Cyclooxygenase (COX) is the rate limiting enzyme that catalyses the production of prostanoids, which are crucial to vascular homeostasis. Evidence suggests that endothelial dysfunction and inflammation play a role in vascular complications in aging and diabetes. Previous animal studies by our laboratory at RMIT University reported enhanced COX expression with aging in rat aortas, platelets and monocytes. Potentially, alteration in COX expression may result in an imbalanced prostanoid production favoring the synthesis of vasoconstrictors and hence increase the risk of cardiovascular events in the aging population. The regulation of altered COX expression in aging, however, is not clear. It has been suggested that histone hyperacetylation may be an important mechanism that regulates COX levels during the aging process as increased histone acetylation has been shown to occur with aging. Thus, we hypothesized that COX expression is modulated by histone hyperacetylati on. This was investigated by measuring COX expression in histone hyperacetylated cultured endothelial cells. In the case of diabetes, studies have reported that the development of diabetes and its complications is associated with persistent inflammatory activity, evident with increased inflammatory markers in the circulation. COX-mediated pathways may be involved in this inflammatory process in diabetes. Furthermore, the formation of advanced glycation end products (AGEs) is accelerated in diabetes. AGEs can bind to receptors for AGEs (RAGE), which has also been suggested to play a role in inflammation in diabetes. We hypothesized that COX- and RAGE-mediated pathways contribute to increased inflammation in diabetes and potentiate the development of diabetic vascular complications. This was investigated by measuring changes in COX-mediated pathways in both rat and human diabetic models. The current thesis reports: 1) in cultured endothelial cells, histone hyperacetylation was associated with increased COX expression; 2) an overall increase in inflammation was observed in diabetes involving COX- and RAGE-mediated pathways. This was supported by increased platelet COX-1 and monocyte COX-2 levels in Zucker rats, increased monocyte COX-2 in human Type 1 diabetes and elevated plasma TXB2 and PGE2 levels in both human Type 1 and Type 2 diabetic subjects. Up-regulation of RAGE expression was further found in platelets and monocytes in both human diabetes types. When treated with NSAIDs, plasma prostanoid levels, COX and RAGE expression were reduced significantly in both platelets and monocytes in human diabetic subjects. 3) It is unclear how COX and RAGE expression was regulated, but histone modifications may be one of the mechanisms. Data from cultured cells indicated that increased COX expression was associated with increased histone acetylation levels induced by TSA. Concurrent increases in histone acetylation and COX-2 levels were also observed in human Type 1 diabetes, but similar findings were not observed in human Type 2 diabetes. In addition, we failed to find an age-dependent increase in monocyte histone H4 acetylation in human Type 2 diabetes despite an age-dependent increase in monocyte COX-2 expression. Thus, whether histone hyperacetylation modulates COX expression and in what conditions require further investigation.

