Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 106-140).

Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 72-79).

Modulating chromatin structure is an important step in maintaining control over the eukaryotic genome. SWI/SNF, one of the complexes belonging to the growing family of ATP-dependent chromatin remodeling enzymes, is involved in controlling the expression of a number of inducible genes whose proper regulation is vital for metabolism and progression through mitosis. The mechanism by which SWI/SNF modulates chromatin structure at the nucleosome level is an important aspect of this regulation. The work in this dissertation focuses on how the Saccharomyces cerevisiae SWI/SNF complex uses the energy of ATP-hydrolysis to alter DNA-histone contacts in nucleosomes. This has been approached in a two part fashion. First, the three-dimensional structure and subunit composition of SWI/SNF complex has been determined. From this study we have identified a potential region of the SWI/SNF complex that might [be] a site for nucleosomal interaction. Second, functional analysis of the ATPase domain of Swi2p, the catalytic subunit of SWI/SNF, has revealed that a specific conserved motif is involved in coupling ATP hydrolysis to the mechanism of chromatin remodeling. These results provide a potential model for the function of the SWI/SNF chromatin remodeling complex at the nucleosome level.

Toxoplasma gondii est un eucaryote unicellulaire appartenant au phylum des Apicomplexes. Ce parasite intracellulaire obligatoire est la cause d’une pathologie sévère pour les fœtus des femmes enceintes primo-infectées ainsi que pour les personnes immunodéprimées. Son cycle de vie est complexe et comporte plusieurs étapes de prolifération et différenciation. Le stade tachyzoïte est responsable de la phase aigüe de la maladie chez les humains. Le tachyzoïte exprime des facteurs d'invasion et de virulence cruciaux pour sa survie et le détournement de la cellule hôte. L'expression de ces facteurs de virulence est hautement régulée pour permettre leur adressage correct dans des organites spécifiques appelés rhoptries et micronèmes. Cependant, peu d'informations sont connues sur les acteurs contrôlant l'expression de ces gènes de virulence. Les ApiAP2 appartiennent à une famille conservée de facteur de transcription (FT) et jouent un rôle important dans la régulation de la transcription des gènes chez les parasites apicomplexes. Des études menées au laboratoire ont révélés la capacité du FT TgAP2XI-5 à se fixer sur des promoteurs de gènes transcriptionnellement actifs durant les phases S/M du cycle cellulaire. Ce moment correspond au pic d’expression les gènes de rhoptrie et de micronème. Cependant, l'expression de TgAP2XI-5 est constitutive durant le cycle cellulaire chez le tachyzoïte. Dans le but de comprendre comment sa fonction dépendante du cycle cellulaire est régulée, nous avons identifié des potentiels partenaires d'interactions dont TgAP2X-5, un autre FT ApiAP2 dont l’expression est régulée durant les phases S/M du cycle. L'utilisation d'un système d'expression inductible ainsi que des expériences de séquençage des ARN nous ont permis de démontrer que la perte d'expression de TgAP2X-5 induit une diminution du nombre de transcrits codant pour les protéines de rhoptrie et de micronème. Alors que la perte d'expression de TgAP2X-5 n'influence pas de manière significative l'invasion et la croissance du parasite, nous observons une perte totale de virulence de la souche parasitaire in vivo. Pour mieux comprendre les mécanismes moléculaires mis en jeu, nous nous sommes demandés si la fixation de TgAP2XI-5 sur ces promoteurs cible est conservée en absence de TgAP2X-5. Par des expériences de ChIP-chip, nous avons montrés que l'absence de TgAP2X-5 conduit à une incapacité de fixation de TgAP2XI-5 sur des promoteurs de gènes de rhoptrie. L'ajout d'une copie du gène TgAP2X-5 sous son propre promoteur dans la souche mutante est capable de restaurer l'expression des protéines de rhoptrie préalablement affectée. Toutes ces expériences montrent pour la première fois une coopération des FT APiAP2 dans la régulation des gènes chez les Apicomplexes. / Toxoplasma gondii is a unicellular eukaryote belonging to the Apicomplexa phylum. It is an obligate intracellular parasite of critical importance to primarily infected pregnant women and immunosuppressed patient. Its life cycle is complex, with multiple proliferation and differentiation steps, of which tachyzoite proliferation is the most relevant to pathogenesis in humans. Tachyzoites express invasion and virulence factors that are crucial for their survival and the manipulation of host cell functions. Expression of these virulence factors is tightly regulated permitting their correct targeting in specific organelles named rhoptry and microneme. However, little is known about the factors controlling the expression of genes encoding the virulence factors. ApiAP2 are a family of conserved transcription factors (TF) that play an important role in regulating gene expression in apicomplexan parasites. Previous studies had revealed the ability of one of these TFs, TgAP2XI-5, to bind to transcriptionally active promoters of genes expressed during the S/M phase such as rhoptry and micronemes genes. However, expression of TgAP2XI-5 is constitutive during the tachyzoite cell cycle. To better understand how its function is regulated, we identified proteins interacting with TgAP2XI-5 including a cell cycle regulated ApiAP2 TF, TgAP2X-5. Using an inducible knock-down strategy and RNA-Seq, we demonstrate that the level of expression of number of rhoptry and microneme transcripts is affected by the disruption of TgAP2X-5 expression. While TgAP2X-5 disruption has mild effect on parasite growth and invasion, it leads to the strain avirulence in mice. To better understand the molecular mechanisms at stake, we investigated the binding of TgAP2XI-5 at promoters in the TgAP2X-5 mutant in a genome-wide assay. We show that disruption of TgAP2X-5 expression leads to defects in TgAP2XI-5 binding to multiple rhoptry gene promoters. Complementation of the TgAP2X-5 mutant restores the expression of rhoptry proteins previously affected. This is the first evidence of a cooperative action of ApiAP2 TF in Apicomplexa.

