriptional bevavior, aiming to identify which pathways are modulated by propolis in S. cerevisiae and potentially influencing cell death. Results We were able to observe 1,339 genes modulated in at least one time point when compared to the reference time (propolis untreated samples) (t-test, p-value 0.01). Enrichment analysis performed by Gene Ontology (GO) Term finder tool showed enrichment for several biological categories among the genes up-regulated in the microarray hybridization such as transport and transmembrane transport and response to stress. Real-time RT-PCR analysis of selected genes showed by our microarray hybridization approach was capable of providing information about S. cerevisiae gene expression modulation with a considerably high level of confidence. Finally, a physical protein-protein (PPPI) network design and global topological analysis stressed the importance of these pathways in response of S. cerevisiae to propolis and were correlated with the transcriptional data obtained thorough the microarray analysis. Conclusions In summary, our data indicate that propolis is largely affecting several pathways in the eukaryotic cell. However, the most prominent pathways are related to oxidative stress, mitochondrial electron transport chain, vacuolar acidification, regulation of macroautophagy associated with protein target to vacuole, cellular response to starvation, and negative regulation of transcription from RNA polymerase II promoter. Our work emphasizes again the importance of S. cerevisiae as a model system to understand at molecular level the mechanism whereby propolis causes cell death in this organism at the concentration herein tested. Our study is the first one that investigates systematically by using functional genomics how propolis influences and modulates the mRNA abundance of an organism and may stimulate further work on the propolis-mediated cell death mechanisms in fungi.

High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

Abstract Background The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Functional in vitro studies are fundamental for the comprehension of their role; nevertheless results are highly dependable on the adopted cellular model. Next generation small RNA transcriptomic sequencing data of a tumor cell line and keratinocytes derived from primary culture was generated in order to characterize the microRNA content of these systems, thus helping in their understanding. Both constitute cell models for functional studies of microRNAs in head and neck squamous cell carcinoma (HNSCC), a smoking-related cancer. Known microRNAs were quantified and analyzed in the context of gene regulation. New microRNAs were investigated using similarity and structural search, ab initio classification, and prediction of the location of mature microRNAs within would-be precursor sequences. Results were compared with small RNA transcriptomic sequences from HNSCC samples in order to access the applicability of these cell models for cancer phenotype comprehension and for novel molecule discovery. Results Ten miRNAs represented over 70% of the mature molecules present in each of the cell types. The most expressed molecules were miR-21, miR-24 and miR-205, Accordingly; miR-21 and miR-205 have been previously shown to play a role in epithelial cell biology. Although miR-21 has been implicated in cancer development, and evaluated as a biomarker in HNSCC progression, no significant expression differences were seen between cell types. We demonstrate that differentially expressed mature miRNAs target cell differentiation and apoptosis related biological processes, indicating that they might represent, with acceptable accuracy, the genetic context from which they derive. Most miRNAs identified in the cancer cell line and in keratinocytes were present in tumor samples and cancer-free samples, respectively, with miR-21, miR-24 and miR-205 still among the most prevalent molecules at all instances. Thirteen miRNA-like structures, containing reads identified by the deep sequencing, were predicted from putative miRNA precursor sequences. Strong evidences suggest that one of them could be a new miRNA. This molecule was mostly expressed in the tumor cell line and HNSCC samples indicating a possible biological function in cancer. Conclusions Critical biological features of cells must be fully understood before they can be chosen as models for functional studies. Expression levels of miRNAs relate to cell type and tissue context. This study provides insights on miRNA content of two cell models used for cancer research. Pathways commonly deregulated in HNSCC might be targeted by most expressed and also by differentially expressed miRNAs. Results indicate that the use of cell models for cancer research demands careful assessment of underlying molecular characteristics for proper data interpretation. Additionally, one new miRNA-like molecule with a potential role in cancer was identified in the cell lines and clinical samples.

