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61	The Role of PC4 in Oxidative Stress: A Dissertation Yu, Lijian 29 June 2011 (has links) Oxidative stress is a cellular condition where cells are challenged by elevated levels of reactive oxygen species (ROS) that are produced endogenously or exogenously. ROS can damage vital cellular components, including lipid, protein, DNA and RNA. Oxidative damage to DNA often leads to cell death or mutagenesis, the underlying cause of various human disease states. Previously our laboratory discovered that human PC4 gene can prevent oxidative mutagenesis in the bacterium Escherichia coli and that the yeast homolog SUB1 has a conserved function in oxidation protection. In this thesis I examined the underlying mechanisms of PC4’s oxidation protection function. My initial efforts to examine the predicted role of SUB1 in transcription-coupled DNA repair essentially negated this hypothesis. Instead, results from our experiments suggest that PC4 and yeast SUB1 can directly protect genomic DNA from oxidative damage. While testing SUB1’s role in double strand DNA break (DSB) repair, I found the sub1Δ mutant resects DSB ends rapidly but still ligates chromosomal breaks effectively, suggesting that DSB resection is not inhibitory to nonhomologous end-joining, an important DSB repair pathway. Finally, in the course of studying transcription recovery after UV damage, I found UV induces a longer form of RPB2 mRNA and demonstrated that this is caused by alternative polyadenylation of the RPB2 mRNA and that alternative polyadenylation contributes to UV resistance. Based on results of preliminary experiments, I propose that UV activates an alternative RNA polymerase to transcribe RNA POL II mRNA, a novel mechanism to facilitate recovery from inhibition of transcription resulting from UV damage. The hypothetical polymerase switch may account for the UV-induced alternative polyadenylation of the RPB2 mRNA. Oxidative Stress DNA Damage DNA-Binding Proteins Subtilisins Proprotein Convertases Polyadenylation Cells Enzymes and Coenzymes Genetic Phenomena
62	Studies on the Regulation of Cytoplasmic Polyadenylation Element-Binding Protein: A Dissertation Lin, Chien-Ling 11 January 2012 (has links) Post-transcriptional regulation of gene expression sits at the core of proteomic complexity; trans-acting factors that regulate RNA localization and translation capacity are thus indispensible. In this thesis, I present studies of the cytoplasmic polyadenylation element binding protein (CPEB), a sequence specific RNA-binding protein important for cell cycle progression and neural synaptic plasticity. I focus on CPEB because the activity of RNA-binding proteins affects the destiny of their mRNA substrates. As presented in Chapter II, CPEB, though mostly cytoplasmic at steady state, shuttles between the nucleus and the cytoplasm. Surprisingly, the RNA recognition motifs are essential for the nuclear localization. CPEB associates with the polyadenylation machinery in both compartments, suggesting it is involved in both nuclear mRNA processing and cytoplasmic translational regulation. Moreover, the nuclear translocalization is critical to relay a tight translation repression on CPE-containing mRNAs. Chapter III focuses on the regulation of CPEB dimerization. CPEB dimerizes through the RNA-binding domains to inhibit its own RNA binding ability in a cell cycle-dependent manner. By dimerizing, CPEB has enhanced binding to protein destruction factors so that robust active degradation occurs in the later cell cycle. The degradation of CPEB is required for translation activation of a subset of mRNAs and cell cycle progression. In addition, dimerization protects cells from being overloaded with excess CPEB. In sum, the localization and dimerization status of CPEB is dynamic and highly regulated; they in turn regulate the activity of CPEB, which results in responsive translation control. These studies provide a strong foundation to decipher CPEB-mediated gene expression. RNA-Binding Proteins Poly(A)-Binding Proteins Polyadenylation Amino Acids, Peptides, and Proteins Genetic Phenomena
