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Association of chromatin modifications with transgenerational abiotic stress memory of plants
Vyskočilová, Barbara ; Holá, Dana (advisor) ; Fischer, Lukáš (referee)
Plants are constantly exposed to various stressors which usually leads to changes in the expression of many different genes. This can be controlled at multiple levels, including modifications of chromatin structure. Some of these modifications may persist even after the period when the plant is exposed to stress and could possibly act as a kind of "stress memory". This work deals with so-called meiotic/transgeneration "stress memory" of plants caused by abiotic stressors. Compilation of studies dealing with this topic showed that they are still rather rare and usually originated from only a few laboratories. The majority of these studies was aimed only at the examination of DNA methylation and their design was not always optimal. In my opinion, true proofs of transgeneration "stress memory" of plants still remain to be presented; further, more properly designed studies are necessary. Powered by TCPDF (www.tcpdf.org)
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Histone modifications and methylation of polyomaviral genomes during the infection
Mrkáček, Michal ; Forstová, Jitka (advisor) ; Šmahelová, Jana (referee)
Similarly to other viruses, polyomaviruses require for their successful replication enzymes and other proteins encoded by their host cells. Additionally, because of their relatively small genome with only a few genes, polyomaviruses utilize for their efficient replication cellular regulation mechanisms. One of these regulations are posttranslational modifications of histones, which form nucleosomes together with viral DNA. The spectrum of these modifications is very wide, but in case of polyomaviruses, almost only ones studied are histone acetylations and methylations. Second possible regulation is a methylation of cytosine in CpG dinucleotides, which is associated with repression of gene expression. Current knowledge however suggest that polyomaviruses do not utilise this kind of modification. Moreover, because of a relatively small amount of CpG dinucleotides present in their genomes, they seem to avoid it. The goal of this work is to describe the individual types of these modifications and show their possible importance in the infectious cycle of polyomaviruses. Key words: polyomavirus, epigenetics, histone modification, DNA methylation, CpG dinucleotides
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Epigenetic mechanisms in the interferon γ signalling pathway
Fišerová, Lenka ; Reiniš, Milan (advisor) ; Javorková, Eliška (referee)
IFNγ is an important cytosine mediating imune responses, including antitumor immunity. It can affect expression of a lot of genes, which regulate different cellular processes. In tumor cells defects in signal cascade of IFNγ and mistakes in expression of genes regulated by IFNγ, for example genes for antigen adjustment and presentation (APM) or genes for major histocompatibility complex (MHC), were observed. Epigenetic mechanisms, can play a role in regulation of expression of genes for IFNγ, as well as in regulation of expression of genes regulated by IFNγ, including the components of the IFNγ signalling pathway. In lymphocytes from tumors the ability to produce IFNγ was limited by epigenetic silencing of genes for IFNγ. In tumor cells, epigenetic silencing of genes regulated by IFNγ, of genes of the IFNγ signaling cascade, for example IRF transcription factors, and other genes regulated by IFNγ, such as genes for APM, MHC or indoldioxygenase coding genes (IDO), was demonstrated. In case of their activation by IFNγ, epigenetic changes in regulation sequences of appropriate genes, were observed. IFNγ thus can be considered as an epigenetic agent. Epigenetic modulators are able to activate expression of genes regulated by IFNγ. By this way it's possible to explain some of immunomudullatory effects...
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Epigenetic regulation of HLA class II genes in relation to senescence of organism
Říhová, Adéla ; Kotrbová - Kozak, Anna Katarzyna (advisor) ; Slavčev, Antonij (referee)
Introduction: Glycoproteins of the major histocompatibility complex (MHC) are an irreplaceable part of immune response regulation and immune homeostasis maintenance. The regulation of the expression plays an important role in adaptive immune response. Recently, DNA methylation in regulatory areas, crucial for DNA availability to transcription factors, is one of the most researched mechanisms of this type of regulation. The DNA methylation is, among others, related to the aging processes. Increased predisposition age-related immunosenescence in higher age could result from the changes in methylation status of regulatory areas of MHC class II genes. Aims: The aim of this thesis is to analyze the methylation status of regulatory areas of DQB1 gene and to compare the differences between generations and specific alleles. The differences in the levels of DQB1 gene mRNA transcription between generations and specific alleles is also compared. Methods: Both DNA and RNA were isolated from blood samples obtained from donors of three different age groups. DNA was genotypized and modified by bisulfite conversion. The regulatory areas of DQB1 genes were then amplified and subcloned into bacteria. The positive clones were selected and subjected to DNA methylation analysis. RNA was reverse transcribed into cDNA...
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Epigenetické regulace u autoimunitních onemocnění se zaměřením na revmatoidní artritidu
Horková, Veronika ; Daňková, Pavlína (advisor) ; Hušáková, Markéta (referee)
Exact cause of rheumatoid arthritis, as well as other autoimmune diseases has not been identified yet. In last twenty years, epigenetics showed a new face of immune system. DNA methylation, modification of histones - proteins around which DNA is wrapped, or interference of small RNA sequences - microRNAs, these all are heritable changes outside the DNA sequence that provide another component involved in autoimmunity. Presented epigenetic mechanisms alter gene expression and thus facilitate production of pro- inflammatory factors leading to autoimmune reactions. Moreover, genes regulating apoptosis are also frequently targeted by epigenetic modifications. Not only these mechanisms provide another level of immune defense, they also explain higher female susceptibility to autoimmune diseases and the influence of environment on pathogenesis of these diseases.
