Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Publisher: search.filters.publisher.01. Izmir Institute of TechnologySubject: search.filters.subject.Apoptosis

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  • Master Thesis
    Investigation of the Effects of Gtf2a1-Antisense Long Non-Coding Rna on Cell Fate
    (01. Izmir Institute of Technology, 2022) Çiftçi, Yusuf Cem; Akgül, Bünyamin
    Apoptosis is a distinct mode of programmed cell death whereby cellular contents are broken down and accumulated in the apoptotic bodies. The vast majority of the genome consists of non-coding RNAs (ncRNA). NcRNAs can be divided into groups depending on their length, for example, long non-coding RNA (lncRNA) longer than 200 nucleotides. It has been demonstrated that these have important roles in the development, and treatment of cancer and in other diseases that critically affect human life. Considering the lncRNAs’ mechanisms of action on apoptosis, they modulate activity of transcription factors, regulate miRNAs, and interact with proteins related to histone mechanisms such as chromatin modifier. In this perspective, GTF2A1-AS which is an uncharacterized and novel lncRNA was found as one of highly expressed lncRNA in transcriptomic data obtained from HeLa cells treated with cisplatin. The potential role of GTF2A1-AS within the cell was investigated through the transcriptomic data provided by GTF2A1-AS knockdown. It has been found that specific gene clusters mainly enriched in the pathway which is Defective Homology directed Repair through Homologous Recombination. In this process, double-strand breaks are repaired with the help of BRCA1/2, RAD50, RAD51, PALB2 proteins which are known as DNA damage response proteins. Thus, the genes related with DNA damage response were selected to validate the transcriptomic data. In light of this information, GTF2A1-AS knockdown has resulted in an increase in the early apoptosis in HeLa cells. Additionally, when GTF2A1-AS knockdown was combined with cisplatin, it sensitized HeLa cells against cisplatin by affecting late apoptosis, specifically. Consequently, GTF2A1-AS as a cisplatin inducible lncRNA modulates apoptosis and chemosensitivity in HeLa cells.
  • Master Thesis
    Transcriptomics Profiling of M6a Rna Modifications in Tnf-Alpha Induced Apoptosis
    (01. Izmir Institute of Technology, 2021) Akçaöz, Azime; Akgül, Bünyamin
    Apoptosis is a form of programmed cell death that occurs as a result of physiological or pathological causes. TNF-alpha, which has a regulatory role in immune system cells, stimulates apoptosis through the external pathway. For this reason, it can be used for the treatment of various diseases. Although there are many studies on the regulatory mechanisms of TNF-alpha mediated apoptosis, the contribution of RNA modifications has not been fully elucidated. Regarding the potential role of m6A RNA modification in apoptosis, studies have focused on the effects of regulatory proteins and there is no genome-wide m6A methylation profile yet. In the present thesis, firstly, the gene expression patterns of m6A writer, eraser, and reader were examined in HeLa cells and 632 genes with differential m6A methylation pattern were identified by the miCLIP method. 99 genes involved in apoptotic pathways were determined by GO analysis. Candidates were selected based on m6A methylation fold change, intracellular expression level and apoptotic role of the relevant gene. Methylation points in IGV were confirmed and specific validation experiments were performed on these m6A points. SELECT based validation studies showed 1-2 cycle increase in the TNF-alpha group compared to the control group. This confirms the miCLIP data, which also pointed to an increase in m6A methylation. To elucidate the fate of candidate RNAs, the gene expression levels, and translational status of candidate genes were analyzed. METTL3 KD HeLa cells exposed to TNF-alpha exhibited an increase in the expression of PHLDA1, IFI6 and HRK by almost 2-fold. Polysome fractionation assay showed that translation level decreased in TNF-alpha treated METTL3 KD HeLa cells. As a conclusion, global m6A level affected RNA abundance as well as translation.