Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Investigation of the Interaction Between Dr5-As Long Noncoding Rna and Caprin1 Protein(Izmir Institute of Technology, 2022) Kaçar, Vahide İlayda; Akgül, BünyaminCell proliferation is the crucial process for many physiological incidents such as tissue and organ development, wound healing, and immune system reactions. It is achieved by the growth and division of cells in a multicellular organism. Investigation of molecules involved in the regulation of cell cycle mechanism provides insight into reasons and treatments of the diseases such as cancer. In recent years, information that acquired from deep sequencing reveals that several proteins and non-coding RNAs have crucial role in the regulation of cell cycle and proliferation. Death receptor 5 antisense (DR5-AS) is a novel long non-coding RNA (lncRNA) transcript that is cisplatin inducible and is involved in modulation of cell proliferation and cell cycle in HeLa cells. When DR5-AS lncRNA was knocked down, the morphology of HeLa cells became spherical without inducing apoptosis. Although this lncRNA reduces cell proliferation via a cell cycle arrest at S and G2/M phases, mechanism behind this cell cycle arrest is not known. lncRNAs work in complexes with RNA, DNA, and protein interactions in the cell. There are several experimental and bioinformatical approaches to investigate RNA: protein interactions such as PAR-CLIP. In this approach, proximal protein and RNAs are covalently bonded with UV radiation. Then this complex is immunoprecipitated with specific antibodies. According to PAR-CLIP data of DR5-AS lncRNA, CAPRIN1 is a cell cycle associated protein that has the highest interaction score. The results suggest that CAPRIN1 and DR5-AS work reversely in cell proliferation although under the cisplatin treatment, CAPRIN1 enhances the expression of DR5-AS lncRNA. All these observations were confirmed by many quantitative experiments. Conclusively, this study provides a clue about how DR5-AS lncRNA might regulate cell cycle and proliferation through CAPRIN1 protein.Master Thesis Investigation of the Effect of Dr5-As Long Non-Coding Rna on Cell Proliferation(Izmir Institute of Technology, 2020) Gürer, Dilek Cansu; Akgül, BünyaminCell proliferation is the process of increasing cell number in a multicellular organism. In literature, there are numerous proteins and non-coding RNAs reported as regulators of cell proliferation, yet, many of others are waiting to be explored. Unravelling the mechanism behind the regulation of cell proliferation is crucial to develop new strategies for fighting numerous diseases such as cancer, immune diseases, or neurodegenerative diseases. Long non-coding RNAs (lncRNAs) are known to regulate various cellular processes. To determine which ones are related to cell proliferation and apoptosis in HeLa cells, a transcriptomics study was performed under cisplatin, doxorubicin, TNF-? and Anti-Fas treatments. DR5-AS is a novel lncRNA transcript selected from this transcriptomics study as a promising regulatory lncRNA candidate due to its overlap with DR5 protein-coding gene which is known to regulate apoptosis and proliferation. Several phenotypic characterization methods were performed to understand the function of DR5-AS lncRNA. These studies showed that DR5-AS knockdown causes a significant decrease in cell proliferation, an alteration in the normal HeLa cell morphology, a shift through S and G2/M phases in cell cycle profile, and significant accumulation of cells in the metaphase phase. A second transcriptomics study was performed with DR5-AS knockdown HeLa cells to uncover which pathways are responsible for these changes. The results suggest that DR5-AS lncRNA regulates expression of numerous key proteins in cell cycle regulation. This observation was confirmed by several qPCR experiments. In conclusion, this study provides the first evidence that DR5-AS lncRNA modulates cell cycle and proliferation in HeLa cells.