The CCAAT/Enhancer Binding Protein Beta (C/EBPβ) is part of the leucine zipper family of transcription factors and is involved in a myriad of processes including cellular proliferation and differentiation. C/EBPβ is expressed as three isoforms (LAP*, LAP, LIP), translated from a single mRNA by a leaky ribosomal scanning mechanism. While LAP* and LAP have activating functions, LIP is recognized as being a repressor of transcription due to its lack of activation domains. Numerous studies have shown that C/EBPβ acetylation state modulates its activity in a promoter-specific manner. For instance, the acetyltransferases GCN5/PCAF and the deacetylase complex mSin3A/HDAC1 regulate C/EBPβ activity on the C/EBPa promoter. GCN5/PCAF-mediated acetylation of C/EBPβ was shown to positively affect its transcriptional activity in a steroid-dependent mechanism via the glucocorticoid receptor (GR). GR relieves HDAC1 association from C/EBPβ by targeting the deacetylase for proteasomal degradation, hence favouring GCN5-mediated acetylation of C/EBPβ and allowing maximum activation capacity to be reached. In order to further elucidate C/EBPβ activation, I sought to characterize the interplay between GCN5 and HDAC1 in regulating C/EBPβ LAP/LIP activity during murine adipogenesis by identifying their binding domain in C/EBPβ. I identified a minimal domain located within regulatory domain 1 (RD1) of C/EBPβ that is required for both GCN5 and HDAC1 binding. Furthermore, the loss of the identified domain in C/EBPβ appears to partially mimic the GR effect, thus giving C/EBPβ a higher basal transcriptional activity that accelerates NIH 3T3 and 3T3 L1 adipogenesis. Moreover, I also showed that the LIP isoform inhibitory mode of action is partially mediated through the mSin3A/HDAC1 repressor complex, which gives LIP an active repressor function. In addition to LIP inhibitory function, I also showed that a cysteine residue located in LAP* negatively regulates its transactivating function during murine adipogenesis. Although RD1 of C/EBPβ has been suggested to act as a negative regulatory domain, I showed that only five residues are responsible for most of its inhibitory effect. Hence, in an attempt to further define sub-domains within RD1, I characterized a new positive regulatory domain at its N-terminal region, which seems to be required for C/EBPβ activity in a promoter-specific manner. In conclusion, this study not only supports previously hypothesized mechanisms by which C/EBPβ is regulated, but it also redefines the contribution of LAP*, LAP and LIP in regulating transcription. Most importantly, the results emphasize the countless possibilities by which C/EBPβ transactivation potential could be modulated during cellular differentiation.

The CMG (Cdc45, MCM, GINS) helicase is required for cellular proliferation and functions to unwind double-stranded DNA to allow the replication machinery to duplicate the genome. Cancer cells mismanage helicase activation through a variety of mechanisms, leading to the potential for the development of novel anti-cancer treatments. Mammalian cells load an excess of MCM complexes that act as reserves for new replication origins to be created when replication forks stall due to stress conditions, such as drug treatment. Targeting the helicase through inhibition of the MCM complex has sensitized cancer cells to drugs that inhibit DNA replication, such as aphidicolin and hydroxyurea. However, these drugs are not used in the clinical management of cancer. We hypothesized that the effectiveness of the clinically relevant drugs gemcitabine and 5-FU against pancreatic cancer cells, and oxaliplatin and etoposide against colorectal cells, could be increased through co-suppression of the MCM complex. The oncogene c-Myc also leads to the mismanagement of CMG helicases in part due to a non-transcriptional role in overactivating replication origins and causing DNA damage. We sought to elucidate the mechanism by which Myc causes overactivation of CMG helicases. Herein we demonstrate that co-suppression of reserve MCM complexes in pancreatic or colorectal cancer cell lines treated with clinically applicable chemotherapeutic compounds causes significant loss of proliferative capacity compared with cells containing the full complement of reserve MCMs. This is in part due to an inability to recover DNA replication following drug exposure, leading to an increase in apoptosis. Targeting of Myc to genomic sites induced large-scale decondensation of higher order chromatin that was required for CMG helicase assembly and activation at reserve MCM complexes. The physiological mediators of Myc, GCN5 and Tip60, are required for the chromatin unfolding and Cdc45 recruitment. We conclude that depletion of the reserve MCM complexes causes chemosensitization of multiple human tumor cell types to several chemotherapeutic drugs used in the clinical management of human cancer. This argues for the development and use of anti-MCM drugs in combination with chemotherapeutic compounds, which has the potential to increase the therapeutic index of existing clinical compounds. We have also identified a previously unknown role for Myc in normal cell cycle progression whereby DNA replication initiation is regulated through the assembly and activation of CMG helicases on Myc-mediated open chromatin regions. Our results also provide new mechanistic insight into Myc oncogenic transformation in which overstimulation of DNA replication could result in genomic instability and provide an explanation for Myc driven oncogenic transformation.