63	Translational Control of M Phase Progression: a dissertation Padmanabhan, Kiran 30 May 2006 (has links) A cell integrates mitogenic signals received at the plasma membrane with intracellular biochemical changes to direct the events of cell division. Oocytes from Xenopus laevis offer a system that allows molecular dissection of pathways controlling cell growth and division in response to extracellular cues. Xenopus oocytes, physiologically arrested in a G2 like state, respond to the hormone progesterone to reinitiate meiosis and mature into a fertilizable egg. Signals received at the oocyte membrane induce translation of dormant maternal mRNAs that not only drive meiotic entry but also maintain the cell cycle arrest in an egg. A major pathway controlling the translation of these mRNAs is cytoplasmic polyadenylation, facilitated by the Cytoplasmic Polyadenylation Element Binding protein (CPEB) through cis-acting elements in their 3'untranslated regions (3'UTRs). Cytoplasmic polyadenylation requires the phosphorylation of serine174 on CPEB by Aurora-A as well as the translation of a hitherto unknown mRNA. The transcript of the RINGO/Spy gene is a putative candidate for this unknown upstream regulator of CPEB function. RINGO/Spy mRNA is translationally repressed in immature oocytes by a ribonucleoprotein (RNP) complex consisting of the repressor Pumilio-2, the putative activator Deleted in Azoospermia-like (DAZl) and embryonic poly A binding protein (ePAB). Progesterone signaling leads to the dissociation of Pumilio-2 from the mRNP and the ensuing RINGO/Spy protein synthesis, in turn, promotes cytoplasmic polyadenylation and oocyte maturation. Pumilio and its associated proteins, such as Drosophila Brain tumor (Brat) and DAZl, in addition to their cytoplasmic roles have ill-defined functions within the nucleus. We detected DAZl within the nucleoli of telomerase-immortalized human retinal pigment epithelial (RPE) cells in interphase and on acrocentric chromosomes during mitosis. DAZl colocalizes with the RNA polymerase I associated Upstream Binding transcription Factor (UBF), most likely through pre-ribosomal RNA and is a likely component of the Nucleolar Organization Region (NOR). Stably knocking down DAZl in RPEs using short hairpin RNAs results in loss of nucleolar segregation, the physiological outcome of which is under investigation. These preliminary findings indicate an additional role for DAZl within the nucleolus, one likely to be independent from cytoplasmic translational control. Cell Division Xenopus Proteins 3' Untranslated Regions Cell Cycle Proteins Oocytes Polyadenylation RNA-Binding Proteins Transcription Factors Academic Dissertations Life Sciences Medicine and Health Sciences
64	Post-Transcriptional Control of Human Cellular Senescence: A Dissertation Burns, David M. 15 July 2010 (has links) The central dogma of biology asserts that DNA is transcribed into RNA and RNA is translated into protein. However, this overtly simplistic assertion fails to portray the highly orchestrated and regulated mechanisms of transcription and translation. During the process of transcription, RNA provides the template for translation and protein synthesis as well as the structural and sequence specificity of many RNA and protein-based machines. While only 1-5% of the genome will escape the nucleus to be translated as mRNAs, complex, parallel, highly-conserved mechanisms have evolved to regulate specific mRNAs. Trans-acting factors bind cis-elements in both the 5" and 3" untranslated regions of mRNA to regulate their stability, localization, and translation. While a few salient examples have been elucidated over the last few decades, mRNA translation can be reversibly regulated by the shortening and lengthening of the 3" polyadenylate tail of mRNA. CPEB, an important factor that nucleates a complex of proteins to regulate the polyadenylate tail of mRNA, exemplifies a major paradigm of translational control during oocyte maturation and early development. CPEB function is also conserved in neurons and somatic foreskin fibroblasts where it plays an important role in protein synthesis dependent synaptic plasticity and senescence respectively. Focusing on the function of CPEB and its role in mRNA polyadenylation during human cellular senescence, the following dissertation documents the important finding that CPEB is required for the normal polyadenylation of p53 mRNA necessary for its normal translation and onset of senescence. Cells that lack CPEB have abnormal levels of mitochondria and ROS production, which are demonstrated to arise from the direct result of hypomorphic p53 levels. Finally, in an attempt to recapitulate the model of CPEB complex polyadenylation in human somatic cells, I unexpectedly find that Gld-2, a poly(A) polymerase required for CPEB-mediated polyadenylation in Xenopus laevis oocytes, is not required for p53 polyadenylation, but instead regulates the stability of a microRNA that in turn regulates CPEB mRNA translation. Furthermore, I demonstrate that CPEB requires Gld-4 for the normal polyadenylation and translation of p53 mRNA. Cell Aging Human RNA Processing Post-Transcriptional RNA-Binding Proteins Amino Acids, Peptides, and Proteins Cells
