DNA methylation entails the addition of a methyl group to the 5-carbon of the cytosine base of the DNA. This modification is important during many biological processes such as imprinting, X-chromosome inactivation, cell differentiation as well as silencing of transposable elements (TEs). DNA methylation is dynamic during early mammalian development, despite being a more static mark in somatic cells. Global hypomethylation is a hallmark of epigenetic reprogramming in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). Genome integrity is crucial during early development, as the germline DNA needs to be protected for future generations. Therefore, epigenetic reprogramming presents a critical phase for TE defence since presumably alternative silencing pathways need to be employed to limit their activity. In this thesis, I investigate the role of small RNAs to control TEs during global waves of DNA demethylation in cellular reprogramming, naïve pluripotency as well as early mammalian development. Following an introduction to the research questions, in chapter 3 I investigate the mechanism of TE regulation in an in vitro model of Dnmt1 deletion in mouse ES cells to recapitulate in vivo epigenetic reprogramming. I find that certain classes of TEs become transcriptionally upregulated and subsequently resilenced by a mechanism independent of DNA methylation. I identify ARGONAUTE 2 (AGO2) bound siRNAs as the prominent mechanism to control certain classes of TEs, while others appear to be regulated by redistribution of repressive histone modifications. In chapter 4, I construct Dicer constitutive and conditional KO ESCs in the background of the Dnmt1f l/f l ESCs using CRISPR-Cas9. I dissect the role of DNA methylation and of DICER dependent small RNAs on transcriptional changes of ESCs. Additionally, I find that DICER dependent small interfering RNAs (siRNAs) re-silence transcriptionally active TE classes. Finally, in chapter 5, I examine the role of small RNAs in TE silencing in different models of global hypomethylation in vivo and in vitro PGCs, during iPSC reprogramming and in a transition from serum to 2i culturing of mouse ESCs.

Myelodysplastic syndromes (MDS) represent a group of clonal stem cell disorders characterized by ineffective hematopoiesis, peripheral cytopenia, morphological dysplasia and the risk of transformation to acute myeloid leukemia (AML). MDS belongs to one of the most common hematological diseases in patients over 60 years old. MDS incidence is still increasing. Appropriate therapy of MDS remains challenging. There is no curative approach besides peripheral stem cells transplantation, which is regretfully appropriate only for a small group of patients due to a higher median age of the MDS population. This is why the search for therapeutic alternatives remains paramount. MDS treatment was rather frustrating until the recent introduction of two new therapeutic approaches: immunomodulation therapy with lenalidomide and epigenetic or demethylating therapy with 5-azacytidine. Both new drugs have significantly higher effect than standard therapy. However, the precise mechanism of this effect remains unknown. As a result, we decided to initiate several research projects while introducing this promising treatment to our patients. Our aim is to investigate the mechanism of both agents in relation to disease pathogenesis by examining changes of certain occurrences and factors prior to and during the course of...

Philosophiae Doctor - PhD / The overall aim of this thesis was to prepare nanostructured more processable heteronuclear sulphonated polyanyline nanocomposites with electroconductive properties suitable for applications in biosensors. The sulphonated self-assembled polyaniline and derivatised polyaniline nanocomposites (SPAHs) were prepared by chemical oxidative polymerisation or electrical decomposition. The SPAHs prepared include those of polyaniline (PANi), poly-o-methoxyaniline (POMA) and poly-2.5 dimethoxyaniline (PDMA). Two types of sulphonic acids of heteronuclear aromatic hydrocarbons were used in the production of sulphonated SPAH composites. These were anthracene sulphonic acid (ASA) and naphthalene sulphonic acids (NSA) wich played both doping and surfactant roles. / South Africa

Myelodysplastic syndromes (MDS) represent a group of clonal stem cell disorders characterized by ineffective hematopoiesis, peripheral cytopenia, morphological dysplasia and the risk of transformation to acute myeloid leukemia (AML). MDS belongs to one of the most common hematological diseases in patients over 60 years old. MDS incidence is still increasing. Appropriate therapy of MDS remains challenging. There is no curative approach besides peripheral stem cells transplantation, which is regretfully appropriate only for a small group of patients due to a higher median age of the MDS population. This is why the search for therapeutic alternatives remains paramount. MDS treatment was rather frustrating until the recent introduction of two new therapeutic approaches: immunomodulation therapy with lenalidomide and epigenetic or demethylating therapy with 5-azacytidine. Both new drugs have significantly higher effect than standard therapy. However, the precise mechanism of this effect remains unknown. As a result, we decided to initiate several research projects while introducing this promising treatment to our patients. Our aim is to investigate the mechanism of both agents in relation to disease pathogenesis by examining changes of certain occurrences and factors prior to and during the course of...