The CCAAT/Enhancer Binding Protein Beta (C/EBPβ) is part of the leucine zipper family of transcription factors and is involved in a myriad of processes including cellular proliferation and differentiation. C/EBPβ is expressed as three isoforms (LAP*, LAP, LIP), translated from a single mRNA by a leaky ribosomal scanning mechanism. While LAP* and LAP have activating functions, LIP is recognized as being a repressor of transcription due to its lack of activation domains. Numerous studies have shown that C/EBPβ acetylation state modulates its activity in a promoter-specific manner. For instance, the acetyltransferases GCN5/PCAF and the deacetylase complex mSin3A/HDAC1 regulate C/EBPβ activity on the C/EBPa promoter. GCN5/PCAF-mediated acetylation of C/EBPβ was shown to positively affect its transcriptional activity in a steroid-dependent mechanism via the glucocorticoid receptor (GR). GR relieves HDAC1 association from C/EBPβ by targeting the deacetylase for proteasomal degradation, hence favouring GCN5-mediated acetylation of C/EBPβ and allowing maximum activation capacity to be reached. In order to further elucidate C/EBPβ activation, I sought to characterize the interplay between GCN5 and HDAC1 in regulating C/EBPβ LAP/LIP activity during murine adipogenesis by identifying their binding domain in C/EBPβ. I identified a minimal domain located within regulatory domain 1 (RD1) of C/EBPβ that is required for both GCN5 and HDAC1 binding. Furthermore, the loss of the identified domain in C/EBPβ appears to partially mimic the GR effect, thus giving C/EBPβ a higher basal transcriptional activity that accelerates NIH 3T3 and 3T3 L1 adipogenesis. Moreover, I also showed that the LIP isoform inhibitory mode of action is partially mediated through the mSin3A/HDAC1 repressor complex, which gives LIP an active repressor function. In addition to LIP inhibitory function, I also showed that a cysteine residue located in LAP* negatively regulates its transactivating function during murine adipogenesis. Although RD1 of C/EBPβ has been suggested to act as a negative regulatory domain, I showed that only five residues are responsible for most of its inhibitory effect. Hence, in an attempt to further define sub-domains within RD1, I characterized a new positive regulatory domain at its N-terminal region, which seems to be required for C/EBPβ activity in a promoter-specific manner. In conclusion, this study not only supports previously hypothesized mechanisms by which C/EBPβ is regulated, but it also redefines the contribution of LAP*, LAP and LIP in regulating transcription. Most importantly, the results emphasize the countless possibilities by which C/EBPβ transactivation potential could be modulated during cellular differentiation.