65	Methylome Sequencing Reveals the Context-Specific Functions of DNA Methylation in Indolent Versus Aggressive Prostate Cancer Bhasin, Jeffrey M. January 2016 (has links) No description available. Biomedical Research Molecular Biology Genetics Bioinformatics DNA methylation epigenomics bioinformatics prostate cancer differentially methylated regions gene expression gene regulation epigenetics molecular medicine alternative cleavage and polyadenylation genomic context genomics
66	Analysis of human non-canonical 3’end formation signals Da Rocha Oliveira Nunes, Nuno Miguel January 2012 (has links) Cleavage and polyadenylation are essential pre-mRNA processing reactions maturing the 3’end of almost all protein encoding eukaryotic mRNAs. Analysis of the sequences required for cleavage and polyadenylation in the human melanocortin 4 receptor (MC4R) and the human transcription factors JUNB and JUND pre-mRNAs revealed that, at least for some mammalian genes, 3’end processing of the primary transcript is independent of previously described auxiliary sequence elements located upstream or downstream of the core poly(A) sequences. The analysis of the MC4R poly(A) site, contrary to the current understanding of mammalian poly(A) sites, showed that mutations of the AUUAAA hexamer sequence had no effect on 3’end processing levels while mutations in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site uses a potent DSE and to direct maximal cleavage efficiency requires only a short upstream adenosine rich sequence. Furthermore, analysis of the endogenous A-rich human JUNB poly(A) signal validated upstream A-rich core sequences as genuine 3’end formation directing sequences in human non-canonical 3’end formation signals. The results show that a minimal human poly(A) site, similar to yeast and plants, can be defined by an adenosine rich sequence adjacent to a U/GU-rich sequence element and a cleavage site. These findings further imply that some human non-canonical poly(A) sites may be recognised via a similar DSE-dependent mechanism and may not require additional auxiliary sequence elements. Finally, results on the analysis of the EDF1 poly(A) signal show that, in a spliced environment, A-rich sequences are also 3’end formation effectors but depend on an competent upstream splicing reaction for efficient definition of the 3’end processing site. 572.88
67	Role MAPK v regulaci cytoplazmatické polyadenylace během meiotického zrání savčích oocytů / Role of MAPK in regulation of cytoplasmic polyadenylation during meiotic maturation of mammalian oocytes Kráčmarová, Jana January 2017 (has links) Mammalian oocytes undergoing meiotic maturation are transcriptionally silent and gene expression is therefore regulated at the level of translation. One of the well established mechanisms employed in translational regulation of maternal mRNAs in oocytes is cytoplasmic polyadenylation. This process is generally controlled by phosphorylation and activation of cytoplasmic polyadenylation element binding protein (CPEB). The aim of this thesis is to determine the role of mitogen-activated protein kinase (MAPK) in regulation of CPEB-mediated cytoplasmic polyadenylation in maturing mouse and porcine oocytes. For this purpose, MAPK activity was inhibited using its specific inhibitor, GDC-0994 and the effect of MAPK inhibition on cyclin B1 mRNA polyadenylation was monitored. In mouse oocytes, MAPK inhibition impaired neither cyclin B1 mRNA polyadenylation nor its translation and MAPK is thus unlikely to be involved in regulation of cytoplasmic polyadenylation in this species. Based on the results of experiments performed using porcine oocytes, the possible role of MAPK in CPEB-mediated cytoplasmic polyadenylation can neither be confirmed nor ruled out. Keywords: cytoplasmic polyadenylation, mouse oocyte, porcine oocyte, mitogen-activated protein kinase (MAPK), cyclin B1, GDC-0994 inhibitor
68	Analysis of CPEB Family Protein Member CPEB4 Function in Mammalian Neurons: A Dissertation Kan, Ming-Chung 01 June 2008 (has links) Local protein synthesis is required for long-term memory formation in the brain. One protein family, Cytoplasmic Polyadenylation Element binding Protein (CPEB) that regulates protein synthesis is found to be important for long-term memory formation possibly through regulating local protein synthesis in neurons. The well-studied member of this family, CPEB1, mediates both translational repression and activation of its target mRNAs by regulating mRNA polyadenylation. Mouse with CPEB1 KO shows defect in memory extinction but not long-term memory formation. Three more CPEB1 homologs (CPEB2-4) are identified