Thesis (Ph.D. in Microbiology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 198-225). Online version available via ProQuest Digital Dissertations.

Human Immunodeficiency Virus type I genome consists of two identical RNA molecules that are non-covalently linked to form a dimer. HIV-1 immature and mature genomic RNA (gRNA) dimers were found in protease defective (PR -) and wild type virions, respectively, and the 5'untranslated region (5' UTR) was shown to play key roles during the genome dimerization process; but the dimerization mechanism still remains to be clarified My research project is to characterize the dimerization process and the role of 5' UTR in genome dimerization in virions produced by tissue culture cells. I'll firstly show the dimer maturation processes of HIV-1 gRNA isolated from newly released to grown-up (≥10h old) wild type, PR-, and SL1 defective (DeltaIDS) virions respectively. The results showed that HIV-1 gRNA dimer maturation process was protease-dependent and involved multiple steps: from low to high dimerization level and dimer thermostability, and from low dimer mobility to intermediate and high mobility. PR- virions did not freeze gRNA conformation in the primordial nascent state and gRNA changed from monomeric in newly released virions to half dimeric in grown-up virions, which showed that genome was packaged in the form of monomeric RNA or fragile dimers, more thermolabile than immature dimers in grown-up PR- virions. DeltaDIS inhibited gRNA dimerization by about 50% in newly released virions, though grown-up DeltaDIS gRNA was fully dimeric, which indicated that the DIS played the initiation role in gRNA dimerization in HIV-1 virions. The gRNA dimerization rate in PR- or DeltaDIS virions was much slower than that in wild type virions. These results show for the first time the whole process of dimer maturation after virion release, the gRNA conformation rearrangement in PR- virions, and the initiation role of the DIS in HIV-1 virions. Next, I'll provide a rather systematic search for the contribution of different regions in 5' UTR to HIV-1 gRNA dimerization by studying selected mutations singly or together with defective SL1. The results showed that the 5'trans-activation response element (5'TAR) was directly involved in gRNA dimerization, and a long distance base-pairing interaction between a sequence in U5 region (nts105-1l5) and another around the initiation codon of the gag gene (nts334-344) was structurally contributive to gRNA dimerization. Deletions of sequences around the 3'end of Primer Binding Site (PBS) stem-loop moderately decreased gRNA dimerization level. Other sequences in 5' UTR except DIS/SL1, which was previously known to play important roles, didn't show any systematic role. Here the results suggested that the absence of inhibition on gRNA dimerization level with defective DIS might be the compensation of the direct role of 5'TAR; and wild type-like dimerization level of DeltaTAR must be the direct contribution of the DIS.

Thesis (Ph.D. in Biochemistry & Molecular Genetics) -- University of Colorado at Denver and Health Sciences Center, 2006. / Typescript. Includes bibliographical references (leaves 119-131). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 126-146).

The purpose of this project was to identify and evaluate nucleotide sequences enhancing translation of proteins in Chinese hamster ovary (CHO) cells. Candidate sequences were placed in the 5´-untranslated region (UTR) or 3´ UTR respectively and evaluated in a CHO-based expression system with a fluorescent Fc-fusion protein as a model protein.Five plasmid vectors were constructed, two of which designed to have a randomized nucleotide library in their 5´ and 3´ UTR respectively, and three of which designed to hold varying repeats of a known enhancing translation (ET) sequence in their 5´ or 3´ UTR. The plasmid constructs were transfected into CHO cells and the protein expression was analyzed both by fluorescence intensity in single cells using flow cytometry and in bulk by monoclonal antibody titer analysis based on Protein A affinity.The main result is that both flow cytometry and titer analysis indicate that insertion of five repeats of the ET in the 5´UTR has a negative effect on protein expression as compared to the control which had no ET repeats. Results related to the insertion of three ETs in the 5´ UTR were ambiguous. The titer analysis indicated that it had a negative effect on the protein expression compared to the control which had no ET repeats, whereas the flow cytometry results suggest that the effect is negligible. Transfection of library plasmids was unsuccessful; hence no library expression analysis results were achieved. Due to the time constraints of the project, the reason for the unsuccessful transfection of library plasmids was not investigated, but the LTX transfection method is stated as a highly plausible cause.Based on the outcome of this study, two recommendations for future work are suggested. The first one is to continue the focus on UTR sequences in terms of library screening, and to improve the method of transfecting library plasmid constructs into CHO cells using lipofection. The second suggestion for further studies is to test different UTR sequence lengths without involving potential ETs, to rule out the effect and positions of the ETs and investigate the expressional effect of UTR length solely.

