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Ziel der folgenden Arbeit ist es epigenetische Muster regulatorischer Elemente in hämatopoetischen multipotenten Vorläuferzellen aufzudecken. Neueste Fortschritte der Einzelzell-Technologien ermöglichen Einblicke in die Komplexität der Regulationsmechanismen auf molekularer Ebene und werden zu einem umfassenderen Verständnis der epigenetischen Komponente in der Zelldifferenzierung führen. Für diese Arbeit wurden sechsunddreißig hämatopoetische multipotente Vorläuferzellen aus dem Oberschenkelknochen einer Maus entnommen. Durch FACS wurden die Zellkerne der Vorläuferzellen vom Zytoplasma getrennt. Es wurde eine Bisulfit-Sequenzierung mit den Zellkernen durchgeführt, um die DNA-Methylierungsmuster durch Umwandlung von unmethylierten Cytosinen in CpGs und die Chromatinzugänglichkeit durch in vitro Methylierung mit M.CviPI in GpCs zu untersuchen. Die DNA-Reinigung nach der Amplifikation wurde mit magnetischen Beads durchgeführt. Siebzehn der sechsunddreißig multipotenten Vorläuferzellen haben die Qualitätskontrolle bestanden. Die Promotorregionen der Zellen weisen eine Chromatinzugänglichkeit von 60% auf, während die codierende Gensequenz eine konstante DNA-Methylierungsrate zwischen 60% und 80% zeigt. Es wurde bestätigt, dass transponierbare Elemente (LINEs und LTRs) mit einer Rate von 90% stark methyliert sind, um die genomische Integrität zu bewahren. Die Bindungsstellen von zwei Architekturproteinen (p300 und CTCF) sind nachweislich bis zu 45% zugänglich, während die DNA-Methylierung an den Bindungsstellen von 60% bzw. 80% auf 30% bzw. 40% abnimmt. DNase I hypersensitive Regionen wurden untersucht, um zu überprüfen, ob die in vitro Methylierung durch M.CviPI erfolgreich zugängliches Chromatin annotieren kann. Es hat sich gezeigt, dass die Bisulfit-Sequenzierung in Einzelzellen hochauflösende Ergebnisse über die epigenetischen Muster in verschiedenen regulatorischen Regionen liefert und ein besseres Verständnis über die heterogenen Zustände in der Hämatopoese ermöglichen wird. The objective of the following work is to elucidate epigenetic patterns in regulatory elements of hematopoietic multipotent progenitor cells (MPPs) on a single-cell level. Recent advances in single-cell technologies have enabled new insights into the complexity of regulatory mechanisms on a molecular level and will lead to a broader understanding of the epigenetic component in the establishment of cell identity. For this work, thirty-six hematopoietic MPPs have been collected from the femur of a mouse. Through cell sorting, the nuclei of the MPPs have been separated from the cytoplasm. Single-cell bisulfite sequencing (scBS-seq) was performed on the nuclei to investigate DNA methylation patterns by bisulfite conversion of unmethylated cytosines in CpG sites and chromatin accessibility by in vitro methylation with M.CviPI in GpC sites. Purification after amplification of the DNA was completed using magnetic beads. Seventeen out of the thirty-six MPPs passed the quality control for sufficient genomic coverage and have been assessed in more detail. Promoter regions show chromatin accessibility up to 60%, while gene bodies maintain a constant rate of DNA methylation between 60% to 80%. Transposable elements (LINEs and LTRs) were confirmed to be highly methylated at a rate of 90% to preserve genomic integrity. The binding sites of two architectural proteins (p300 and CTCF) are shown to be accessible up to 45%, while DNA methylation at the binding sites decreases to 30% and 40% from 60% and 80%, respectively. DNase I hypersensitive sites have been investigated to verify that in vitro DNA methylation was used successfully to annotate accessible chromatin. ScBS-seq was shown to provide high-resolution results of epigenetic states at various regulatory regions in single progenitor cells and will enable further understanding of heterogeneity in hematopoiesis.