Gene expression and phenotypic traits of Aggregatibacter actinomycetemcomitans in response to environmental changes

Background and Objective: Periodontopathogens experience several challenges in the oral cavity that may influence their transcription profile and resulting phenotype. This study evaluated the effect of environmental changes on phenotype and gene expression in a serotype b Aggregatibacter actinomycetemcomitans isolate. Material and Methods: Cultures in early exponential phase and at the start of stationary growth phase in microaerophilic and anaerobic atmospheres were evaluated. Cell hydrophobic properties were measured by adherence to n-hexadecane; in addition, adhesion to, and the ability to invade, KB cells was evaluated. Relative transcription of 12 virulence-associated genes was determined by real-time reverse transcritption quantitative PCR. Results: The culture conditions tested in this study were found to influence the phenotypic and genotypic traits of A. actinomycetemcomitans. Cells cultured in microaerophilic conditions were the most hydrophobic, reached the highest adhesion efficiency and showed up-regulation of omp100 (which encodes an adhesion) and pga (related to polysaccharide synthesis). Cells grown anaerobically were more invasive to epithelial cells and showed up-regulation of genes involved in host-cell invasion or apoptosis induction (such as apaH, omp29, cagE and cdtB) and in adhesion to extracellular matrix protein (emaA). Conclusion: Environmental conditions of different oral habitats may influence the expression of factors involved in the binding of A. actinomycetemcomitans to host tissues and the damage resulting thereby, and thus should be considered in in-vitro studies assessing its pathogenic potential.

Hepatocyte nuclear factors 1α/4α and forkhead box A2 regulate the solute carrier 2A2 (Slc2a2) gene expression in the liver and kidney of diabetic rats

AIMS: Solute carrier 2a2 (Slc2a2) gene codifies the glucose transporter GLUT2, a key protein for glucose flux in hepatocytes and renal epithelial cells of proximal tubule. In diabetes mellitus, hepatic and tubular glucose output has been related to Slc2a2/GLUT2 overexpression; and controlling the expression of this gene may be an important adjuvant way to improve glycemic homeostasis. Thus, the present study investigated transcriptional mechanisms involved in the diabetes-induced overexpression of the Slc2a2 gene. MAIN METHODS: Hepatocyte nuclear factors 1α and 4α (HNF-1α and HNF-4α), forkhead box A2 (FOXA2), sterol regulatory element binding protein-1c (SREBP-1c) and the CCAAT-enhancer-binding protein (C/EBPβ) mRNA expression (RT-PCR) and binding activity into the Slc2a2 promoter (electrophoretic mobility assay) were analyzed in the liver and kidney of diabetic and 6-day insulin-treated diabetic rats. KEY FINDINGS: Slc2a2/GLUT2 expression increased by more than 50% (P<0.001) in the liver and kidney of diabetic rats, and 6-day insulin treatment restores these values to those observed in non-diabetic animals. Similarly, the mRNA expression and the binding activity of HNF-1α, HNF-4α and FOXA2 increased by 50 to 100% (P<0.05 to P<0.001), also returning to values of non-diabetic rats after insulin treatment. Neither the Srebf1 and Cebpb mRNA expression, nor the SREBP-1c and C/EBP-β binding activity was altered in diabetic rats. SIGNIFICANCE: HNF-1α, HNF-4α and FOXA2 transcriptional factors are involved in diabetes-induced overexpression of Slc2a2 gene in the liver and kidney. These data point out that these transcriptional factors are important targets to control GLUT2 expression in these tissues, which can contribute to glycemic homeostasis in diabetes.

Global transcriptional response of Caulobacter crescentus to iron availability

BACKGROUND: In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. RESULTS: In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility. CONCLUSIONS: Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms

Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

Tetracycline-inducible RNAi Knockdown of SCL (Stem Cell Leukaemia) in Mice

RNAi (RNA interference) is a powerful technology for sequence-specific targeting of mRNAs. This thesis was aimed at establishing conditions for conditional RNAi-mediated silencing first in vitro and subsequently also in transgenic mice. As a target the basic helix-loop-helix transcription factor encoding gene SCL (stem cell leukaemia also known as Tal-1 or TCL5) was used. SCL is a key regulator for haematopoietic development and ectopic expression of SCL is correlated with acute T-lymphoblastic leukaemias. Loss of SCL function studies demonstrated that ab initio deletion of SCL resulted in embryonic lethality around day E9 in gestation. To be able to conditionally inactivate SCL, RNAi technology was combined with the tetracycline-dependent regulatory system. This strategy allowed to exogenously control the induction of RNAi in a reversible fashion and consequently the generation of a completely switchable RNAi knockdown. First a suitable vector allowing for co-expression of tetracycline-controlled shRNAs (small hairpin RNAs) and constitutively active EGFP (enhanced green fluorescent protein) was generated. This novel vector, pRNAi-EGFP, was then evaluated for EGFP expression and tetracycline-mediated expression of shRNAs. Four sequences targeting different regions within the SCL mRNA were tested for their efficiency to specifically knockdown SCL. These experiments were performed in M1 murine leukaemia cells and subsequently in the HEK 293 cell line, expressing an engineered HA-tagged SCL protein. The second assay provided a solid experimental method for determining the efficiency of different SCL-siRNA knockdown constructs in tissue culture. Western blotting analyses revealed a down regulation of SCL protein for all four tested SCL-specific target sequences albeit with different knockdown efficiencies (between 25% and 100%). Furthermore, stringent tetracycline-dependent switchability of shRNA expression was confirmed by co-transfecting the SCL-specific pRNAi-EGFP vector (SCL-siRNA) together with the HA-tagged SCL expression plasmid into the HEK 293TR /T-REx cell line constitutively expressing the tetracycline repressor (TetR). These series of experiments demonstrated tight regulation of siRNA expression without background activity. To be able to control the SCL knockdown in vivo and especially to circumvent any possible embryonic lethality a transgenic mouse line with general expression of a tetracycline repressor was needed. Two alternative methods were used to generate TetR mice. The first approach was to co-inject the tetracycline-regulated RNAi vector together with a commercially available and here specifically modified T-REx expression vector (SCL-siRNA T-REx FRT LoxP mouse line). The second method involved the generation of a TetR expressor mouse line, which was then used for donating TetR-positive oocytes for pronuclear injection of the RNAi vector (SCL-siRNA T-REx mouse line). As expected, and in agreement with data from conditional Cre-controlled adult SCL knockout mice, post-transcriptional silencing of SCL by RNAi caused a shift in the maturation of red blood cell populations. This was shown in the bone marrow and peripheral blood by FACS analysis with the red blood cell-specific TER119 and CD71 markers which can be used to define erythrocyte differentiation (Lodish plot technique). In conclusion this study established conditions for effective SCL RNAi-mediated silencing in vitro and in vivo providing an important tool for further investigations into the role of SCL and, more generally, of its in vivo function in haematopoiesis and leukaemia. Most importantly, the here acquired knowledge will now allow the establishment of other completely conditional and reversible knockdown phenotypes in mice.

Strategies to identify and further characterize novel and known genes involved in regulation of skeletogenesis

372 osteochondrodysplasias and genetically determined dysostoses were reported in 2007 [Superti-Furga and Unger, 2007]. For 215 of these conditions, an association with one or more genes can be stated, while the molecular changes for the remaining syndromes remain illusive to date. Thus, the present dissertation aims at the identification of novel genes involved in processes regarding cartilage/ bone formation, growth, differentiation and homeostasis, which may serve as candidate genes for the above mentioned conditions. Two different approaches were undertaken. Firstly, a high throughput EST sequencing project from a human fetal cartilage library was performed to identify novel genes in early skeletal development (20th week of gestation until 2nd year of life) that could be investigated as potential candidate genes. 5000 EST sequences were generated and analyzed representing 1573 individual transcripts, corresponding to known (1400) and to novel, yet uncharacterized genes (173). About 7% of the proteins were already described in cartilage/ bone development or homeostasis, showing that the generated library is tissue specific. The remaining profile of this library was compared to previously published libraries from different time points (8th–12th, 18th–20th week and adult human cartilage) that also showed a similar distribution, reflecting the quality of the presented library analyzed. Furthermore, three potential candidate genes (LRRC59, CRELD2, ZNF577) were further investigated and their potential involvement in skeletogenesis was discussed. Secondly, a disease-orientated approach was undertaken to identify downstream targets of LMX1B, the gene causing Nail-Patella syndrome (NPS), and to investigate similar conditions. Like NPS, Genitopatellar syndrome (GPS) is characterized by aplasia or hypoplasia of the patella and renal anomalies. Therefore, six GPS patients were enrolled in a study to investigate the molecular changes responsible for this relatively rare disease. A 3.07 Mb deletion including LMX1B and NR5A1 (SF1) was found in one female patient that showed features of both NPS and GPS and investigations revealed a 46,XY karyotype and ovotestes indicating true hermaphroditism. The microdeletion was not seen in any of the five other patients with GPS features only, but a potential regulatory element between the two genes cannot be ruled out yet. Since Lmx1b is expressed in the dorsal limb bud and in podocytes, proteomic approaches and expression profiling were performed with murine material of the limbs and the kidneys to identify its downstream targets. After 2D-gel electrophoresis with protein extracts from E13.5 fore limb buds and newborn kidneys of Lmx1b wild type and knock-out mice and mass spectrometry analysis, only two proteins, agrin and carbonic anhydrase 2, remained of interest, but further analysis of the two genes did not show a transcriptional down regulation by Lmx1b. The focus was switched to expression profiles and RNA from newborn Lmx1b wild type and knock-out kidneys was compared by microarray analysis. Potential Lmx1b targets were almost impossible to study, because of the early death of Lmx1b deficient mice, when the glomeruli, containing podocytes, are still immature. Because Lmx1b is also expressed during limb development, RNA from wild type and knock-out Lmx1b E11.5 fore limb buds was investigated by microarray, revealing four potential Lmx1b downstream targets: neuropilin 2, single-stranded DNA binding protein 2, peroxisome proliferative activated receptor, gamma, co-activator 1 alpha, and short stature homeobox 2. Whole mount in situ hybridization strengthened a potential down regulation of neuropilin 2 by Lmx1b, but further investigations including in situ hybridization and protein-protein interaction studies will be needed.

