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Model for study of transcription regulation of granulocytic genes MPO and MMP9 by different levels of PU.1 transcription factor
Chramostová, Kamila ; Pospíšil, Vít (advisor) ; Kleibl, Zdeněk (referee)
9 Abstract Enhancers are distal cis - regulatory DNA sequences that regulate (enhance) transcription of the respective gene driven by its promoter. Enhancers are found in non-coding DNA upstream or downstream of the gene coding sequence, or in introns or coding regions that are located up to hundreds kb away from the gene. Superenhancers are newly discovered clusters of multiple enhancers that play a vital role in activating tissue-specific genes, determining cell identity and regulating differentiation. PU.1 is the transcription factor (TF) that is necessary for normal haematopoiesis, specifically for the development of myeloid and lymphoid blood lineages. Distinct levels of PU.1 induce differentiation of hematopoietic cells into different cell lineages whereby disruption of PU.1 levels leads to leukemogenesis. High PU.1 levels stimulate macrophage development, while intermediate levels stimulate the development of granulocytes. This diploma thesis seeks to contribute to addressing the interesting biological question of what are the regulatory mechanisms to ensure that granulocytic genes are activated only at the intermediate concentration of PU.1, whereas macrophage genes are activated only at its high levels. The aim of this diploma thesis was to create a series of reporter vectors carrying regulatory...
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Regulation of expression of Ms1, a sRNA from Mycobacterium smegmatis
Páleníková, Petra ; Krásný, Libor (advisor) ; Lichá, Irena (referee)
Bacteria are exposed to various environmental conditions during their growth. They have to cope with rapid changes in temperature, lack of nutrition, etc. To survive, bacteria alter their gene expression. One type of regulation of gene expression is regulation by small RNAs (sRNAs). In bacteria, a well-studied sRNA is 6S RNA that binds to the RNA polymerase holoenzyme. However, 6S RNA has not been identified in several bacterial species. Mycobacteria are a genus that probably does not have 6S RNA. Instead, Mycobacterium smegmatis possess another sRNA - Ms1. Ms1 structurally resembles 6S RNA and indeed it was first identified as a 6S RNA structural homologue. However, Ms1 binds to RNAP devoid of any sigma factor, and, therefore, is significantly distinct from 6S RNA. This work describes regulation of expression of Ms1. DNA fragments of different length from the region upstream of the Ms1 gene were prepared. These fragments were fused to the lacZ reporter gene and their activity was tested in different growth phases and under stress. This allowed identification and characterization of the core promoter sequence and regulatory sequences that might interact with transcription factor(s). Promoter activity increased with increased length of the promoter fragment and after transition into stationary...
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Regulatory mechanisms of ornithin transcarbamylase and beta-glucocerebrosidase gene expression and their relevance to diagnostics
Lukšan, Ondřej ; Jirsa, Milan (advisor) ; Kožich, Viktor (referee) ; Kříž, Vítězslav (referee)
5 Abstract Definitive diagnosis of inherited metabolic disorders commonly depends on the measurement of enzyme activity (which is often complicated) and/or molecular genetic testing. Yet even the standard mutation analysis can bring false negative results in the case of gross chromosomal rearrangements or incorrect regulation of gene expression due to the mutations in regulatory regions. In the present study I focused on characterization of complex mutations affecting the gene encoding ornithin transcarbamylase (OTC) followed by studies of regulatory regions of OTC and GBA (the gene encoding β-glucocerebrosidase). In the first study we identified 14 novel mutations including three large deletions in a cohort of 37 patients with OTC deficiency (OTCD). Subsequently we evaluated clinical significance of all these mutations. We also found a heterozygote carrying a hypomorphic mutation and manifesting OTCD most likely due to unfavorable X-inactivation which was observed independently in three different peripheral tissues. In order to evaluate the clinical significance of a promoter variation c.-366A>G found in a family with mild OTCD we identified three alternative transcription start sites (TSSs) of human OTC and delimited the promoter. We also found a distal enhancer and performed functional analysis of both...