The bovine papillomavirus type 1 E2 protein is a multifunctional early viral protein with roles in all phases of the cell cycle. E2 is required during G1 as a transcription factor, in S phase to initiate viral replication and during mitosis to tether the viral genome to dividing DNA. The viral genome contains 17 E2 binding sites, the majority of which are concentrated in the long control region (LCR), a regulatory region that is upstream of the viral coding sequence. The role of these binding sites has been explored in vitro using small plasmids and E1 and E2 proteins expressed in bacteria and insect cells. In this study we attempt to examine the placement of E2 on its binding sites during all phases of the cell cycle and in the context of a stably replicating viral system. As part of the examination of the role of E2 during mitosis, we have also examined the role of the cohesin protein Scc1 in viral tethering. Two groups have published disparate reports identifying the cellular protein that binds to the transactivation domain of E2 to stably maintain viral genomes during cell division. Our group has published that it is the DNA helicase ChlR1 that is required for viral tethering, while it has been reported that it is the bromodomain protein Brd4 that is responsible. In this study we contribute to a report that shows that the cellular protein Scc1 binds to the viral genome through a ChlR1 independent mechanism. The cohesin protein binds to BPV-1 E2 at intermittent stages of the cell cycle and may be a factor in viral genome tethering. This interaction may also be important for regulating viral transcription.

DNA-binding proteins (DBPs) such as repair proteins, DNA polymerases, re- combinases, transcription factors, etc. manifest diverse stochastic behaviours dependent on physiological conditions inside the cell. Now that multiple independent in vitro studies have extensively characterised different aspects of the biochemistry of DBPs, computational and mathematical tools that would be able to integrate this information into a coherent framework are in huge demand, especially when attempting a transition to in vivo characterisation of these systems. ChIP-Seq is the method commonly used to study DBPs in vivo. This method generates high resolution sequencing data { population scale readout of the activity of DBPs on the DNA. The mathematical tools available for the analysis of this type of data are at the moment very restrictive in their ability to extract mechanistic and quantitative details on the activity of DBPs. The main trouble that researchers experience when analysing such population scale sequencing data is effectively disentangling complexity in these data, since the observed output often combines diverse outcomes of multiple unsynchronised processes reflecting biomolecular variability. Although being a static snapshot ChIP-Seq can be effectively utilised as a readout for the dynamics of DBPs in vivo. This thesis features a new approach to ChIP-Seq analysis { namely accessing the concealed details of the dynamic behaviour of DBPs on DNA using probabilistic modelling, statistical inference and numerical optimisation. In order to achieve this I propose to integrate previously acquired assumptions about the behaviour of DBPs into a Markov- Chain model which would allow to take into account their intrinsic stochasticity. By incorporating this model into a statistical model of data acquisition, the experimentally observed output can be simulated and then compared to in vivo data to reverse engineer the stochastic activity of DBPs on the DNA. Conventional tools normally employ simple empirical models where the parameters have no link with the mechanistic reality of the process under scrutiny. This thesis marks the transition from qualitative analysis to mechanistic modelling in an attempt to make the most of the high resolution sequencing data. It is also worth noting that from a computer science point of view DBPs are of great interest since they are able to perform stochastic computation on DNA by responding in a probabilistic manner to the patterns encoded in the DNA. The theoretical framework proposed here allows to quantitatively characterise complex responses of these molecular machines to the sequence features.

No description available.

Abstract Human prostatic acid phosphatase (hPAP) was the first laboratory parameter used for prostate cancer diagnosis, whereas the mechanisms behind the androgen regulation and tissue-specific expression of this prostate epithelium-specific differentiation antigen are not yet clear. In this study, a transient transfection model and transgenic animal model have been set up for functional analysis of the promoter and first intron region of the hPAP gene. The promoter constructs covering the region-734/+467 of the gene were functional in both prostatic and nonprostatic cells. Although hPAP constructs included two putative AREs with in vitro AR-binding ability at -178 and +336, androgen treatment had little effect on the promoter activity of the gene in transiently transfected cells. The hPAP fragment -734/+467 could trigger the expression of the CAT reporter gene and restrict the expression mainly in the prostates of transgenic mice. The DNA-binding site with the sequence GAAAATATGATA of a regulatory protein involved in prostate-specific and androgen receptor-dependent gene expression was identified from rPB promoter. The exact same 12 bp sequence was found in the first intron +1144/+1155 of the hPAP gene. Five homologous sequence, A, B, C, D and E, were located in the -734/+467 region of the hPAP gene, where site C and E could bind the regulatory protein in EMSA. Deletion of site C decreased the transcriptional activities significantly compared to those of corresponding wild-type constructs in LNCaP cells when androgens were present. Deletion of site E or both sites D and E increased the promoter activity in LNCaP when androgens were absent. In conclusion, androgens could not directly regulate hPAP expression via receptor-binding to the AREs in LNCaP cells. The promoter and first intron fragment -734/+467 of the hPAP gene could direct and restrict the gene expression mainly in prostate epithelium. A prostatic regulatory protein binds to multiple sites with the GAAAATATGATA or homologous sequences along the regulatory areas of the hPAP gene with different affinities, modulating the prostate-specific expression of the gene in a bidirectional manner, depending on the hormone status.

No description available.

No description available.