In der Epigenetik werden die Veränderungen der Erbinformationen neben der DNS erforscht. Dabei werden den Histonen, um die sich die DNS im Zellkern wickelt, eine große Bedeutung zugeordnet. In dieser Arbeit werden die Ergebnisse eines neuen Segmentierungsverfahrens ausgewertet und visualisiert. Dabei werden die vorliegenden Daten mittels des k-means++ Algorithmus geclustert.Zuerst werden die Clusterergebnisse statistisch ausgewertet, um sie dann mit den durch vorgehenden Arbeiten erworbenen Kenntnissen zu vergleichen. Mittels dieses Vergleichs werden dann die idealen Parameter für das Clustering bestimmt. Die Ergebnisse dieses idealen Clusterings werden dann mittels Starplots, Scatterplots und Binningplots visualisiert. Für die Erstellung der Scatter- und Binningplots wird eine PCA genutzt, um die Daten auf zwei Dimensionen zu reduzieren.

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...

Methylation of histone 3 (H3) at lysine 36 (K36) has been implicated in several biological processes, such as DNA replication, DNA repair, and transcription. To date, at least eight distinct mammalian enzymes have been described to methylate H3K36 in vitro and/or in vivo. In this work, Set2, Nsd1, and Nsd3 Venus tagged proteins were successfully expressed in mouse embryonic stem cells and, then, analyzed by confocal microscopy, mass spectrometry (MS), and chromatin immunoprecipitation sequencing (ChIP-seq). MS analysis revealed that Setd2, Nsd1, and Nsd3 do not associate in protein complexes with each other. Setd2 was associated with RNA polymerase II subunits and two transcription elongation factors (Supt5 and Supt6), whereas Nsd1 associated with the transcription factor Zfx. In contrast, Nsd3 interacted with multiple protein complexes including Kdm1b and Brd4 complexes. Interestingly, Nsd1 and Zfx seem to be bound to chromatin during cell division. ChIP-seq analysis of the H3K36 methyltransferases showed different binding profiles at transcribed genes: Nsd1 binds near the transcription start site (TSS), Setd2 loading starts near the TSS and spreads along the gene body, while, Nsd3 is preferentially enriched at the 5’ and 3’ gene regions. Sequential deletion of PWWP and zinger-finger like domains was achieved to study any possible changes in Nsd1 and Nsd3 function. Deletion of either PHD1-4 or PHD5/C5HCH domains decreased Nsd1 recruitment to chromatin. Particularly, the PHD5/C5HCH were identified as the protein-protein interface for Zfx interaction. In agreement, Zfx knockdown also decreased Nsd1 deposition at the Oct4 and Tcl1 promoter regions. Furthermore, Nsd1 depletion reduced bulk histone H3K36me2 and histone H3K36me3 loading at the coding regions of Oct4, Rif1, Brd2, and Ccnd1. In addition, Nsd1 knockdown led to an increased Zfx deposition at promoters. Our findings suggest Zfx recruits Nsd1 to its target loci, whereas Nsd1 regulates Zfx chromatin release and further contributes to transcription regulation through its H3K36 dimethylase activity. On the other hand, loss of Nsd3’s PHD5/C5HCH or PWWP domains decreased Nsd3 binding to DNA. In addition, we demonstrate that Nsd3 is recruited to target genes in a Brd4-dependent manner. Herein, we provided further insights on how H3K36 methyltransferases are regulated, and how they contribute to changes in the epigenetic landscape in mouse embryonic stem cells.fi

No description available.