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Molecular mechanisms in diabetic embryopathy
Čerychová, Radka ; Pavlínková, Gabriela (advisor) ; Kolář, František (referee)
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...
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Study of expression of the nuclear receptor nhr-97 in Caenorhabditis elegans
Boušová, Kristýna ; Stiborová, Marie (advisor) ; Vaněk, Ondřej (referee)
Nuclear hormone receptors (NHR) are important transcription factors that regulate development and metabolism in the large group of animals. Caenorhabditis elegans contains 284 nuclear receptors, which is unusually large amount compared to receptors of Drosophila melanogaster (18) and humans (48). 15 receptors of the C. elegans have homologous receptor structure with receptors of D. melanogaster and mammals. The remaining 269 NHR are specific to nematodes and belong to the group of supplementary nuclear receptors (SupNRs), the evolutionary precursor of the HNF4 - an important transcription factor in humans. In this work we describe the nuclear hormone receptor nhr-97 C. elegans, whose expression and function have not yet been studied. The gene is encoded in the genome of C. elegans and is among SupNRs. Nhr-97 consists of two isoforms A and B, whose expression in C. elegans tissues is different. Localization of gene expression in vivo was determined using lines expressing nhr-97:: GFP. For the A isoform expression of nhr-97::GFP was localized in neurons in the pharynx and the tail, in the intestine and hypodermis, in isoform B in the pharynx, in neurons around the corpus of pharynx, the head mesodermal cell and in anal sphincter. Nhr-97 expression during development of C. elegans was determined by...
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Study of effect of Bacillus subtilis yxkO gene on motility during stress response to osmotic upshift.
Streitová, Eliška ; Lichá, Irena (advisor) ; Krásný, Libor (referee)
Bacillus subtilis is gram-positive soil bacteria. In its natural environment it is constantly exposed to changes of chemical and physical conditons, including changes of osmolality. It responds to high osmolality by transporting of potassium ions and afterthat transporting and/or synthetising of compatible solutes. In last years the mutant strain Bacillus subtilis L-42 was isolated with non-specific insertional mutagenesis (mini Tn10) in our laboratory. This strain displays limited growth and inability to cope with hyperosmotic shock in a defined medium with potassium concentration of < 1 mmol/l. Insertion of transposon was located in yxkO gene which encodes a protein of unknown biological function. Some other data also indicate a possible role of disruption of yxkO gene in regulation of expression of hag gene, which encodes flagelin - a pivotal protein of bacterial flagellum. The goal of this thesis was to clarify if the disruption of yxkO gene influences motility and whether is affected the transcription of hag gene. With integrative vector pMUTIN4 a mutant strain with specific mutation of yxkO gene was prepared. Vector was pasted into chromosome of Bacillus subtilis strain 1A839 - genotype of this strain allows to extrude the known transcriptional regulation of hag gene. Cell's motility was...
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DNA-binding properties of the CSL proteins of Schizosaccharomyces pombe
Ptáčková, Martina ; Půta, František (advisor) ; Doležal, Pavel (referee)
As the effector component of the Notch signaling pathway the transcription factors of the CSL family (CBF1/RBP-Jκ/Suppressor of Hairless/Lag-1) are essential for many developmental processes in metazoan organisms, but they can function also independently of Notch. Recently, their presence was proved in fungal organisms lacking the Notch pathway as well as most of the known metazoan interacting partners. Cbf11 and Cbf12, the CSL proteins of the unicellular yeast Schizosaccharomyces pombe, were determined experimentally as non-essential nuclear transcription factors, which regulate cell adhesion, extracellular material production, colony morphology, septation and daughter cell separation, coordination of nuclear and cell division, and ploidy maintenance in an antagonistic way. The responsive genes of these factors are not known yet. In this study, genes of S. pombe, whose promoter regions represent potential direct targets for the Cbf proteins binding, were predicted. The binding of the Cbf11 and Cbf12 proteins, and of a truncated version Cbf12∆N to CSL response elements contained in the regulatory regions of selected S. pombe genes was tested in vitro by EMSA, and consequently, in the case of the Cbf11 protein, also in vivo by ChIP. Cbf11 and Cbf12∆N recognize specifically the response elements in...