Regulation der Selenoproteinsynthese durch den Mevalonatweg

Im Rahmen dieser Arbeit sollte der Einfluss des Mevalonatpfads auf die Expression von Selenoproteinen untersucht werden. Im Mevalonatpfad, einem universellen Stoffwechselweg eukaryontischer Zellen, entstehen neben Cholesterol auch verschiedene Isoprenoide, die z.B. für die post-transkriptionelle Modifikation der Selenocystein-tRNA herangezogen werden. Selenocystein ist funktioneller Bestandteil von Selenoproteinen, welche häufig in den Abbau von oxidativem Stress involviert sind. rnDer Mevalonatpfad wird hauptsächlich durch die HMG-CoA-Reduktase (HMGCR) reguliert. Pharmaka vom „Statin“-Typ gelten als wirkungsvolle kompetitive Inhibitoren dieses Enzyms und finden ihren Einsatz bei Patienten zur Behandlung von Hypercholesterolämie, welche eine Grundlage für vaskuläre Krankheiten bildet. Trotz der allgemein guten Verträglichkeit der Statine treten jedoch auch unerwünschte Nebeneffekte, wie Erhöhung der Leberenzyme oder Myopathien auf, deren biochemischer Hintergrund bislang noch im Dunkeln liegt. rnDie in dieser Arbeit durchgeführten Experimente belegen, dass Atorvastatin, Cerivastatin und Lovastatin in klinisch relevanten Dosen die Synthese bestimmter Selenoproteine, wie der Glutathionperoxidase (GPx), in klonalen humanen Hepatocyten post-transkriptionell unterdrücken, wodurch die Zellen anfälliger für oxidativen Stress in Form von Peroxiden werden. Dieser Mechanismus könnte eine Erklärung für die häufig beobachteten abnormen Leberwerte von Statin-behandelten Patienten darstellen.rnEndogenes Cholesterol gilt ebenfalls als potenter Inhibitor der HMGCR. Die in dieser Arbeit erzielten Ergebnisse zeigen, dass Cholesterol in verschiedenen Formen, als Low-Density-Lipoprotein (LDL), als 25-Hydroxycholesterol, und als Methylcyclodextrin-Komplex in unterschiedlichen humanen Zelltypen die Selenoproteinsynthese ebenfalls unterdrücken. Der negative Zusammenhang zwischen Cholesterol und bestimmten Selenoproteinen konnte auch in vivo beobachtet werden. In juvenilen Mäusen konnte gezeigt werden, dass ein Knockout des LDL-Rezeptors sowie auch ein Knockout von Apolipoprotein E zu einer Senkung des Lebercholesterols führte, was in einer Zunahme der GPx in der Leber resultierte.rnDie vorliegenden Daten belegen erstmals einen direkten und funktionellen Zusammenhang zwischen dem Mevalonatpfad und der Selenoproteinsynthese. Unterdrückung dieses Pfades, entweder durch exogene Substanzen wie Statine, oder durch endogene Substanzen wie Cholesterol, hat offenbar zur Folge, dass essentielle Zwischenprodukte für die Modifizierung der Selenocystein-tRNA fehlen, was in einer post-transkriptionellen Verminderung der induzierbaren Selenoproteine resultiert. Dies könnte die biochemische Grundlage für einen Teil der vielfältigen gesundheitlich negativen Auswirkungen schon geringfügig erhöhter Cholesterolspiegel sein.