<p>Prostate cancer is (PCa) the second leading cause of cancer death in males in the United State, with 174,650 new cases and 31,620 deaths estimated in 2019. Polo-like kinase 1 (PLK1) has been postulated to have a pro-tumorigenesis function, besides its critical role in regulation of cell cycle, and to be overexpressed in various types of human cancer, including prostate cancer (PCa). However, our understanding remains unclear regarding the pro-tumor properties of PLK1 partially due to a lack of proper animal model. Integrating our recently generated prostate-specific PLK1 knock-in genetically engineered mouse model (GEM) and the transcriptome data of human PCa patients, we identify an oncogenic role of PLK1 in the prostate adenocarcinoma progression, castration resistance and metastatic dissemination. To elucidate the underlying mechanism, we investigate the link between PLK1 and tumor microenvironment in PCa using the transgenic mouse model, and find that PLK1overexpression enable the macrophages polarization towards M2 phenotype via driving the activation of IL4/IL13/STAT6 pathway. These findings first validates PLK1 as a critical oncogene closely associated with PCa progression in vivo, and uncover a novel function of PLK1 to facilitate IL4/STAT6 signaling and M2 macrophage polarization. Importantly, these findings suggest an efficient therapeutic strategy targeting STAT6 for treatment of advanced PCa which usually possessing a high level of PLK1 expression. To further explore the molecular mechanism underlying PLK1-induced PCa progression and resistance to therapy, we turned our eyes to epigenetic modifications. It has been documented that epigenetic deregulation such as histone modification and DNA methylation contributes to PCa initiation and progression. Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of Polycomb-repressive complex 2 (PRC2), plays a critical role in repressing gene expression by tri-methylation of histone 3 at lysine 27 (H3K27me3). Emerging data have demonstrated that there is a link between EZH2 and oncogenesis as EZH2-mediated methylation acts as an important factor in epigenetic silencing of tumor suppressor genes in cancer. Expression of EZH2 is often upregulated in castration-resistant prestate cancer (CRPC), thus EZH2 has been proposed as a target for CRPC. Importantly, it has been demonstrated that EZH2 becomes hyperphosphorylated in CPRC cells. Further, it has been shown that the oncogenic function of EZH2 is usually regulated by the post-translational modifications. PLK1 acting as a serine/threonine kinase to regulate multiple signaling pathways in human cancer, however, whether PLK1 is involved in EZH2 phosphorylation is not known. Herein, we show that Plk1 physically interacts with EZH2 and negatively regulates H3K27 trimethylation (H3K27me3). Furthermore, Plk1 can phosphorylate EZH2 at T144, and Plk1-mediated phosphorylation of EZH2 is involved in inhibiting EZH2 activity toward H3K27me3. More importantly, EZH2 phosphorylation by Plk1 is inhibitory for PRC2-mediated gene repression but required for transcriptional activation toward oncogenesis. Finally, by combination with Plk1 inhibitor BI2536, we show a robust sensitization of EZH2 inhibitors in CRPC cell lines, as well as in CRPC xenograft tumors. Our findings provide a new mechanism to define the oncogenic activity of EZH2 and suggest that inhibition of Plk1-mediated EZH2 activity may provide a promising therapeutic approach for CRPC.</p>

The "omics" is a concept of biological disciplines that globally characterizes and quantifies biomolecules involved in the key functions of an organism. The "omics" methods are used e.g. in molecular epidemiology, where they help to evaluate potential biomarkers that identify the impact of environmental factors for human health. In this thesis, the "omics" methods were applied in samples collected from newborns born in localities of the Czech Republic mostly differing by pollution levels from industrial sources. The principal aim was to determine whether environmental changes during prenatal development can affect gene expression and its regulation in newborns. The thesis further aimed to evaluate the level of air pollution at the time of biological samples collection. Using the whole genome approach, differentially expressed genes (DEGs) in newborns from districts Karvina and Ceske Budejovice (CB) were identified. In a pilot study of a small group of newborns from districts Most and CB, differentially methylated CpG sites in DNA were assessed. These sites attenuate gene activity and could be responsible for long-term changes at the genetic level. Finally, the aim was to find differentially expressed small non-coding RNA (DE miRNA) in newborns from Most and CB. Samples of umbilical cord blood from...

