京都大学 / 0048 / 新制・課程博士 / 博士(生命科学) / 甲第21228号 / 生博第397号 / 新制||生||52(附属図書館) / 京都大学大学院生命科学研究科高次生命科学専攻 / (主査)教授 朝長 啓造, 教授 藤田 尚志, 教授 野田 岳志 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

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mRNA molecules form an intermediate in the transfer of sequences from DNA to ribosomes in order to guide protein production. Errors can be introduced into mRNA, producing aberrant proteins which place a strain on cellular regulatory machinery, causing increased risks of apoptosis, cancer, and decreased fitness. These errors may be introduced due to decreased transcriptional proofreading capabilities, exposure to chemicals, or mistakes in RNA editing machinery. It is important to investigate these causes of transcription errors to better understand the long-neglected area of mRNA fidelity which has such significant impacts on our cellular functions. In this paper, it was determined that addition of adenine opposite from abasic sites, not genomic uracil pairing with adenine, are a probable cause of G-to-A transcription errors. That exposure to Roundup causes increased levels of transcription errors, potentially due to oxidative stress. And finally, that off-target ADAR gene editing of transcripts occurs at high levels.

The development of super-resolution microscopy made it possible to surpass the diffraction limit of optical microscopy, enabling researchers to gain a nanometer scale understanding of cellular structures. While many applications have benefited from standard super-resolution microscopy, gaps remained making high-speed dynamic imaging in live cells impossible. To address this problem, single-point edge-excitation sub-diffraction (SPEED) microscopy was developed. This methodology enables the nanometer imaging of dynamic cell processes within live cells, the evaluation of subcellular structural information, the capacity to derive three-dimensional information from two-dimensional images within rotationally symmetric structures, and the interrogation of novel questions regarding the transport dynamics of macromolecules in a variety of cellular structures. Here, I have described the theory and method behind the current iteration of SPEED microscopy that we have developed and validated via Monte Carlo simulation. Further, a detailed description of how we have further developed SPEED microscopy to derive structural information within the nuclear pore complex as well as how SPEED has been applied to evaluate the export kinetics of mRNA. / Biology

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In this study we have focused on the codon usage bias in E. coli. In chapter 3, we use the population genetics model and the data available on the protein and mRNA levels of the E. coli genes to understand the pattern of codon usage in different genes with different expression levels and see which measure best explains the codon usage pattern. Besides codon bias, by testing for the over-parametrization of the model, we are able to test for the existence of context dependent mutation. We have also fitted the model for the codon usage patter in the Yeast and also tested for the context dependent mutation in this organism. In chapter 4, we focus on the first 10-15 codons in the genes of E. coli. Motivated by the fact that in this region we observe two phenomena, reduction in translation efficiency and suppression of mRNA secondary structures, we investigate whether the former is a side effect of selection for the latter. For this matter we have generated a set of synonymous randomized sequences, and then by selecting the ones which show weak secondary structures in the mentioned region, we would be able to test the theory. We will also look at the frequencies of the amino acids in E. coli genes and see whether the selection for weak secondary structures in the translation initiation region could be strong enough to not only affect the codon usage, but also the choice of amino acids. We would also provide information on the correlation between the strength of the mRNA secondary structure in the first 13 codons and the overall translation efficiency of the genes. / Thesis / Master of Science (MSc)

H1 and core histone mRNA levels have been examined in the presence of portein synthesis inhibitors with different mechanisms of action. Total HeLa cell RNAs were analyzed by Northern Blot hybridization using cloned human histone genes as probes. Inhibition of DNA replication resulted in a rapid decline in histone mRNA levels. However, in the presence of cycloheximide or puromycin, H1 and core mRNAs did not decrease in parallel with DNA synthesis, but were stabilized and accumulated. Inhibition of DNA synthesis with hydroxyurea after the inhibition of protein synthesis did not lead to a decline in histone mRNA levels. These results suggest that synthesis of a protein(s) - perhaps a histone protein(s) - is required for the coordination of DNA synthesis and histone mRNA levels.

Hepatitis B virus (HBV) represents one of the hot topics of current basic and pharmaceutical research. Although an effective vaccine against HBV exists since 1982, the world prevalence of chronic infection is still alarming. The infection can lead to significant liver damage, often resulting in hepatocellular carcinoma. Chronic HBV infection cannot be cured due to the fact that the viral genome persists in the infected hepatocyte hidden from the host immune response as well as from the antiviral treatment. One of the novel approaches aiming for HBV cure suggests that this cccDNA pool could be destroyed using gene editing tools such as CRISPR/Cas9 system. In order to shift this gene editing system to possible medicinal application, CRISPR/Cas9 has to be specifically delivered into the target cell in order to minimize its putative off-target activity. This thesis focuses at first on the design and efficacy testing of new sgRNAs targeting HBV cccDNA and secondly, it describes modular lipid nanoparticles developed specially for delivery of the CRISPR/Cas9 system in the form of RNA. Keywords: hepatitis B virus, CRISPR/Cas9, gene editing, lipid nanoparticles, mRNA delivery, targeted delivery

The physiological responses of angiotensin II (Ang II) are mediated across the cell membrane through the angiotensin II type 1 receptor (AT1R), a heptahelical membrane protein coupled to trimeric G-proteins on the cytosolic side. AT1R on binding its ligand, Ang II, leads to downregulation of cell-surface receptor and also its mRNA. We have investigated whether the 3'- and 5'-untranslated regions of the human AT1R mRNA mediate the degradation of hAT1R mRNA by post-transcriptional mechanisms in human adrenocortical carcinoma cell line (H295R cells). Protein kinase C (PKC) activator, phorbol-12-myristate-13-acetate (PMA), showed that the downregulation of hAT1R mRNA is mediated by the PKC pathway. Experiments performed in the presence of cycloheximide and/or Ang II demonstrated that protein translation is essential for hAT1R mRNA downregulation. In vitro cell-free RNA degradation assays did not show any increase in the rate of degradation of in vitro transcribed RNA in the presence of cytoplasmic extract from cells treated with Ang II, which suggested that hAT1R steady state mRNA levels may not be mediated by changes in mRNA degradation rates. Luciferase assay after transient transfection of chimeric plasmids of luciferase and hAT1R-3'-UTR showed that Ang II stabilizes the mRNA rather than increase the rate of degradation. Similar results were observed in Northern blot experiments utilizing beta-globin fusion with 3'-UTR that led to stabilization of the chimeric mRNA. Luciferase fusion constructs with both 5'- and 3'-UTRs demonstrated that UTRs are not involved in the Ang II-mediated degradation of hAT1R mRNA. Experiments using transcriptional inhibitor actinomycin D demonstrated that the hAT1R mRNA is not destabilized in response to Ang II activation in H295R cells. Nuclear run-on assay performed in the adrenocortical carcinoma cells demonstrated that the Ang II-stimulated downregulation of hAT1R is mediated by transcriptional inhibition. The transcription of hAT1R mRNA was reduced by 44 and 70% after Ang II treatment for 1 and 2 hours, respectively. Taken together, these findings suggest that the Ang II-induced downregulation of hAT1R steady state mRNA levels is transcriptionally controlled and is not mediated by post-transcriptional mechanisms.