Yes / Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes, catalyzing 5-methylcytosine oxidation in DNA. Here, by using Keratin 14–Cre–driven ablation of Tet genes in skin epithelial cells, we demonstrate that ablation of Tet2/Tet3 results in marked alterations of hair shape and length followed by hair loss. We show that, through DNA demethylation, Tet2/Tet3 control chromatin accessibility and Dlx3 binding and promoter activity of the Krt25 and Krt28 genes regulating hair shape, as well as regulate interactions between the Krt28 gene promoter and distal enhancer. Moreover, Tet2/Tet3 also control three-dimensional chromatin topology in Keratin type I/II gene loci via DNA methylation–independent mechanisms. These data demonstrate the essential roles for Tet2/3 in establishment of lineage-specific gene expression program and control of Dlx3/Krt25/Krt28 axis in hair follicle epithelial cells and implicate modulation of DNA methylation as a novel approach for hair growth control. / This work was supported by the National Institutes of Health grant 5R01 AR075776 (V.A.B. and A.A.S.) and grant 5R01 AR071727 (V.A.B. and A.A.S.) and the National Science Foundation of China (G.-L.X.). / Research Development Fund Publication Prize Award winner, Dec 2022.

Les polyphénols et les phénols sont des molécules organiques largement présentes dans le règne végétal et souvent évaluées pour leur potentiel pharmacologique. Ces travaux de thèse concernent la synthèse totale de gallotannins, une classe importante de polyphénols, et l’hémisynthèse de la norbergénine, un C-arylglucoside naturel. Les gallotannins font partie des tannins hydrolysables dont la biosynthèse conduit à des structures chimiques caractérisées par la présence, sur un cœur glucopyranose, de plusieurs unités galloyle liées les unes aux autres par des liaisons méta-depside. Aucune synthèse chimique de ces composés n’ayant été décrite à ce jour, nous avons réalisé la synthèse totale de gallotannins naturels et de leurs anomères non naturels porteurs de motifs di- ou tri-galloyle depside. Ces travaux ont également permis d’étudier l’équilibre méta-para de ces motifs en solution. Quant à l’hémisynthèse de la norbergénine, elle a été réalisée avec succès en une seule étape à partir de la bergénine, un C-arylglucoside commercial, par réaction de O-déméthylation oxydante au SIBX (version stabilisée commerciale du iodane_λ5 IBX). Cette réaction chimiosélective a également été appliquée à des 2-méthoxyphénols et a notamment permis l’obtention de l’hydroxytyrosol à partir de l’alcool homovanillique. / Polyphenols and phenols are organic molecules widely found in the plant kingdom and very often evaluated for their pharmacological potential. This thesis work describes the total synthesis of gallotannins, an important class of polyphenols, and the hemisynthesis of norbergenin, a natural C-arylglucoside. The gallotannins belong to the hydrolysable tannins whose biosynthesis leads to chemical structures characterized by the presence, on a glucopyranose core, of several galloyl units linked ones to the others by meta-depside bonds. No chemical synthesis of these compounds have been reported to date, so we completed the total synthesis of several naturally occurring meta-depsidic gallotannins and their non natural anomers that contain di- or tri-galloyl motifs. This work also allowed the study of the meta-para equilibrium of these motifs in solution. For the norbergenin hemisynthesis, it was successfully achieved in a one step reaction from bergenin, a commercial C-arylglucoside, by a SIBX-mediated oxidative O-demethylation (SIBX = commercially available stabilized version of the λ5 _iodane IBX). This chemoselective reaction was also applied to 2-methoxyphenols and notably allowed the hemisynthesis of hydroxytyrosol from homovanillyl alcohol.