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The study of epigenetic regulation of HLA class II genes at the level of histone modification
Černoch, Marek ; Černá, Marie (advisor) ; Hirsch, Ivan (referee)
Introduction: The epigenetic modifications can significantly affect and alter the gene activity by regulating their expression, having direct impact on various processes in human body. Epigenetic processes are involved in ethiopathogenesis of many diseases. From this point of view, MHC genes are very important as they were linked to many autoimmune disorders, for example type 1 diabetes mellitus. In general autoimmune diseases appear to be connected to certain MHC class II genes. Aims: The aim of this thesis is to determine the relationship between expression levels and histone modifications present in the promoter area of MHC class II gene, DQA1. Moreover, we also analyze and compare the DQA1 gene mRNA expression depending on the QAP promoter allele. Methods: We isolated both nucleic acids (DNA and RNA) and leukocytes from peripheral blood samples collected from voluntary donors. DNA was utilized for genotypization of individuals. RNA was subjected to reverse transcription and the quantitative PCR was performed in order to determine the level of expression. Leukocytes were used for chromatin immunoprecipitation, which was evaluated using quantitative PCR. Results: The expression level of QAP allele 3.1 was found to be higher than for the rest of the alleles Allele 4.1A showed, on the other hand,...
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Forensic analysis of epigenetic factors and mRNA
Andreasová, Karolina ; Šimková, Halina (advisor) ; Zachová, Markéta (referee)
In last years, forensic genetics focused on a research of epigenetic factors and mRNA. It turned out that their analysis provides valuable information that can be obtained from a small amount of a biological trace and which included e.g. estimation of circumstances of death, age estimation, discrimination within monozygotic twins, identification of tissues and body fluids, sample authentication, determination of paternal allele, etc. In this thesis, it is discussed methods of epigenetic factors and mRNA analysis and their potential application in future forensic practice.
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Functional genome analysis using the retroviral integration sites permissive for provirus expression in human cells
Miklík, Dalibor ; Hejnar, Jiří (advisor) ; Španielová, Hana (referee)
The expression of retroviral genes depends on the establishment of the provirus - the DNA copy of retroviral genome integrated into the host genome. The transcriptional state of provirus is then influenced by the environment at the site of integration. The phenomenon of proviral silencing is an obstacle to the usage of retroviral vectors and a barrier to the eradication of human immunodeficiency virus type 1 (HIV-1) from infected individuals. Taking advantage of single cell clones bearing one provirus, this diploma thesis investigates the distribution of (epi)genomic features at the sites occupied by stably expressed proviruses. In total, long-term expression profiles of 245 and 255 clones carrying avian sarcoma-leucosis virus (ASLV) and HIV-1, respectively, were obtained. The database-based analysis of 42 integration sites of ASLV and three integration sites of HIV-1 proviruses shows that proviral stable expression highly correlates with the transcriptional start sites (TSS) at the sites of integration. Histone marks characteristic for the proximity of active TSSs and regulatory elements at the sites of integration of stably expressed proviruses confirm this finding. The results presented in this thesis could inspire other analyses investigating the relationship between the integration site and the...
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Genome reprogramming during the first cell cycle of embryonic development
Barnetová, Irena ; Fulka, Josef (advisor) ; Pěknicová, Jana (referee) ; Strejček, František (referee)
The sperm head contains highly compacted genome. This compaction is mediated by protamines. Sperm protamines are replaced by cytoplasmic histones after the sperm entry into the oocyte. Beside the proteins replacement, also some epigenetic remodeling occurs. One of the most studied epigenetic remodeling in early zygotes is DNA demethylation. This phenomenon was observed in some mammals (mouse, rat, monkey) but not in some other mammals (sheep) and what is more, in some of them quite inconsistent data were published (pig, human, goat, rabbit). In our work we were mostly concentrated on porcine zygotes and attempted to explain the reasons of inconsistency in observed data. Three factors were evaluated in our work - the technique of embryo production, sperm factors, and the oocyte quality. In the first part of the study (the technique of embryo production) we compared the zygotes produced by conventional in vitro fertilization and zygotes produced by intracytoplasmic sperm injection. The epigenetic remodeling was evaluated by immunolabeling. There were no differences between zygotes produced by the two mentioned techniques. The paternal genome was not demethylated in any of zygotes. The labeling with anti-H3/K9- me2 (anti dimethyl group on lysine 9 of histone 3) showed the positive labeling of both...
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The study of epigenetic regulation of gene HLA II. Clas within family relationships
Chmel, Martin ; Černá, Marie (advisor) ; Urbanová, Jana (referee)
Introduction: At our post-genomic era the studies of epigenetic regulation constitutes one of the tools for understanding the function of genes. Epigenetic regulation can directly control the temporal and spatial gene activity or silencing. The molecular basis of these regulations are DNA bases modifications, chromatin remodeling and RNA interference. At the same time, these mechanisms have a special way of transferring genetic information to subsequent generations called epigenetic inheritance. It has been proven epigenetic deregulation of certain genes as cause for many disease. For this reason, the study of epigenome HLA genes seems particularly important because these genes play a fundamental role in regulating the immune system. Aims: The aim of this work is to create a description of epigenetic modifications within families. It is an analysis of histone modifications and DNA methylation in the promoter region of the gene HLA DQA1. The aim was also to compare the differences in epigenetic modifications between alleles and compared the differences in these modifications between generations. The results will be compared with the analysis of the level of expression of the gene HLA DQA1. Methods: From collected peripheral blood of donors were isolated DNA, RNA, and leukocytes. DNA was used for...
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