Transcriptional dynamics of the human DMD locus

The human DMD locus encodes dystrophin protein. Absence or reduced levels of dystrophin (DMD or BMD phenotype, respectively) lead to progressive muscle wasting. Little is known about the complex coordination of dystrophin expression and its transcriptional regulation is a field of intense interest. In this work we found that DMD locus harbours multiple long non coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. These lncRNAs are tissue-specific and highly expressed during myogenesis, suggesting a possible role in tissue-specific expression of DMD gene isoforms. Their forced ectopic expression in human muscle and neuronal cells leads to a specific and negative regulation of endogenous dystrophin full lenght isoforms. An intriguing aspect regarding the transcription of the DMD locus is the gene size (2.4Mb). The mechanism that ensures the complete synthesis of the primary transcript and the coordinated splicing of 79 exons is still completely unknown. By ChIP-on-chip analyses, we discovered novel regions never been involved before in the transcription regulation of the DMD locus. Specifically, we observed enrichments for Pol II, P-Ser2, P-Ser5, Ac-H3 and 2Me-H3K4 in an intronic region of 3Kb (approximately 21Kb) downstream of the end of DMD exon 52 and in a region of 4Kb spanning the DMD exon 62. Interestingly, this latter region and the TSS of Dp71 are strongly marked by 3Me-H3K36, an histone modification associated with the regulation of splicing process. Furthermore, we also observed strong presence of open chromatin marks (Ac-H3 and 2Me-H3K4) around intron 34 and the exon 45 without presence of RNA pol II. We speculate that these two regions may exert an enhancer-like function on Dp427m promoter, although further investigations are necessary. Finally, we investigated the nuclear-cytoplasmic compartmentalization of the muscular dystrophin mRNA and, specifically, we verified whether the exon skipping therapy could influence its cellular distribution.

Mechanistic study of the effects of 8-oxo-7,8-dihydroguanine (8-oxoG) on reporter gene expression in mammalian cells

DNA damage causes replication errors, leading to genetic instability or cell death. Besides that, many types of DNA base modifications have been shown to interfere with transcriptional elongation if they are located in the transcribed DNA strand of active genes, acting as roadblocks for RNA polymerases. It is widely assumed that transcription blockage by endogenous DNA damage is responsible for the early cell senescence in organs and accelerated ageing observed in individuals with compromised nucleotide excision repair.rnThe aims of this work were to design new experimental systems for testing transcription blocking potentials of DNA base modifications in an individual gene and to apply these test systems to the investigation of the effects of a frequent endogenously generated base modification, namely 8-oxo-7,8-hydroxyguanine (8-oxoG), on the gene transcription in cells. Several experimental strategies were employed for this purpose. First, I constructed an episomal vector encoding for a short-lived EGFP-ODC fusion protein and measured expression of the reporter gene in permanently transfected clonal cell lines exposed to DNA damaging agents. Second, the expression of plasmid-borne EGFP gene damaged with photosensitisers to obtain one or several oxidative purine modifications per plasmid molecule was determined in transiently transfected human and mouse host cells in an approach known as “host cell reactivation”. As a prerequisite for these experiments, a robust method of precise quantitative measurement of the EGFP gene expression in transiently transfected cells by flow cytometry was developed and validated. Third, I elaborated a very efficient procedure for insertion of synthetic oligonucleotides carrying 8-oxoG into plasmid DNA, avoiding any unwanted base damage and strand breaks. The consequences of 8-oxoG placed in defined positions in opposing DNA strands of the EGFP gene for transcription were measured by host cell reactivation in cells with functional 8-oxoguanine DNA glycosylase (OGG1) gene and in OGG1 null cells.rnThe results obtained in Ogg1-/- cells demonstrated that unrepaired 8-oxoG, even if situated in the transcribed DNA strand, does not have any negative effect on the reporter gene transcription. On the other hand, as few as one 8-oxoG was sufficient to cause a significant decrease of the gene expression in OGG1-proficient cell lines, i.e. in the presence of base excision repair. For two analysed positions of 8-oxoG in the plasmid DNA, the inhibition of gene transcription by the base modification correlated with the efficiency of its excision by purified OGG1 protein under cell-free conditions. Based on these findings, it has to be concluded that the observed decrease of transcription is mediated by excision of the base modification by OGG1 and probably caused by the repair-induced single-strand breaks. The mechanism of transcription inhibition by 8-oxoG is therefore clearly distinct from stalling of elongating RNA polymerase II complexes at the modified base.