Indiana University-Purdue University Indianapolis (IUPUI) / Infection with the single-celled parasite Toxoplasma gondii (phylum Apicomplexa) is usually benign in normal healthy individuals, but can cause congenital birth defects, ocular disease, and also life-threatening infection in immunocompromised patients. Acute infection caused by tachyzoites is controlled by a healthy immune response, but the parasite differentiates into a latent cyst form (bradyzoite) leading to permanent infection and chronic disease. Current therapies are effective only against tachyzoites, are highly toxic to the patient, and do not eradicate the encysted bradyzoites, thus highlighting the need for novel therapeutics. Inhibitors of histone deacetylases have been shown to reduce parasite viability in vitro demonstrating that chromatin remodeling enzymes, key mediators in epigenetic regulation, might serve as potential drug targets. Furthermore, epigenetic regulation has been shown to contribute to gene expression and differentiation in Toxoplasma. This dissertation focused on investigating the physiological role of a Toxoplasma GCN5-family histone acetyltransferase (HAT), termed TgGCN5-B. It was hypothesized that TgGCN5-B is an essential HAT that resides within a unique, multi-subunit complex in the parasite nucleus. Studies of TgGCN5-B have revealed that this HAT possesses a unique nuclear localization signal (311RPAENKKRGR320) that is both necessary and sufficient to translocate the protein to the parasite nucleus. Although no other protein motifs have been identified in the N-terminal extension of TgGCN5-B, it is likely that this extension plays a role in protein-protein interactions. All GCN5 homologues function within large multi-subunit complexes, many being conserved among species, but bioinformatic analysis of the Toxoplasma genome revealed a lack of many of these conserved components. Biochemical studies identified several potential TgGCN5-B associating proteins, including several novel apicomplexan transcription factors. Preliminary evidence suggested that TgGCN5-B was essential for tachyzoites; therefore, a dominant-negative approach was utilized to examine the role of TgGCN5-B in the physiology of Toxoplasma. When catalytically inactive TgGCN5-B protein was over-expressed in the parasites, there was a significant decrease in tachyzoite growth and viability, with initial observations suggesting defects in nuclear division and daughter cell budding. These results demonstrate that TgGCN5-B is important for tachyzoite development and indicate that therapeutic targeting of this HAT could be a novel approach to treat toxoplasmosis.

Generation and characterization of activation tagged potato mutants could aid in functional genomic studies. Morphological and molecular studies were conducted to compare potato cv. Bintje, its two mutants, underperformer (up), and nikku generated using the activation tagging vector pSKI074, and nikku revertant plants. Mutant up exhibited a dwarf phenotype (plant height 42 cm vs. 73 cm in cv. Bintje), abundant axillary shoot growth (3.1 shoots/plant compared to 0.7 shoots/plant in cv. Bintje; in vitro plants), greater tuber yield, altered tuber traits and early senescence compared to wild-type Bintje under in vitro conditions. Under in vivo conditions, the dwarf and early senescence phenotypes of the mutant were consistent, but the tuber yield of up was less (250 g/plant compared to 610 g/plant in wild-type Bintje) and had fewer axillary shoots compared to wild-type (1.9 shoots/plant in up vs. 4.7 shoots/plant in Bintje). Mutant nikku plants exhibited an extremely dwarf phenotype (plant height 2 cm in nikku vs. 6 cm in Bintje), had small hyponastic leaves, were rootless, and infrequently produced small tubers when compared to cv. Bintje. The overall nikku phenotype was suggestive of a constitutive stress response, which was further supported by the higher expression levels of several stress-responsive genes in nikku. The nikku revertant plants exhibited near normal stem elongation, larger leaves and consistent rooting, and it was a case of partial reversion. Southern blot analyses indicated the presence of single T-DNA insertions on chromosome 10 in the up and on chromosome 12 in the nikku mutant. The reversion in the nikku plants was not associated with the loss of enhancer copies from the original nikku mutant. Reverse transcriptase PCR analyses indicated transcriptional activation/repression of several genes in the up and nikku mutants, suggesting pleiotropic effects. In revertant, the expression levels of several genes which were differentially regulated in the nikku mutant were similar to Bintje. The gene immediately flanking the right border of the T-DNA insertion, which encoded a novel BTB/POZ (Broad complex, Tramtrac, Bric a brac; also known as Pox virus and Zinc finger) domain-containing protein, was highly up-regulated in the up mutant. This protein domain plays an important role in several important developmental, transcriptional and regulatory pathways. The mRNA-seq analyses resulted in 1,632 genes that were differentially expressed between mutant up and Bintje and the total number of up-regulated genes (661) were less than the number of genes down-regulated (971 genes) in the up mutant. Further analyses indicated that a variety of biological processes including decreased cell division, cell cycle activity, and abiotic stress responses were modified in the up mutant. In the nikku mutant, two potato genes, encoding an Acyl-CoA N-acyltransferases (NAT) superfamily protein, and a predicted major facilitator superfamily protein (MFS) were identified and overexpression lines Bintje/35S::NAT1 and Bintje/35S::PMT1 were created for recapitulation of the nikku mutant phenotype. Methylated DNA-PCR between the nikku and the revertant indicated a change in methylation status of the 35S enhancers, suggesting that the nikku revertant phenotype may be associated with some epigenetic modification. / Ph. D.