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Transcriptional regulation of miR-17-92 microRNA cluster during macrophage differentiation.
Rybářová, Jana ; Stopka, Tomáš (advisor) ; Pospíšek, Martin (referee)
miR-17-92 cluster (Oncomir1) encodes seven microRNAs (miRNA, miR) regulating many biological processes including proliferation, differentiation or apoptosis. Overexpression of microRNAs encoded by miR-17-92 cluster is found in a number of tumors including acute and chronic myeloid leukemias (Dixon-McIver et al., 2008; Li et al., 2008; Venturini et al., 2007). Myeloid progenitors express miR-17-92 cluster at a high level, while macrophage differentiation associates with its downregulation. Our laboratory found, that miR-17-92 cluster is repressed by transcription factor Early growth response 2 (Egr2) upon differentiation of primary myeloid PUER progenitors, induced with transcription factor PU.1. Aim of this thesis is to further test the abovementioned data by preparing a reporter vectors set, carrying various fragments of miR-17-92 putative promoter, which enables us to study regulation of transcription of miR-17-92 cluster. This task complicated by presence of increased GC content of the miR-17-92 promoter was successfully accomplished resulting in amplification of eight fragments containing the various parts of miR-17-92 promoter including region -3.3 to 0 kb relative to the start of miR-17-5p sequence, that were inserted into pGL3 reporter vector. Transfection of pGL3 reporter vector carrying...
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The molecular mechanism of CSL protein participation in oxidative stress response in Schizosaccharomyces pombe
Daněk, Petr ; Převorovský, Martin (advisor) ; Sipiczki, Matthias (referee)
Redox homeostasis maintenance is important for proper organism and cell function, for while relatively low amount of reactive oxygen (and nitrogen) species contributes to the fine tuning of signal transduction, excessive concentration of ROS (oxidative stress) has demonstrably harmful effects and is tightly connected to many pathological states. Cells therefore evolved broad palette of antioxidant mechanisms that express striking level of conservation among different species. Large, intricate stress response signaling networks have been already described; nonetheless, novel molecules employed in stress-related signaling are still being discovered. Several studies recently suggested transcription factors CSL, proteins essential for regulation of metazoan development as effectors of Notch signaling, are also involved in response to oxidative stress. The fission yeast Schizosaccharomyces pombe, well established model of response to various stresses, comprises two paralogs of CSL proteins - Cbf11 and Cbf12. We have found cells depleted of cbf11 are highly resistant to hydrogen peroxide. This resistance appears to be caused by upregulation of important stress responsive genes including ctt1, gst2, pyp2, and atf1. Cbf11 is therefore negative regulator of these genes, which suppresses their expression...
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The transcriptional regulation by the nuclear receptor NHR-25 in \kur{Caenorhabditis elegans}
MERGLOVÁ, Linda
NHR-25 is a one of few conserved nuclear receptors in C. elegans and its family is involved in many developmental processes not only in the worm but also in flies, fish, mice and humans. Yet, the cellular mechanism of the action of this gene family is poorly understood. In C. elegans, it is likely to function as a transcription factor but its direct target gene has not been identified to date. In this study, I utilized the defined NHR-25 binding (target) sequence and GFP as a marker to visualize a possibility that NHR-25 regulates transcription of other gene(s) in vivo. I have also tried the "candidate approach" of two genes utilizing existing transgenic worm strains carrying promoter::GFP fusion transgenes expressed in epithelial cells to see if those genes can be regulated by NHR-25. According to the results it seems, that there could be an interaction between one of these genes and nhr-25 and that NHR-25 can play some role in endocytosis.
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