La schistosomiase est la deuxième endémie parasitaire mondiale après le paludisme; 200 millions d'individus sont infectés à travers le monde et la morbidité reste élevée (environ 200 000 morts par an) malgré l'utilisation du praziquantel, seule drogue disponible. Cinq espèces de schistosomes infectent l'Homme dont celle que nous étudions, Schistosoma mansoni. Ce parasite possède un cycle de vie complexe, comportant 4 stades de développement morphologiquement distincts et 2 hôtes successifs, un hôte intermédiaire, le mollusque Biomphalaria glabrata et un hôte définitif, l'Homme. Afin de déterminer les mécanismes mis en jeu dans le contrôle du développement du schistosome et de caractériser des cibles potentielles de nouveaux agents chimiothérapeutiques, nous nous intéressons à certains acteurs impliqués dans la régulation génique, et plus particulièrement, les histones déacétylases, ou HDACs. Les HDACs sont des enzymes bien conservées dans le règne du vivant. Elles contrôlent l'expression de 5 à 10% des gènes, majoritairement en réprimant la transcription via la déacétylation des histones. Elles sont réparties en 3 classes, les classes I et II sont composées d'enzymes dont le site catalytique comporte un ion de zinc ; tandis que la classe III est composée des sirtuines, dépendantes du NAD+. Chez le parasite, une partie de nos études porte sur les 3 enzymes de classe I que nous avons identifiées et caractérisées au niveau moléculaire, SmHDAC1, 3 et 8. Ensuite nous avons réalisé une étude fonctionnelle de SmHDAC1 et mis en évidence sa capacité de répression de la transcription en système hétérologue. Puis nous nous sommes intéressés à l'inhibition de l'activité HDAC chez le parasite, grâce à l'utilisation de différents inhibiteurs des classes 1 et 2 des HDACs. Nous avons montré que des parasites cultivés en présence de trichostatine A (TSA) mouraient de manière dose dépendante. Nous avons approfondi notre étude au niveau moléculaire et avons étudié la variation d'acétylation des histones des parasites en présence de TSA et d'acide valproique. Nous avons montré une augmentation de l'acétylation de manière dose-dépendante de l'histone H4. Le traitement par la TSA entraîne la mort de nombreux types cellulaires par apoptose et provoque une surexpression de certains gènes impliqués dans ce processus. Nous avons démontré que ce traitement induit l'apoptose chez des larves maintenues en culture, ainsi qu'une activation des Caspases 3/7. Ensuite, la caractérisation des ADNc des Caspases 3 et 7 nous a permis de montrer par RT-PCR en temps réelle que les transcrits correspondants sont surexprimés après traitement par la TSA, tandis que celle-ci n'a aucun effet sur la transcription de SmHDAC1 et 3. Par la suite, nous avons corrélé cette augmentation avec le taux d'acétylation de H4 sur le promoteur de caspase7. Cette étude sera poursuivie à l'avenir par l'investigation de la relation structure/fonction des HDACs afin de développer des inhibiteurs spécifiques. En parallèle, nous étudions une HDAC de classe III, SmSirt1, que nous avons identifiée et caractérisée. La présence d'une grande insertion dans son domaine catalytique présage des fonctions modifiées par rapport à ses orthologues chez d'autres espèces. Nous souhaitons nous focaliser sur les conséquences de cette insertion spécifique chez S. mansoni. En effet, elle semble être la cible de potentielles modifications post-traductionnelles (site de phosphorylation par PKB/Akt), que nous voulons mettre en évidence. De plus, l'une des fonctions de Sirt1 est l'interaction avec le facteur de transcription FoxO et la régulation de la voie de signalisation insuline dépendante (impliquant PKB/Akt). Par ce biais FoxO et Sirt1 contrôlent le métabolisme, des mécanismes de survie cellulaire et la longévité. Une modification de la fonction de SmSirt1 pourrait être à la base de la durée de vie anormalement longue de S. mansoni. Nous avons donc également réalisé la caractérisation moléculaire de SmFoxO, afin de mettre en évidence son interaction avec Sirt1 ainsi que l'implication de cette interaction dans le contrôle de la transcription de gènes cibles. Par la suite nous étudierons le rôle de Sirt1 et FoxO dans la régulation de la signalisation insuline dépendante sur des parasites en culture

Les interactions protéine–protéine jouent un rôle essentiel dans le fonctionnement cellulaire et sont impliquées dans diverses pathologies. L'étude de ces interactions est donc primordiale. Nous avons entrepris de développer une méthode de « footprinting » basée sur la différence d'accessibilité à l'eau des acides aminés d'une protéine selon qu'elle est seule ou en interaction. Le principe de cette méthode de caractérisation des zones d'interactions protéine–ligand, est basé sur une étape de génération de radicaux carbo-centrés sur les chaînes latérales des acides aminés de la protéine, et sur une étape de réparation de ces radicaux par un atome de tritium.<br /> <br />La première étape a été de déterminer la réactivité des 20 acides aminés communs vis-à-vis de notre méthode : <br />Lys>Leu>Arg>Ile>Trp>Phe>Val>Cys>Met>His>Tyr>Glu>Thr>Asp><br />Gln>Pro>Ala>Asn> Ser>Gly. Notre méthode ensuite appliquée à l'étude du complexe entre la protéine hAsf11-156 et un fragment de l'histone H3 a permis de caractériser sans ambiguïté les trois résidus principaux de H3 (L126, R129 et I130) impliqués dans cette interaction. De plus, nous avons mis en évidence que notre méthode de caractérisation des interactions protéique est à la fois sensible aux phénomènes d'interaction et de repliement.

Chaque spermatozoïde transmet non seulement le génome paternel, mais également une information épigénétique, portée par l'organisation structurale du génome, ou épigénome. Malgré son importance lors du développement embryonnaire, peu de données décrivent l'épigénome transmis par le gamète mâle. Ce travail étudie la reprogrammation de l'épigénome lors de la différenciation post-méiotique des cellules germinales males, ou spermiogenèse. Ce processus implique une restructuration globale de la chromatine caractérisée par l'enlèvement de la majorité des histones, associées à l'ADN dans les cellules somatiques, et leur remplacement par des protéines nucléaires spécifiques du gamète male. <br />Ce travail met en évidence dans les cellules post-méiotiques, un dialogue original entre les modifications post-traductionnelles des histones et la présence de nouveaux variants d'histones associés à l'hétérochromatine péricentrique. La reprogrammation épigénétique des régions de contrôle de l'empreinte parentale a également été analysée. De plus, de nouvelles fonctions ont été mises en évidence pour plusieurs protéines chaperones, notamment HSP70.2, Npm3 et NAP1L4, qui seraient impliquées dans l'incorporation de variants d'histones ou de protéines basiques spécifiques lors des étapes tardives de la spermiogenèse.<br />Ainsi, l'action coordonnée de plusieurs voies de réorganisation de la chromatine participe à la mise en place de l'épigénome transmis par les spermatozoïdes.