in mammalian system. To test if CPEB2-4 may have redundant role in replacing CPEB1 in mediating local protein synthesis, the RNA binding specificity of these homologs are studied by SELEX. The result shows CPEB2-4 bind to RNAs with consensus sequence that is distinct from CPE, the binding site of CPEB1. This distinction RNA binding specificity between CPEB1 and CPEB2-4 suggests CPEB2-4 cannot replace CPEB1 in mediating local protein synthesis. For CPEB2-4 have distinct RNA binding specificity compared to CPEB1, they are referred as CPEB-like proteins. One of CPEB-like protein, CPEB3, binds GluR2 mRNA and represses its translation. The subcellular localization of CPEB family proteins during glutamate over stimulation is also studied. The CPEB family proteins are identified as nucleus/cytoplasm shuttling proteins that depend on CRM1 for nuclear export. CPEB-like proteins share similar nuclear export ciselement that is not present in CPEB1. Over-stimulation of neuron by glutamate induces the nuclear accumulation of CPEB family proteins possibly through disrupted nuclear export. This nuclear accumulation of CPEB family protein is induced by imbalance of calcium metabolism in the neurons. Biochemical and cytological results suggest CPEB4 protein is associated with ER membrane peripherally in RNA independent manner. This research provides general description of biochemical, cytological properties of CPEB family proteins. Neurons Protein Biosynthesis RNA Messenger RNA-Binding Proteins Receptors AMPA Memory Transcription Factors Gene Expression Regulation Amino Acids, Peptides, and Proteins Cells Genetic Phenomena Nervous System
69	Spindle-Localized CPE-Mediated Translation Controls Mediotic Chromosome Segregation Eliscovich, Carolina 11 June 2008 (has links) La progresión meiótica y el desarrollo embrionario temprano están programados, en parte, por la activación tradcuccional de mRNAs maternos como lo son los que codifican para las proteinas de ciclina B1 o mos. Estos mRNAs no son traducidos al mismo tiempo ni en el mismo lugar. Por lo contrario, su traducción está especificamente regulada por elementos de poliadenilación citoplasmática (CPEs) presentes en sus 3'UTRs. Los elementos CPEs reclutan a la proteina de unión a CPE (CPE-binding protein CPEB (Colegrove-Otero et al., 2005; de Moor et al., 2005; Mendez and Richter, 2001; Richter, 2007)). Esta proteina de unión al RNA no sólo determina cuándo y en qué medida un mRNA será activado traduccionalmente por poliadenilación citoplasmática (Mendez et al., 2000a; Mendez et al., 2000b; Mendez et al., 2002) sino que también participa, junto con el represor de la traducción Maskin, en el transporte y la localización de sus mRNAs diana hacia los sitios de localización subcelular donde su traducción ocurrirá (Huang et al., 2003; Huang and Richter, 2004). Durante el desarrollo embrionario de Xenopus, CPEB se encuentra localizada en el polo animal de los oocitos y más tarde, sobre el huso mitótico y centrosomas en el embrión (Groisman et al., 2000). Se ha demostrado que embriones de Xenopus inyectados con agentes que interrumpen la traducción dependiente de poliadenilación citoplasmática, detienen la división celular y presentan estructuras mitóticas anormales (Groisman et al., 2000). En este trabajo que derivó en mi tesis doctoral, hemos demostrado que la activación traduccional localizada en el huso mitótico de mRNAs regulados por CPEB que codifican para proteinas con una conocida función en aspectos estructurales del ciclo celular como la formación del huso mitótico y la segregación cromosómica, es esencial para completar la primera división meiótica y para la correcta segregación cromosómica en oocitos de Xenopus. interkinesis microtubule organizing center microtubule-cytoskeleton chromosome segregation centrosomes spindle assembly germinal vesicle breakdown prophase-I arrest meiotic cell cycle progression Poly(A) tail lengthening animal and vegetal hemispheres xenopus oocytes and development RNA-binding proteins translational activation untranslated regions (UTRs) translational repression mRNA Localization Cytoplasmic polyadenylation translation CPEB vesícula Germinal profase-I formación del huso mitótico progresión del ciclo meiótico elongamiento de la cola de poli(A) polo animal y vegetal oocitos de Xenopus al RNA proteínas de unión regiones no traducidas (UTRs) activación traduccional citoesqueleto de microtúbulos localización de mRNAs represión traduccional poliadenilación citoplasmática traducción centro organizador de microtúbulos centrosomas segregación cromosómica Xkid TPX2 interquinesis CPEB Xkid TPX2 57

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