No description available.

Afin d'initier la transcription par l'ARN Polymérase II, la chromatine est modifiée par des coactivateurs, dont certains catalysent des modifications post-traductionnelles des queues des histones. La protéine GCN5 est une enzyme qui possède une activité histone acétyltransférase (HAT). Elle fait partie du complexe coactivateur SAGA, qui acétyle les histones H3. Or, il existe un second complexe HAT contenant GCN5 : le complexe ATAC, mis en évidence chez la drosophile. Chez l'homme en revanche, l'existence d'un tel complexe n'avait pas encore été démontrée au début de ma thèse.L'objectif de ma thèse a consisté tout d'abord en la purification et la caractérisation du complexe HAT ATAC chez l'homme. Puis, j'ai cherché à comprendre le fonctionnement et la spécificité d'action du complexe ATAC, par rapport au complexe SAGA.Dans une première partie, j'ai ainsi pu montrer que GCN5 fait partie d'un second complexe chez l'homme, le complexe ATAC. La composition en sous-unités du complexe ATAC a été déterminée et l'activité de ce dernier sur les histones étudiée. Nous avons pu démontrer que, comme hSAGA, hATAC acétyle les histones in vitro et in vivo, et préférentiellement la lysine 14 de l'histone H3. Chez les vertébrés, un paralogue de GCN5, PCAF peut se substituer à GCN5 dans les complexes ATAC ou SAGA.Par la suite, j'ai poursuivi la caractérisation de ces complexes HAT afin de comprendre le rôle des enzymes au sein des complexes et leurs fonctions. Pour cela, j'ai voulu comprendre le rôle des sous-unités, comment elles influencent l'activité de l'enzyme, et ainsi identifier les protéines qui permettent la spécificité de hATAC par rapport à hSAGA.

In Schizosaccharomyces pombe, the MAPK pathway Sty1 is activated upon several stress situations, like osmotic and oxidative stress, stationary phase, UV radiation or heat shock. Since the modulation of gene expression is one of the main outputs of this response, we focused this Thesis work on the charactherization of the transcription regulation by the activation of the Sty1 pathway and through the transcription factors Atf1 and Pcr1. Moreover, we extend our field of interest investigating how stress–related chromatin remodelers are affecting the stress defence transcription of the cells. / En Schizosaccharomyces pombe, la vía de la MAPK Sty1 es activada ante diferentes situaciones de estrés, como son el estrés oxidativo u osmótico, fase estacionaria, radiación UV o choque de calor. Al ser la modulación de la expresión génica uno de los más importantes objetivos de esta respuesta, hemos focalizado el trabajo de esta Tesis doctoral en la caracterización de la regulación transcripcional mediada por la activación de la ruta de Sty1 y los factores de transcripción Atf1 y Pcr1. Además, hemos ampliado nuestra área de interés investigando el papel de remodeladores de cromatina relacionados con la respuesta a estrés y cómo a participan en la transcripción estrés-dependiente.