No description available.

No description available.

The formation of the mRNP complex is a critical component of translational regulation and mRNA decay. Both the 5 ' and 3 ' UTRs of CSF-1 mRNA are involved in post-transcriptional regulation. In CSF-1 mRNA, a small hairpin loop structure is predicted to form at the extreme 5 ' end (2-21 nt) of the 5 ' UTR. Nucleolin binds the hairpin loop structure in the 5 ' UTR of CSF-1 mRNA and enhances translation, while removal of this hairpin loop nucleolin binding element dramatically represses translation. Thus in CSF-1 mRNA, the hairpin loop nucleolin binding element is critical for translational regulation. In addition, nucleolin interacts with the 3 ' UTR of CSF-1 mRNA and facilitates the miRISC formation which results in poly (A) tail shortening. The overexpression of nucleolin increases the association of CSF-1 mRNA containing short poly (A)(n), <= 26, with polyribosomes. Nucleolin both forms an mRNP complex with the eIF4G and CSF-1 mRNA, and is co-localized with the eIF4G in the cytoplasm further supporting nucleolin's role in translational regulation. The distinct foci formation of nucleolin in the cytoplasm of ovarian and breast cancer cells implicates the translational promoting role of nucleolin in these cancers.

abstract: Multicellular organisms use precise gene regulation, executed throughout development, to build and sustain various cell and tissue types. Post-transcriptional gene regulation is essential for metazoan development and acts on mRNA to determine its localization, stability, and translation. MicroRNAs (miRNAs) and RNA binding proteins (RBPs) are the principal effectors of post-transcriptional gene regulation and act by targeting the 3'untranslated regions (3'UTRs) of mRNA. MiRNAs are small non-coding RNAs that have the potential to regulate hundreds to thousands of genes and are dysregulated in many prevalent human diseases such as diabetes, Alzheimer's disease, Duchenne muscular dystrophy, and cancer. However, the precise contribution of miRNAs to the pathology of these diseases is not known. MiRNA-based gene regulation occurs in a tissue-specific manner and is implemented by an interplay of poorly understood and complex mechanisms, which control both the presence of the miRNAs and their targets. As a consequence, the precise contributions of miRNAs to gene regulation are not well known. The research presented in this thesis systematically explores the targets and effects of miRNA-based gene regulation in cell lines and tissues. I hypothesize that miRNAs have distinct tissue-specific roles that contribute to the gene expression differences seen across tissues. To address this hypothesis and expand our understanding of miRNA-based gene regulation, 1) I developed the human 3'UTRome v1, a resource for studying post-transcriptional gene regulation. Using this resource, I explored the targets of two cancer-associated miRNAs miR-221 and let-7c. I identified novel targets of both these miRNAs, which present potential mechanisms by which they contribute to cancer. 2) Identified in vivo, tissue-specific targets in the intestine and body muscle of the model organism Caenorhabditis elegans. The results from this study revealed that miRNAs regulate tissue homeostasis, and that alternative polyadenylation and miRNA expression patterns modulate miRNA targeting at the tissue-specific level. 3) Explored the functional relevance of miRNA targeting to tissue-specific gene expression, where I found that miRNAs contribute to the biogenesis of mRNAs, through alternative splicing, by regulating tissue-specific expression of splicing factors. These results expand our understanding of the mechanisms that guide miRNA targeting and its effects on tissue-specific gene expression. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2019