Single cell multi omics techniques have shown an advancement in unrevealing complex diseases like cancer heterogeneity by providing multi-faceted insight into their individual cellular regulations. In this study, a machine learning approach, Bayesian network (BN), has been applied to integrate genomic, epigenomic, and transcriptomic data in hepatocellular carcinoma at single cell resolution. Hepatocellular carcinoma (HCC) is the most common type of liver cancer with a high metastatic rate and reckoned for poor prognosis. Heterogeneity of tumor cells is concerned with cancer progression, metastasis, therapeutic resistance, and mortality. For this purpose, a dataset from a published study of 25 single cell sequencing of hepatocellular carcinoma were used. First, DNA methylome and transcriptome data were analyzed on their own. Copy number variations were estimated from DNA methylome data by using the Hidden Markov Model method. To reveal the causal relationship between the omics, three BN models were constructed. The models were fitted to their parameters by using maximum likelihood estimation. For model evaluation, score-based criteria, Akaike information criterion and Bayesian information criterion, were used. 207 genes with significant models have been detected. The heterogeneity of the omics and their regulation mechanisms with each other have been shown, by pointing to genes that follow different BN models that take place in major pathways in HCC. Tek hücreli çoklu omik teknikleri, kendi bireysel hücresel düzenlemelerine çok yönlü bir bakış açısı sağlayarak kanser heterojenliği gibi kompleks hastalıkların ortaya çıkarmada bir ilerleme göstermiştir. Bu çalışmada, tek hücre temelli hepatoselüler karsinomda genomik, epigenomik ve transkriptomik verileri entegre etmek için bir makine öğrenimi yaklaşımı olan Bayesian ağları (BN) uygulanmıştır. Bu amaçla, yayınlanmış bir çalışmadan hepatoselüler karsinomun 25 tekil hücre dizileme veri seti kullanılmıştır. Hepatosellüler karsinom (HSK), yüksek metastatik oranla en yaygın karaciğer kanseri türüdür ve kötü prognoza sahip olduğu düşünülmektedir. Tümör hücrelerinin heterojenliği, kanserin ilerlemesi, metastaz, terapötik direnç ve mortalite ile ilgilidir. Önce, DNA metilom ve transkriptom verileri tek başlarına analiz edilmiştir. Kopya sayısı varyasyonu, Gizli Markov Modeli yöntemi kullanılarak DNA metilom verilerinden tahmin edilmiştir. Omikler arasındaki nedensel ilişkiyi incelemek için üç BN modeli oluşturulmuştur. Modeller, en çok olabilirlik kestirimi (MLE) kullanılarak parametrelerine uydurulmuştur. Model değerlendirme için puana dayalı kriterler, Akaike bilgi kriteri (AIC) ve Bayes bilgi kriteri (BIC) kullanılmıştır. Anlamlı modele sahip 207 gen tespit edilmiştir. Farklı BN model izleyen genlerin HCC’de aynı yolakta yer aldığına işaret ederek, omiklerin ve birbirleriyle regülasyon mekanizmalarının heterojenliği gösterilmiştir.

Rapid industrial and agricultural development brought, besides the indisputable advances, also risks related to the environmental pollution. Widespread soil deterioration represents a global problem. Chernobyl area contaminated by radionuclides after nuclear accident in 1986 provides the opportunity to analyze in situ the impact of radiation on plant systems. Unlike animals and humans, plants are not able to move to another place with better living conditions. Therefore, plants are an ideal object to study adaptation to the conditions of environmental stress. Long- term exposure to the ionizing radiation causes widespread changes in plant genome and epigenome. Also, these alterations may result in changed phenotype. In particular, this review discusses the effect of ionizing radiation on genetic and epigenetic stability of plant genome., Rozvoj priemyslu a poľnohospodárstva priniesol okrem nesporných výhod aj riziká súvisiace so znečistením životného prostredia. Rádioaktívnymi prvkami kontaminovaná oblasť Černobyľu po jadrovej havárii v roku 1986 poskytuje možnosť analyzovať vplyv radiácie na rastliny v podmienkach in situ. Rastliny na rozdiel od živočíchov a človeka nie sú schopné presídliť sa na iné miesto s vyhovujúcejšími životnými podmienkami. Z tohto dôvodu sú ideálnymi objektom pre štúdium adaptácie na podmienky prostredia zmenené pôsobením stresu. Dlhodobé pôsobenie ionizujúceho žiarenia môže mať za ásledok rozsiahle zmeny v genóme a epigenóme rastlín. Tieto zmeny môžu mať za následok zmenený fenotyp. Prehľad diskutuje najmä vplyv ionizujúceho žiarenia na genetickú a epigenetickú stabilitu rastlín.