<p>  </p> <p>Aging is characterized by changes in transcriptional outputs that correlate with physiological changes observed as we age, including decreased function, and increased cell death. Importantly, many of these changes are conserved across tissues and organisms . Because one of the molecular hallmarks of aging is epigenetic dysregulation, we are interested in understanding how age-associated changes in chromatin contribute to the aging transcriptome. To accomplish this, we use the <em>Drosophila </em>visual system as a model for aging, with a particular focus on photoreceptor neurons. </p> <p>To perform cell-type specific genomic studies in <em>Drosophila, </em>we previously developed a nuclei immuno-enrichment method that was compatible with RNA-seq. However, due to low nuclei yields, this protocol was not amenable to chromatin-based studies, such as ChIP-seq and ATAC-seq. In Chapter 1, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein that increased yields without compromising efficiency. We further demonstrate that this protocol is compatible with several chromatin profiling techniques, such as Assay of Transposable-Accessible Chromatin (ATAC)-seq, Chromatin Immunoprecipitation (ChIP-seq), and CUT&Tag. </p> <p>Chromatin accessibility is enriched for transcription factors. Thus, in Chapter 2, we profiled accessible chromatin in aging photoreceptors and integrated this data with RNA-seq to identify transcription factors that showed differential activity in aging Drosophila photoreceptors. Surprisingly, we found that 57 transcription factors had differential binding activity during aging, including two circadian regulators, Clock and Cycle, that showed sustained increased activity during aging. When we disrupted the Clock:Cycle complex by expressing a dominant negative version of Clock (ClkDN) in adult photoreceptors, we observed changes in expression of 15–20% of genes including key components of the phototransduction machinery and many eye-specific transcription factors. Using ATAC-seq, we showed that expression of ClkDN in photoreceptors leads to changes in activity of 37 transcription factors and causes a progressive decrease in global levels of chromatin accessibility in photoreceptors. Supporting a key role for Clock-dependent transcription in the eye, expression of ClkDN in photoreceptors also induced light-dependent retinal degeneration and increased oxidative stress, independent of light exposure. Together, our data suggests that the circadian regulators Clock and Cycle act as neuroprotective factors in the aging eye by directing gene regulatory networks that maintain expression of the phototransduction machinery and counteract oxidative stress.</p> <p>Previous work in the Weake lab found that long, highly expressed genes were more susceptible to be downregulated with age. DNA:RNA hybrids are co-transcriptional structures that form when the nascent RNA hybridizes with the template strand, resulting in a displaced non-template ssDNA. Importantly, accumulation of R-loops is associated with transcriptional inhibition and genomic instability, both hallmarks of aging. In Chapter 3, I characterized R-loop in maintaining proper transcriptional outputs and regulating visual function during aging. Bulk assays to measure R-loop levels revealed a significant increase in nuclear R-loops with age. Further, genome-wide mapping of R-loops revealed that transcribed genes accumulated R-loops over gene bodies during aging, which correlated with decreased expression of long and highly expressed genes. Importantly, while photoreceptor-specific down-regulation of Top3β, a DNA/RNA topoisomerase associated with R-loop resolution, lead to decreased visual function, over-expression of Top3β or nuclear-localized RNase H1, which resolves R-loops, enhanced positive light response during aging. </p> <p>Together, these studies underscore the importance of understanding how age-related changes in genomic processes, such as circadian transcription and maintenance of R-loops, contribute to physiological changes observed during aging. </p>