Orientador: Sérgio Roberto Peres Line / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-22T18:59:49Z (GMT). No. of bitstreams: 1 Urioste_EduardoArcanjo_M.pdf: 1274507 bytes, checksum: 0f7136d4dabaf0e810ad2bdf1b2ee815 (MD5) Previous issue date: 2013 / Resumo: Estima-se que cada indivíduo carregue cerca de 120 a 430 variantes raras em regiões UTRs (Abecasis et al, 2012). Apesar da tolerância a variação na região 5' UTR, a patofisiologia de várias doenças está ligada a mutações na mesma (Cazzola & Skoda, 2000; Reynolds, 2002; Chatterjee & Pal, 2009; Wethmar et al 2010), sendo necessário o entendimento a determinação dos mecanismos regulatórios. O objetivo deste trabalho é descobrir assinaturas genéticas encontradas no contexto genômico de mutações pontuais de região 5' UTR que permitam prever o impacto funcional de outras variações pontuais na mesma região. As mutações, causadora de doença, foram selecionadas do banco de dados do Human Gene Mutation Database (HGMD) (Stenson et al, 2008); e os polimorfismos, de impacto funcional desconhecido, foram obtidos no banco de dados NHLBI Grand Opportunity Exome Sequencing Project (ESP), sendo originados do trabalho de Tenessen et al (2012). No total foram utilizadas 235 mutações e 21.542 polimorfismos. Para as variações foram calculados parâmetros de variação da estabilidade da estrutura secundária do contexto das variações (??Gfolding), presença de sítios de ligação de fatores de transcrição (JASPAR), tipo de variação (transição/transversão, tipoV), distância do início da sequência codificante (DiSC), distância do início de transcrição (DiTr) e conservação filogenética por distância de Levenshtein do contexto (Lev). A estatística foi calculada pelos testes de Wilcoxon e Binomial. A partir destes foram gerados modelos de regressão logísticos analisados através de curva ROC. Os parâmetros ??Gfolding máximo, tipoV, DiSC, e Lev permitiram a distinção significativa (? = 0,05) entres os polimorfismos e as mutações permitindo modelos explicativos, mas incompletos (área da Curva ROC 0, 772). ??Gfolding max. indicou uma relação entre as mutações e entre estruturas secundárias mais estáveis geradas pelas mesmas. Os parâmetros Lev e tipoV sugerem a origem das mutações como resultantes de hotspots. O parâmetro DiSC indicou regiões com provável funcionalidade. Apesar de não ter sido possível estabelecer relação causal entre os parâmetros e o impacto funcional das variações, encontrou-se correlações importantes / Abstract: It is estimated that each individual carries about 120 to 430 rare variante in the UTR regions (Abecasis et al, 2012). Despite the increased tolerance towards variations in 5' UTR region, the patho-phisiology of several diseases is linked to its mutations (Cazzola & Skoda, 2000; Reynolds, 2002; Chatterjee & Pal, 2009; Wethmar et al 2010). Therefore it is necessary the understanding and the determination of the regulatory elements. The objective of this study is the discovery of genetic signatures found in the genomic context of disease causing point mutations in 5' UTR, thus allowing the prediction of the functional impact of other point variations in the same region. The disease causing mutations were selected from Human Gene Mutation Database (HGMD) (Stenson et al, 2008). The polymorphisms of unknown functional impact were obtained from the NHLBI Grand Opportunity Exome Sequencing Project (ESP), originated from the work of Tenessen et al (2012). A total of 235 mutations and 21,542 polymorphisms were used. For each variation, parameters related with the differences of the variation's context folding stability (??Gfolding), presence of transcription factor binding sites (JASPAR), type of variation (transition/transversion, tipoV), distance from coding sequence start (DiSC), distance from transcription start site (DiTr) and phylogenetic conservations by distance of Levenshtein from wild type to variant context (Lev). The statistical test was done by Wilcoxon and Binomial. Logistical regressions models were generated from the parameters and its performance was evaluated by a ROC curve. The parameters maximal ??Gfolding, tipoV, logarithm of DiSC and Lev allowed a significant distinction (? = 0,05) between the groups, generating models of reasonable explanation but incomplete (area under the ROC curve 0,772). Maximal ??Gfolding showed a relationship between mutations and stable secondary structures generated by them. Lev and tipoV suggested the origin of the mutation from hotspots. The DiSC parameter identified regions with possible functionality. While it was not possible to establish any clear causal relationship between the parameters and the functional impact of the variations, important correlations were found / Mestrado / Histologia e Embriologia / Mestre em Biologia Buco-Dental