<p>The human tumour suppressor protein p53 is an effective inhibitor of cell growth, by inducing cell cycle arrest and apoptosis. However, p53-induced cell growth inhibition can be detrimental for virus multiplication. Therefore, viruses encode for proteins, which can interfere with the functions of the p53 protein. Human adenoviruses encode for a transcription repressor protein named E1B-55K, which inhibits the activity of the p53 protein during a lytic adenovirus infection.</p><p>In this thesis, we have studied the biochemical characteristics of the E1B-55K protein and how the E1B-55K protein interferes with the function of p53 as a transcription factor.</p><p>Our data show that the E1B-55K protein interacts with the Sin3 co-repressor complex in adenovirus transformed and in adenovirus infected cells. Furthermore, the E1B-55K protein recruites a histone deacetylase activity, indicating that the E1B-55K protein is associated with a functional chromatin modifying complex. We also show that in addition to repressing p53-activated transcription, E1B-55K could also relieve p53-mediated repression of the survivin and Map4 promoters.</p><p>Previous results have shown that E1B-55K inhibits p53 as a transcriptional activator of the p21/CDKN1A promoter. Here we show that the E1B-55K protein prevents p53 from inducing histone H3 and H4 acetylation on p21/CDKN1A promoter, which coincided with the inhibition of p21/CDKN1A protein expression. Notably, the Sin3 complex was detected in the vicinity of the p53 binding site on the p21/CDKN1A promoter, suggesting that the E1B-55K protein blocked p53-mediated histone acetylation by recruitment of a histone deacetylase activity. Inhibition of p21/CDKN1A protein expression might be the reason, why the E1B-55K protein alleviates p53-dependent transcriptional repression of the survivin promoter. </p><p>Finally, we show that oligomerisation of the E1B-55K protein is important for the defined subcellular localization of the protein and for its function as a repressor of p53-activated transcription.</p>

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 104-113).

The human tumour suppressor protein p53 is an effective inhibitor of cell growth, by inducing cell cycle arrest and apoptosis. However, p53-induced cell growth inhibition can be detrimental for virus multiplication. Therefore, viruses encode for proteins, which can interfere with the functions of the p53 protein. Human adenoviruses encode for a transcription repressor protein named E1B-55K, which inhibits the activity of the p53 protein during a lytic adenovirus infection. In this thesis, we have studied the biochemical characteristics of the E1B-55K protein and how the E1B-55K protein interferes with the function of p53 as a transcription factor. Our data show that the E1B-55K protein interacts with the Sin3 co-repressor complex in adenovirus transformed and in adenovirus infected cells. Furthermore, the E1B-55K protein recruites a histone deacetylase activity, indicating that the E1B-55K protein is associated with a functional chromatin modifying complex. We also show that in addition to repressing p53-activated transcription, E1B-55K could also relieve p53-mediated repression of the survivin and Map4 promoters. Previous results have shown that E1B-55K inhibits p53 as a transcriptional activator of the p21/CDKN1A promoter. Here we show that the E1B-55K protein prevents p53 from inducing histone H3 and H4 acetylation on p21/CDKN1A promoter, which coincided with the inhibition of p21/CDKN1A protein expression. Notably, the Sin3 complex was detected in the vicinity of the p53 binding site on the p21/CDKN1A promoter, suggesting that the E1B-55K protein blocked p53-mediated histone acetylation by recruitment of a histone deacetylase activity. Inhibition of p21/CDKN1A protein expression might be the reason, why the E1B-55K protein alleviates p53-dependent transcriptional repression of the survivin promoter. Finally, we show that oligomerisation of the E1B-55K protein is important for the defined subcellular localization of the protein and for its function as a repressor of p53-activated transcription.