A subset of eukaryotic heterochromatin is located around the nucleoli, and this localization is correlated with gene silencing. Although there is some evidence for trans-acting factors organizing genomic loci around the nucleolus, the characterization of proteins and /or RNAs involved in perinculeolar heterochromatin localization and maintenance is incomplete. Notably, the mammalian female inactive X chromosome, a well-studied model of facultative heterochromatin, frequently resides in the perinucleolar regions during mid to late S phase. The disruption of the Xi–nucleolus association results in the erosion of heterochromatin compartment and silencing, which renders it a good model to investigate the mechanism and biological relevance of heterochromatin organization around the nucleolus. This dissertation will present evidence showing that Ki-67 regulates inactive X (Xi) chromosome association with nucleoli, maintains Xi heterochromatic structures, and regulates cell cycle progression, in cell-type-specific manner dependent on checkpoint proficiency. Ki-67 protein plays roles in heterochromatin organization during interphase. Upon Ki-67 depletion, a subset of Xi in human female hTERT-RPE1 moved away from nucleolus and displayed several features of compromised heterochromatin maintenance. These chromatin alterations were limited to Xi chromosomes localized away from the nuclear lamina and were not observed in virally transformed 293T cells upon Ki-67 depletion. Furthermore, I demonstrated that the different Xi heterochromatin alteration responses result from cell-type-specific reduced proportion of cells in S phase upon Ki-67 depletion. In human hTERT-RPE1, WI-38, IMR90, hTERT-BJ cell lines, depletion of Ki-67 slowed entry into S phase and coordinately downregulated genes related to DNA replication. These cell lines are able to induce p21 expression upon Ki-67 depletion. On the contrary, alteration of transcription and cell cycle progression were not observed in tumor-derived HeLa, U2OS and 293T cell lines. These cell lines do not induce p21 expression either. I additionally examined the Ki-67 function in mouse cell cultures. Depletion of Ki-67 neither redistributes inactive X chromosome nor regulates S phase progression in primary female mouse embryonic cells.

Down Syndrome (DS), the most common aneuploidy seen in live-borns, is caused by trisomy for chromosome 21. DS imposes high risks for multiple health issues involving various systems of the body. The genetic complexity of trisomy 21 and natural variation between all individuals has impeded understanding of the specific cell pathologies and pathways involved. In addition, chromosomal disorders have been considered outside the hopeful progress in gene therapies for single-gene disorders. Here we test the feasibility of correcting imbalanced expression of genes across an extra chromosome by expression of a single gene, XIST, the key player in X chromosome inactivation. We targeted a large XIST transgene into one chromosome 21 in DS iPS cells, and demonstrated XIST RNA spreads and induces heterochromatin and gene silencing across that autosome in cis. By making XIST inducible, this allows direct comparison of effects of trisomy 21 expression on cell function and phenotypes. Importantly, XIST-induction during in vitro hematopoiesis normalized excess production of differentiated blood cell types (megakaryocytes and erythrocytes), known to confer high risk for myeloproliferative disorder and leukemia. In contrast, trisomy silencing enhances production of iPS and neural stem cells, consistent with DS clinical features. Further analysis revealed that trisomy 21 initially impacts the endothelial hematopoietic transition (EHT) to generate excess CD43+ progenitors, and also increases their colony forming potential. Furthermore, results provide evidence for a key role for enhanced IGF signaling, involving over-expression of non-chromosome 21 genes controlled by trisomy 21. Finally, experiments to examine trisomy effects on angiogenesis showed no effect on production of endothelial cells, but it remains unclear whether trisomic cells may differ in ability to form vessels. Collectively, this thesis demonstrates proof-of-principle for XIST-mediated “trisomy silencing”. Phenotypic improvement of hematopoietic and neural stem cells demonstrates the value for research into DS pathogenesis, but also provides a foundation of potential for future development of “chromosome therapy” for DS patients.