L'arthrose (OA) est une maladie articulaire dégénérative, classée comme la forme la plus fréquente au monde. Elle est caractérisée par la dégénérescence du cartilage articulaire, l’inflammation de la membrane synoviale, et le remodelage de l’os sous-chondral. Ces changements structurels et fonctionnels sont dues à de nombreux facteurs. Les cytokines, les prostaglandines (PG), et les espèces réactives de l'oxygène sont les principaux médiateurs impliqués dans la pathophysiologie de l'OA. L'interleukine-1β (IL-1β) est une cytokine pro-inflammatoire majeure qui joue un rôle crucial dans l'OA. L'IL-1β induit l'expression de la cyclooxygénase-2 (COX-2), la microsomale prostaglandine E synthase-1 (mPGES-1), la synthase inductible de l'oxyde nitrique (iNOS), ainsi que leurs produits la prostaglandine E2 (PGE2) et l'oxyde nitrique (NO). Ce sont des médiateurs essentiels de la réponse inflammatoire au cours de l'OA qui contribuent aux mécanismes des douleurs, de gonflement, et de destruction des tissus articulaires. Les modifications épigénétiques jouent un rôle très important dans la régulation de l’expression de ces gènes pro-inflammatoires. Parmi ces modifications, la méthylation/ déméthylation des histones joue un rôle critique dans la régulation des gènes. La méthylation/ déméthylation des histones est médiée par deux types d'enzymes: les histones méthyltransférases (HMT) et les histones déméthylases (HDM) qui favorisent l’activation et/ou la répression de la transcription. Il est donc nécessaire de comprendre les mécanismes moléculaires qui contrôlent l’expression des gènes de la COX-2, la mPGES-1, et l’iNOS. L'objectif de cette étude est de déterminer si la méthylation/déméthylation des histones contribute à la régulation de l’expression des gènes COX-2, mPGES-1, et iNOS dans des chondrocytes OA humains induits par l'IL-1β. Nous avons montré que la méthylation de la lysine K4 de l'histone H3 (H3K4) par SET-1A contribue à l’activation des gènes COX-2 et iNOS dans les chondrocytes humains OA induite par l'IL-1β. Nous avons également montré que la lysine K9 de l’histone H3 (H3K9) est déméthylée par LSD1, et que cette déméthylation contribue à l’expression de la mPGES-1 induite par IL-1β dans les chondrocytes humains OA. Nous avons aussi trouvé que les niveaux d'expression des enzymes SET-1A et LSD1 sont élevés au niveau du cartilage OA. Nos résultats montrent, pour la première fois, l'implication de la méthylation/ déméthylation des histones dans la régulation de l’expression des gènes COX-2, mPGES-1, et iNOS. Ces données suggèrent que ces mécanismes pourraient être une cible potentielle pour une intervention pharmacologique dans le traitement de la physiopathologie de l'OA. / Osteoarthritis (OA) is a disabling disease classified as the most common form of arthritis worldwide. It is characterized by cartilage degeneration, synovium inflammation, and subchondral bone remodeling resulting in a loss of joint function. These structural and functional changes are due to numerous factors. Cytokines, prostaglandins (PG), and reactive oxygen species are the major mediators implicated in the pathophysiology of OA. Interleukin-1 (IL-1) is a major pro-inflammatory cytokine that plays a crucial role in OA. IL-1 induces the expression of Cyclo-oxygenase-2 (COX-2), microsomal prostaglandin E synthase-1 (mPGES-1), inducible nitric oxide synthase (iNOS), as well as their products prostaglandin E2 (PGE2) and nitric oxide (NO). These are critical mediators of the inflammatory response during OA causing pain, swelling, and joint tissue destruction. The activation of these pro-inflammatory genes results from different changes at the level of chromatin known as epigenetic modifications. Epigenetic modifications such as DNA methylation and histone modifications play a crucial role in gene expression. Among these modifications, histone methylation/demethylation is the most critical one. Histone methylation/demethylation is mediated by two types of enzymes: histone methyltransferases (HMT) and histone demethylases (HDM) which can either activate or repress transcription. It is therefore necessary to understand the molecular mechanisms which underlie the regulation of COX-2, mPGES-1, and iNOS expression. The objective of this study is to investigate whether histone methylation/demethylation can modulate COX-2, mPGES-1, and iNOS expression in IL-1 induced OA human chondrocytes. We demonstrated that histone H3 lysine K4 (H3K4) methylation by SET-1A contributes to IL-1-induced COX-2 and iNOS expression in human OA Chondrocytes. We showed also that LSD1-mediated demethylation of histone H3 lysine 9 (H3K9) contributes to IL-1β-induced mPGES-1 expression in human OA chondrocytes. We found that levels of SET-1A and LSD1 expression are elevated in OA cartilage as compared with normal cartilage. Our data demonstrates, for the first time, the implication of histone methylation/demethylation in COX-2, mPGES-1, and iNOS regulation suggesting that these mechanisms could be a potential target for pharmacological intervention in the treatment of the pathophysiology of OA.