Epigenetičke promjene imaju značajan utjecaj na evolucijski proces, njihovo djelovanje na specijaciju i prirodnu selekciju je posredovano okolišnim faktorima i time su usko povezane s ekologijom i evolucijom. U radu je dan pregled znanstvenih istraživanja čija tematika istražuje uzajamno djelovanje okolišnih čimbenika i fenotipskih promjena te njihov utjecaj na evolucijski proces. Također, na koji način promjene okolišnih čimbenika uzrokuju promjene u genskoj zalihi populacije te njihov utjecaj na socijalnu dinamiku populacije i potencijalno specijaciju.

This theoretical thesis covers the issues of Autism Spectrum Disorders (ASD) in relation to the brain connectome research. ASD belong to the group of neurodevelopmental syndromes and are characterized by deficits in communication skills, social interaction and stereotypic behaviors. The prevalence of ASD increases, its etiopathogenesis is very likely multifactorial. Within the ASD syndrome, precise differential diagnostic algorithms are difficult to implement in the absence of objective biomarkers. Extensive neuroscientific research, including the connectome projects, might improve the diagnostic and therapeutic procedures in the field of Psychiatry, including ASD. The individual's connectome profile might well serve as a new biomarker in psychiatric diagnostic and therapeutic approaches. The brain connectome represents the net of all neuronal connections in the brain. Mapping of the connectome across all ages, in health and in disease, is the main goal of the Human Connectome Project (HCP). The first HCP data show great interindividual variability with the environmental factors playing a crucial role. Extensive neurobiology research data on mechanisms of memory support the vital role of environmental stimulation in compensating for behavioral symptoms in ASD. Applied behavior analysis (ABA) is an...

Epigenetika proučava nasljedne promjene u ekspresiji gena i fenotipa, koje ne ostavljaju trag na molekuli DNA i transgeneracijski učinak okolišnih čimbenika. Za bolje razumijevanje definicije epigenetike, u diplomskom radu opisani su osnovni pojmovi u genetici, mehanizmi regulacije ekspresije pojedinih gena, te glavni molekularni mehanizmi epigenetike: metilacija DNA, modifikacija histona i RNA interferencija. Svaki od navedenih mehanizama možemo usporediti s prekidačem, koji 'pali ili gasi' određeni gen i time odlučuje o njihovoj ekspresiji. Epigenom upravo zbog toga možemo nazvati 'dodatnim slojem' genetičkih informacija koji mehanizmi (de)aktiviraju ukoliko postoji neki vanjski čimbenik koji utječe na njih, kojeg nazivamo epigenatorom. Hrana je čovjeku osnovno gorivo za organizam i iz nje dobivamo korisne, ali i neke štetne tvari. Opisana su dva istraživanja na miševima, u kojima su hranjeni određenom hranom, koja je mijenjala neka fenotipska obilježja njihovih potomaka. Tim spoznajama čovjek je shvatio kako naš život određuju ne samo naslijeđeni geni, već i niz drugih okolišnih čimbenika, na koje možemo utjecati., Epigenetics studies hereditary changes in gene and phenotypic expression, which do not leave any trace on the DNA molecule, as well as transgenerational effects of environmental factors. For a clear perception of the definition of epigenetics, this graduation thesis describes some basic notions of genetics, regulatory mechanisms controlling gene expression, and the main molecular mechanisms of epigenetics: DNA methylation, histone modifications, and RNA interference. Each of the mechanisms listed above can be compared to a switch, which 'turns off or on' a specific gene, thus deciding upon their expression. This is the reason we can refer to the epigenome as 'an additional layer' of genetic information, (de)activated by certain mechanisms if there is an external factor, called epigenator, influencing them. Food is the basic fuel for human organism from which we extract usefull, as well as some harmfull substances too. Two experiments conducted on mice have been described. The mice were fed by specific food, which than changed certain phenotypic characteristics of their offsprings. This made us realize that human life is determined not just by inherited genes, but also by a number of external factors, which we can influence.