Analysen zur Expression proinflammatorischer Mediatoren in humanen Zellkulturmodellen und murinen Tiermodellen chronisch-inflammatorischer Erkrankungen

Die humane induzierbare NO-Synthase (iNOS) spielt bei zahlreichen Erkrankungen wie Asthma, Krebs und der rheumatoiden Arthritis eine entscheidende Rolle. Durch Fehlregulation der iNOS-Expression kommt es häufig zu massiven Gewebeschädigungen. Aus diesem Grund ist es wichtig die Mechanismen der Genregulation der iNOS-Expression zu verstehen. Bei Affinitätschromatographie-Analysen wurde das zytosolische PolyA-bindende Protein (PABP) als direkter Interaktionspartner der 3´UTR der humanen iNOS identifiziert. Weitere Bindungsanalysen konnten eine spezifische Bindestelle für PABP in der 5´UTR und zwei Bindestellen im AU-reichen Bereich der 3´UTR der humanen iNOS nachweisen. Eine siRNA-mediierte Herabregulation von PABP mit Hilfe der stabilen Expression spezifischer siRNAs in DLD-1 Zellen (siPABP Zellen) zeigte eine signifikant verringerte Expression der humanen iNOS und damit einhergehend eine verringerte NO-Produktion nach Zytokinstimulation. Promotoranalysen zeigten keine Veränderung der Induzierbarkeit des humanen 16 kb iNOS-Promotors in siPABP Zellen. RNA-Stabilitätsanalysen zeigten einen verstärkten Abbau der iNOS-mRNA in diesen Zellen, so dass davon auszugehen ist, dass die Regulation der humanen iNOS über die mRNA-Stabilität erfolgt. Reportergen-Analysen mit Plasmiden, welche die 5’ und/oder 3’UTR Sequenzen der humanen iNOS mit den identifizierten PABP-Bindestellen oder Mutationen in diesen Bindestellen enthielten, zeigten, dass PABP die iNOS-mRNA über die 5´UTR stabilisiert und anscheinend über die 3´UTR einen destabilisierenden Effekt auf die mRNA ausübt. Ebenfalls scheint PABP über die 3’UTR dieTranslation der iNOS mRNA zu hemmen. Die Ergebnisse dieser Arbeit zeigen, dass PABP, über seine allgemeinen Funktionen hinaus, eine spezifische Rolle in der Regulation der Expression der humanen iNOS einnimmt.rnDie rheumatoide Arthritis (RA) ist eine chronisch entzündliche Autoimmunerkrankung, welche überwiegend die peripheren Gelenke der Hände und Füße betrifft. Die aktuellen Therapiemöglichkeiten sind immer noch mit einer Vielzahl von Nebenwirkungen behaftet und führen nicht zur vollständigen Remission der Erkrankung, so dass die Entwicklung neuer Medikamente unerlässlich ist. In dieser Arbeit wurden die antiinflammatorischen Substanzen Gallielalacton (Gal) und Oxacyclododecindion (Oxa) im Mausmodell der kollagen-induzierten Arthritis (CIA) getestet. Leider waren beide Substanzen nicht in der Lage die Symptome der CIA zu vermindern, obwohl beide im Modell der LPS-induzierten akuten Entzündung die Expression proinflammatorischer Mediatoren senken konnten. Die Substanz S-Curvularin (SC) hat sich im CIA-Modell bereits bewährt und wurde in dieser Arbeit weiter untersucht. SC war in der Lage die Expression knorpel- und knochendestruktiver Markergene signifikant zu verrindern. rnIn der vorliegenden Arbeit wurden neue microRNAs identifiziert, die in der Pathogenese der CIA eine Dysregulation zeigen. Die Expression dieser microRNAs wurde von SC wieder auf das Normalniveau gebracht, so dass SC eine vielversprechende Substanz in der Therapie chronisch inflammatorische Erkrangungen sein könnte. Die neu identifizierten CIA-relevanten microRNAs könnten als neueRA-Marker oder als Zielstrukturen für neue Medikamente dienen.rn

Tetracycline regulator expression alters the transcriptional program of mammalian cells

Tetracycline regulated ectopic gene expression is a widely used tool to study gene function. However, the tetracycline regulator (tetR) itself has been reported to cause certain phenotypic changes in mammalian cells. We, therefore, asked whether human myeloid U937 cells expressing the tetR in an autoregulated manner would exhibit alterations in gene expression upon removal of tetracycline.