Endogenous retrovirus ERVWE1 is an integral part of the human genome. In the course of evolution, a protein encoded by the env gene of this retrovirus - Syncytin-1 - has gained unique function in human development. It mediates cell-to-cell fusion of placental cytotrophoblasts. Receptor that binds to Syncytin-1 is expressed in different cell types. Syncytin-1-mediated fusion is essential in placenta, but it can cause disruption of tissue integrity in other cell types. ERVWE1 expression is regulated by promoter DNA methylation, transcription factor GCM1 and efficient mRNA splicing. This thesis concerns the ERVWE1 expression and its regulation in non-placental tissues. It was found out that the moderate GCM1 overexpression was not sufficient to induce Syncytin-1 expression. Neither treatment with DNA demethylation agent 5-azacytidine nor with Syncytin-1 activator forskolin was able to manage Syncytin-1 expression. This thesis extends previous findings concerning high syncytin-1 expression in seminomas. In same tissues, there was found elevated TET1 expression on mRNA level in comparison with controls. The presence of the TET1 demethylation enzyme can influence ERVWE1 promoter DNA methylation. Previously unreported splicing variant of TET1 has been found during the construction of human TET1 expression...

Bei Säugerkeimzellen, Zygoten und Embryos in frühen Stadien kommt der epigenetischen Neuprogammierung eine außergewöhnlich wichtige Rolle in der Regulation der Genomfunktionen in entscheidenden Entwicklungsstadien zu. Die epigenetische Neuprogrammierung in Keimzellen löscht zuerst die Imprinting-Markierungen und Epi-Mutationen und stellt dann geschlechtsspezifische Markierungen (genomische Prägung) wieder her. Die vorliegende Arbeit bezieht sich auf das Löschen epigenetischer Modifikationen in primordialen Mauskeimzellen (primordial germ cells (PGCs)) zwischen dem 10.5 bis 13.5 Tag nach der Befruchtung. Entgegen früheren Annahmen zeigen unsere Ergebnisse, daß primordiale Mauskeimzellen (PGCs) beim Eintritt in die embryonalen Keimdrüsen noch immer DNS Methylierungsmarker besitzen, die ähnlich dem Marker in somatischen Zellen sind. Kurz nach dem Eintritt in die Keimdrüsen werden die DNS Methylierungsmarker, die in Verbindung mit geprägten und nicht geprägten Genen stehen, gelöscht. Für die Mehrzahl der Gene beginnt die Löschung der Marker in männlichen und weiblichen Embryos gleichzeitig und ist innerhalb eines Entwicklungstages abgeschlossen. Diese Kinetik deutet auf einen aktiven Demethylierungsprozess hin, initiiert durch ein somatisches Signal, ausgehend von der embryonalen Keimdrüse. Der Zeitpunkt der Neuprogrammierung in den primordialen Keimzellen ist entscheidend, da er sicherstellt, daß Keimzellen beiden Geschlechts einen epigenetisch äquivalenten Status erhalten, bevor sie geschlechtsspezifisch ausdifferenzieren und anschließend neu elterlich geprägt werden. Vollständiges Verständnis des Prozesses der Neuprogrammierung der Keimzellen ist nicht nur im Hinblick auf genomisches Imprinting wichtig, sondern auch für die Erforschung von Mechanismen für die Wiederherstellung von omnipotenten Zellen bei Klonierung und Stammzellenerhaltung. / Epigenetic reprogramming in mammalian germ cells, zygote and early embryos, plays a crucial role in regulating genome functions at critical stages of development. Germ line epigenetic reprogramming assures erasure of all the imprinting marks and epi-mutations and establishment of new sex-specific gametic imprints. The presented work focuses on the erasure of epigenetic modifications that occur in mouse primordial germ cells (PGCs) between day 10.5 to 13.5 post coitum (dpc). Contrary to previous assumptions, our results show that as they enter the genital ridge the PGCs still possess DNA methylation marks comparable to those found in somatic cells. Shortly after the entry of PGCs into the gonadal anlagen the DNA methylation marks associated