Za razliku od genetike koja se temelji na proučavanju građe gena, epigenetika se temelji na proučavanju tzv. fiziologije gena, odnosno promjena u njihovoj aktivnosti. Temeljne epigenetske promjene su metilacija DNA i posttranslacijske promjene histona, procesi koji se međusobno nadopunjuju i stvaraju genetički profil kojim se regulira genska aktivnost. Prehrana je važan čimbenik u životu svih organizama te je poznato blagotvorno i štetno djelovanje sastojaka hrane koju unosimo. Niz istraživanja je pokazao da povećan unos određene skupine hrane može smanjiti rizik nastanka bolesti kao što su kardiovaskularne i neurološke bolesti, dijabetes i rak, moguće zbog toga što pojedini sastojci te hrane mogu izazvati epigenetske promjene kod ljudi. U ovom radu opisane su najučestalije epigenetske promjene s naglaskom na mehanizme njihovog djelovanja, utjecaja određenih nutrijenata i biološki aktivnih tvari koje unosimo prehranom.

Diese Masterarbeit beschäftigt sich mit der Frage der Relevanz epigenetischer Kenntnisse für die Ausbildung Klinischer Sozialer Arbeit. Das junge Forschungsgebiet Epigenetik erweitert das Wissen der Genetik und befasst sich mit den biochemischen Möglichkeiten einer Zelle, ihre Gene zu regulieren, ohne deren Substanz zu verändern. Wissenschaftliche Studien zeigen den Einfluss von Umweltfaktoren auf epigenetische Prozesse, die wiederum Auswirkungen auf die psychische und physische Gesundheit eines Menschen haben können. Die Frage ob auch die Möglichkeit einer Vererbung epigenetischer Veränderungen an nächste Generationen besteht, wird mit beleuchtet. Die Epigenetik ist ein Gebiet mit großem und weitreichendem Potenzial, dem die Wissenschaft vermehrt Aufmerksamkeit widmet und welches zunehmend auch öffentliches und interdisziplinäres Interesse weckt. In einer qualitativen Erhebung, sowohl mit FachexpertInnen der Epigenetik als auch der Klinischen Sozialen Arbeit, wurde erörtert, wie wichtig und förderlich die Erkenntnisse zu Epigenetik für die Profession sein können/sind. Das Ergebnis zeigt, dass epigenetische Fachkenntnisse ein wesentliches und ergänzendes Hintergrundwissen für Theorien, wie beispielsweise das bio-psycho-soziale Modell, klinisches Fallverstehen sowie ein wertvoller Beitrag für ethische Grundhaltung, Behandlungsimpulse und Disziplinentwicklung sein können. Wesentlich dabei ist eine wissenschaftlich fundierte Grundlagenvermittlung, mit basalem Einblick in biochemische Prozesse, um Studienergebnisse und ihre Tragweite für den Menschen realistisch einschätzen und in klinischem Kontext verwerten zu können. Ebenso erörtert wurden unterschiedliche Ansätze und Möglichkeiten das Wissen in die Ausbildung zu integrieren. Empfehlenswert wären die Behandlung der Thematik innerhalb einer bestehenden Lehrveranstaltung, beispielsweise im Zuge der bio-psycho-sozialen Perspektive, sowie das Angebot eines Weiterbildungsseminares für bereits Berufstätige in der Praxis. This master thesis deals with the question of relevance of epigenetic knowledge for the training of clinical social work. The young research area of epigenetic extends the knowledge of genetics and deals with the biochemical options of a cell to regulate its genes without changing its substance. Scientific research studies show the influence of environmental factors on epigenetic processes, which by themselves can cause effects on the psychic and physical health of a person. There is also a focus on the question, if there is the possibility of inheriting epigenetic changes to the next generation Epigenetics is a field with a large and extensive potential which science pays more and more attention to and which increasingly raises public and interdisciplinary interest. In a qualitative study together with epigenetic experts as well as clinical social work it was discussed how important and beneficial epigenetic findings can be for that profession. The results show that epigenetic expert knowledge is a decisive and supplementary background for theories such as the bio-psycho-social model, for the clinical understanding of cases and a valuable input for ethical disposition. Furthermore, it is impetus for treatment and development of disciplines. An important element is a scientifically grounded teaching of basics with a basal view into biochemical processes to evaluate realistically study results and their significance for the human being and to make use of them in clinical context. Alike different approaches and possibilities were discussed to integrate knowledge into training. It is recommendable to deal with the topic during an existing course, e.g. in the event of the bio-psycho-social perspective and the offer of a seminar of advanced training for persons already employed. Wien, FH Campus Wien, Masterarb., 2017