Epigenetic modifications were shown to play an essential role in tumorigenesis. Epigenetic mechanisms can alter transcription in several ways, through DNA methylation and/or through histone modification. DNA methylation at the TSS (transcriptional start site) has been implicated in tumor development and gene silencing. However, several examples of atypical methylation were shown. In Paper I we present the ICSBP/IRF8 gene that belongs to the IRF family and has characteristics of a tumor suppressor gene. The ICSBP/IRF8 is fully methylated in the promoter and TSS regions in U-937 and despite high expression of the gene. Presence of positive histone marks suggests that methylated DNA can be overridden by histone modification. In Paper II a panel of 13 MM (multiple myeloma) cell lines and 9 primary patient tumors were analysed for methylation status of the ICSBP/IRF8 gene. In most cell lines (8/13) the gene was partially or fully methylated and partial methylation was also observed in 1/9 primary tumors. In vitro methylation analysis and treatment with 5-aza-2’deoxycytidine (DAC) proved that the ICSBP/IRF8 gene is silenced by methylation and may be associated with the malignant phenotype. In Paper III and IV the NFκB signalling pathway was analysed and the role of ATRA and TNFα induction. In Paper III the data shows that activation of the NFκB pathway is essential in ATRA-induced terminal differentiation in the U-937 cell line and IκBα (S32A/S36A) inhibits ATRA-induced differentiation and G1 cell cycle arrest. This was accompanied by delayed down-regulation of several cyclins (A and E) and up-regulation of p21WAF1/CIP1 (CDKN1A) and p27KIP1 (CDKN1B). TNFα alone did not induce expression of RA-induced genes analysed in Paper IV. However, ATRA in combination with TNFα showed enhanced activation of RA-induced genes. TNFα triggers demethylation of H3K9me3/H3K9me2 and H3K4me3 at RAR/RXR target genes, which were not accompanied by changes in the level of H3K9-ac. This decrease in H3 methylation by TNFα may pave way for the later ATRA-induced gene transcription.

<p>The accurate and timely replication of eukaryotic DNA during S-phase is of critical importance for the cell and for the inheritance of genetic information. Missteps in the replication program can activate cell cycle checkpoints or, worse, trigger the genomic instability and aneuploidy associated with diseases such as cancer. Eukaryotic DNA replication initiates asynchronously from hundreds to tens of thousands of replication origins spread across the genome. The origins are acted upon independently, but patterns emerge in the form of large-scale replication timing domains. Each of these origins must be localized, and the activation time determined by a system of signals that, though they have yet to be fully understood, are not dependent on the primary DNA sequence. This regulation of DNA replication has been shown to be extremely plastic, changing to fit the needs of cells in development or effected by replication stress. </p><p>We have investigated the role of chromatin in specifying the eukaryotic DNA replication program. Chromatin elements, including histone variants, histone modifications and nucleosome positioning, are an attractive candidate for DNA replication control, as they are not specified fully by sequence, and they can be modified to fit the unique needs of a cell without altering the DNA template. The origin recognition complex (ORC) specifies replication origin location by binding the DNA of origins. The <italic>S. cerevisiae</italic> ORC recognizes the ARS (autonomously replicating sequence) consensus sequence (ACS), but only a subset of potential genomic sites are bound, suggesting other chromosomal features influence ORC binding. Using high-throughput sequencing to map ORC binding and nucleosome positioning, we show that yeast origins are characterized by an asymmetric pattern of positioned nucleosomes flanking the ACS. The origin sequences are sufficient to maintain a nucleosome-free origin; however, ORC is required for the precise positioning of nucleosomes flanking the origin. These findings identify local nucleosomes as an important determinant for origin selection and function. Next, we describe the <italic>D. melanogaster</italic> replication program in the context of the chromatin and transcription landscape for multiple cell lines using data generated by the modENCODE consortium. We find that while the cell lines exhibit similar replication programs, there are numerous cell line-specific differences that correlate with changes in the chromatin architecture. We identify chromatin features that are associated with replication timing, early origin usage, and ORC binding. Primary sequence, activating chromatin marks, and DNA-binding proteins (including chromatin remodelers) contribute in an additive manner to specify ORC-binding sites. We also generate accurate and predictive models from the chromatin data to describe origin usage and strength between cell lines. Multiple activating chromatin modifications contribute to the function and relative strength of replication origins, suggesting that the chromatin environment does not regulate origins of replication as a simple binary switch, but rather acts as a tunable rheostat to regulate replication initiation events. </p><p>Taken together our data and analyses imply that the chromatin contains sufficient information to direct the DNA replication program.</p> / Dissertation

The mixed lineage leukemia (MLL) proteins regulate an array of developmental and differentiation processes. Similar to other members of the SET1 family, association of MLL1-4 with Ash2L, RbBP5 and WDR5, collectively termed the MLL core complex, is required for MLL mediated histone H3 Lys-4 di/tri-methylation. Each member of the core complex has a unique role in modulating the activity of MLL1. WDR5 is key in nucleating the formation of the core complex by acting as a structural scaffold, whereas Ash2L and RbBP5 are responsible for stimulating MLL methyltransferase activity. Currently, the structural and biochemical mechanisms utilized by the core complex to regulate MLL1 activity are unknown. Through structural and biochemical dissection of the core complex we have assigned specific functions to core complex subunits and have identified the minimal structural requirements for methyltransferase activity. Furthermore, through structure based drug design, we have identified a peptidomimetic inhibitor of MLL1 methyltransferase activity.