with imprinted and non-imprinted genes are erased. For most genes the erasure commences simultaneously in PGCs of both male and female embryos and is completed within only one day of development. The kinetics of this process indicates that is an active demethylation process initiated by a somatic signal emanating from the stroma of the genital ridge. The timing of reprogramming in PGCs is crucial since it ensures that germ cells of both sexes acquire an equivalent epigenetic state prior to the differentiation of the definitive male and female germ cells in which, new parental imprints are established subsequently. Complete understanding of the germline reprogramming processes is important not only in the light of genomic imprinting but also for resolving other mechanisms connected with restoring cellular totipotency, such as cloning and stem cell derivation.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-02-16T14:00:28Z No. of bitstreams: 1 Alba Valeria da Silva Pereira.pdf: 458155 bytes, checksum: 80e5a16e6ef2e1ee3b97cac4fbc53703 (MD5) / Made available in DSpace on 2017-02-16T14:00:28Z (GMT). No. of bitstreams: 1 Alba Valeria da Silva Pereira.pdf: 458155 bytes, checksum: 80e5a16e6ef2e1ee3b97cac4fbc53703 (MD5) Previous issue date: 2009-03-16 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Application of fungicide is the main measure of management to stem-end rot and there is no information on the sensitivity and on the fitness costs arising from the reduction in sensitivity of its causal agent, Lasiodiplodia theobromae. One hundred and twenty monosporic isolates collected in producing areas of the Northeast region of Brazil, were divided into six populations. We evaluated the in vitro sensitivity (inhibition of mycelial growth) of the isolates to class the fungicides belonging to two groups: benzimidazoles and sterol demethylation inhibitors (DMIs). We also evaluated the fitness of isolates with different levels of sensitivity the fungicides both in vitro and in vivo (mycelial growth and aggressiveness). The average EC50 for DMIs ranged from 0,141 to 4,054, 0,045 to 0,691 and from 0,001 to 1,529 for tebuconazole, prochloraz and imazalil, respectively. The level of sensitivity to DMIs did not differ among populations. For the benzimidazoles EC50 of 91.6% of the isolates ranged from 0,002 to 0,14 and 0,36 in 1,272 (benomyl and thiabendazole,respectively).The 8.4% isolates, classified as not sensitive (NS) were not inhibited at the highest concentration evaluated (100μg ml of a.i-1). All NS isolates were from the same population. The aggressiveness of NS isolated was lower. / A aplicação de fungicida é a principal medida de manejo para podridão peduncular e não há informações sobre a sensibilidade e custos adaptativos decorrentes da redução de sensibilidade do seu agente causal, Lasiodiplodia theobromae. Cento e vinte isolados monospóricos, coletados em áreas produtoras da região Nordeste do Brasil, foram divididos em seis populações. Avaliou-se a sensibilidade in vitro (inibição de crescimento micelial) dos isolados aos fungicidas das classes dos benzimidazois e inibidores da biossíntese de ergosterol (IBEs) e a adaptabilidade in vitro e in vivo (crescimento micelial e agressividade) de isolados com níveis distintos de sensibilidade aos fungicidas testados. A CE50 média para os IBEs variou de 0,141 a 4,054, 0,045 a 0,691 e 0,001 a 1,529 para o tebuconazol, prochloraz e imazalil, respectivamente. O nível de sensibilidade aos IBEs não diferiu entre populações. Para os benzimidazóis a CE50 de 91,6% dos isolados variou de 0,002 a 0,14 e 0,36 a 1,272(benomyl e tiabendazol, respectivamente). Os 8,4%, classificados como não sensíveis (NS), não foram inibidos na maior concentração avaliada (100μg de i.a. ml-1). Todos os isolados NS foram oriundos de uma mesma população. A agressividade dos isolados NS foi menor. Para os IBEs, não foi detectado nenhum custo adaptativo.