During the process of spermatogenesis, histones are replaced by protamines, basic proteins enabling transmission of DNA to the oocyte during fertilization. In mouse sperm, there is only 1% of remaining histones whose N-terminal tails contain post-translationally modified residues. In this study, I was interested in contribution of paternal histone H4 acetylated on lysine K12 residues (H4K12ac) that is present in mature sperm head in remaining nucleosomes. Physiologically, H4K12ac has an important role in transcription factor accumulation and in regulation of gene expression. The presence and abundance of H4K12ac modification in various pronuclei stages of 1-cell embryo and parthenotes were assessed by imunnoflourescent detection with utilization of anti-H4K12ac antibody. Altogether, the paternal pronucleus exhibits a strong acetylation signal on H4K12 since its formation, while in the maternal one, there is a slow continual increase of H4K12ac getting on the same level as paternal pronucleus till the pronuclei fusion. Simultaneously DNA methylation status in both pronuclei was detected. In paternal pronucleus there is a continual decrease in the DNA methylation detectable as a decrease of 5mC and an increase of 5hmC signal. Meanwhile, the maternal pronucleus stays widely methylated. DNA...

Her ne kadar DNA‟nın kimyasal ve moleküler yapısı anlaşılmış olsa da, son on yıldır elde edilen bulgular sayesinde artık her şeyin DNA‟da bitmediği bilinmektedir. Yaşamı sürdürebilmek için çevresel uyaranlara uygun tepki göstermeyi gerektirir. Embriyodan yaşamın sonuna kadar geçen süreçte, gen ifadelerinde değişiklikler gözlemlenir. Genomda bulunan genler, belirli hücrelerde ve belirli zamanlarda ifade edilir. Bu yeni kavrama “genler üstü genetik” anlamına gelen “epigenetik” denilmektedir. Epigenetik düzenlemelerde ve mekanizmalarda yer alan tüm oluşumlara ise “epigenom”denir. Epigenetik değişikler bir genin aktivasyonuna ya da sessizleşmesine neden olurlar, bu ise bir geni aktive edici, mutasyon ya da delesyon gibi genetik bir mekanizmaya benzerdir. Fakat, epigenetik değişiklikler baz dizisinde bir değişime neden olmadan ortaya çıkarlar ve çoğu kez geriye dönüşümlüdür. Gen regülasyonunun düzenlenmesi, hücrelerin nasıl differansiye olduklarının belirlenmesinde ve nasıl kansorejen hale geldiklerinin anlaşılmasında hayati önem taşımaktadır. Bu çalışmada en az genetik kadar önemli ve çok yeni olan epigenetik hakkında, bilgiler derlenmiştir. Although the chemical and molecular structure of DNA understood, thanks to the findings of the last ten years, is known that everything is not over the DNA. To sustain of the life are requires of the appropriate response to environmental stimuli. Embryo to until the end of life, changes in gene expression observed. Genes in the genome is expressed at certain times and in certain cells. This new grip is called that "epigenetic". All of the mechanisms of epigenetic regulation is called that "epigenome". Epigenetic alterations cause of the gene silencing or activation, such as a genetic mutation or deletion mechanism. However, epigenetic alterations are emerging without change of the base sequence, and occurring often recyclable. Arrangement of the gene regulation is vital importance to understanding of the cells how they differentiated and they can be carcinogenic. In this study the information is compiled about that epigenetic, which is important at least as genetic.