Dans les cellules souches embryonnaires de souris (mESCs), le groupe de protéines Polycomb (PcG) répriment les gènes de développement en participant ainsi à la maintenance de l’état de pluripotence. Ce complexe dépose la H3K27me3au niveau des éléments régulateurs induisant une compaction de la chromatine. Cette marque forme en plus des marquesactives H3K4me3 présentes des domaines bivalents. Etrangement, des boucles d’ADN dites entre le promoteur et enhancer, généralement associé à l’activation du gènes, sont observées au niveau des gènes bivalents avant leur activation.On suppose que la fonction du PcG pourrait être de neutraliser l'enhancer conférant une future activation rapide des gènes.Au cours de ma thèse, j’ai identifié les boucles d’ADN formé par les réprimés par PcG dans les mESCs. Pour cela,j’ai effectué un profilage épigénomique de 4 marques d'histones et identifié près de 2500 promoteurs bivalents et 13000enhancers. En utilisant des données publiées de Hi-C à haute résolution, j’ai identifié toutes les boucles formées par les domaines bivalents. Etonnement, j’ai pu identifier que de nombreux gènes réprimés par PcG interagissent avec des enhancers actifs. Cette observation a été suivie d'une validation par le 4C-seq. De plus, j’ai effectué une caractérisation fonctionnelle des boucles en utilisant deux approches. Tout d'abord, j'ai mis en place, en collaboration avec D. Bourc'his(Institut Curie), un système de culture de mESCs (2i + VitC) où le taux de H3K27me3 est réduit. J'ai effectué un profilage épigénomique similaire révélant que les promoteurs réprimés par PcG ont perdu la marque H3K27me3. En RNA-seq, j’ai démontré que l’expression des gènes ne change pas après le PcG soit détacher des promoteurs.. Ensuite, par la réalisation de plusieurs validations en 4C-seq j’ai démontré que les interactions avec les enhancers ne sont pas affecté alors que la moitié des enhancers interagissant perdent leurs marques activatrices. Dans le système 2i+VitC, ces gènes semblent être réprimés par un autre mécanisme suite à la perte du PcG. De plus, j’utilise une approche ciblée pour enlever localement laH3K27me3 de deux gènes bivalents en utilisant le système Cette technique est en cours d’optimisation.Notre étude est la plus systématique au niveau génomique des boucles d'ADN dans le cadre de la régulation des gènes PcG. Notre étude révèle une nouvelle fonction du PcG qui est la répression de boucle d’ADN déjà établies entre promoteurs et enhancers. / In the mouse embryonic stem cells (mESCs), Polycomb Group Proteins (PcG) repress developmental genes and thereby participating in the maintenance of the pluripotency. PcG repress genes by depositing the H3K27me3 histone marks on their regulatory elements, followed by chromatin compaction. In addition to the H3K27me3 marks, those genes carry H3K4me3 active marks and were characterized as bivalent. Intriguingly, at many PcG repressed genes, DNA loops can be observed with enhancer elements, which are normally thought to have an activating function. The aim of my project is to both describe and mechanistically dissect the function of Polycomb repressed promoter – enhancer loops.During my PhD, I aimed firstly to identify all promoter–enhancer loops involved by PcG repressed genes in mESCs. I have performed ChIP-seq profiling of 4 histone marks and identified around 2500 PcG repressed promoters and 13000 enhancers. Using a recently published high-resolution Hi-C data in mESCs, I have identified all DNA loops that are formed by PcG repressed promoters. Surprisingly, a high percentage of bivalent promoters were found to contact active enhancers. The presence of those loops were validated by ultra-high 4C-seq on selected genes and imply a small significant increase of the gene expression without leading to a complete activation of the gene. I have established a more physiological ESC model (2i+VitC) where H3K27me3 is reduced at all promoters. I have performed ChIP-seq, where bivalent promoters were all classified as H3K27me3 negative. RNA-seq experiments have showed that those genes do not become activated. 4C-seq experiments have revealed that those loops do not disappear after PcG removal, whereas the half of interacted enhancer loose their H3K27ac active marks. Those genes seem to remain repressed by an unknown mechanism. These results argue for a possible role of PcG in preparing the gene for their activation by blocking the productivity of such DNA loops. Secondly, I aimed to functionally characterize those DNA loops by using a CRISPR/dCas9 approach to completely remove H3K27me3 from two PcG repressed genes that contact active enhancers Pax6 and Nkx1-1 genes. This system is still under optimization steps.My project revealed the most systematic characterization of DNA loops under the regulation of PcG, providing important insight how PcG function to inactivate such loops. I have highlighted an additional function of PcG which the involvement in the repression of already establish loops between active enhancers and promoters and thereby blocking the productivity of such activating loops. This function is an addition to the already described repressive function of PcG on both promoters and poised enhancers.