Master Degree / Yüksek Lisans Tezleri

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

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Author: search.filters.author.Akgül, BünyaminSubject: search.filters.subject.Non-coding RNA

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Now showing 1 - 4 of 4
  • Master Thesis
    Examination of Stable Intronic Sequence Rna Profile Under Apoptotic Conditions
    (Izmir Institute of Technology, 2022) Kara, Merve; Akgül, Bünyamin
    Apoptosis is a process of programmed cell death. Cisplatin, a chemotherapeutic drug, activates intrinsic pathway of apoptosis while TNF-alpha, a death ligand, activates the extrinsic pathway of apoptosis. Noncoding RNAs involve in regulation of apoptotic pathways at post-transcriptional level. Stable intronic sequence RNAs (sisRNAs) are the novel class of non-coding RNAs which can be generated by splicing- dependent and independent mechanisms. sisRNAs transcribed from their intronic promoter may contain 5’ cap and polyA tail. Despite the reports of several studies about sisRNAs in Xenopus and Drosophila, a genome-wide profile of sisRNAs in human is lacking. Therefore, we aimed to identify sisRNAs profile that are transcribed from their intronic promoter under cisplatin- and TNF-alpha- mediated apoptosis conditions. In this thesis study, the deep sequencing of total RNA, polyA + and polyA eliminated fractions from cisplatin-, TNFalpha-, DMSO-treated cells were performed. Differentially expressed intronic transcripts were analysed by DE-kupl algorithm. The intronic transcripts both in total RNA and polyA + RNA fractions but not in polyA eliminated fractions were screened visually on Integrated Genome Viewer (IGV) and selected as sisRNA candidateS. 48 sisRNA candidates were detected in cisplatin-treated data while 33 sisRNA candidates were detected in TNF-alpha- treated data. 5’ and 3’ RACE PCRs were performed for determination of transcriptional units of sisRNA candidates. Overexpression of sisRDOCK7-IT1 caused 8.09% increase in total apoptosis of HeLa cells in 48 hours. sisRDOCK7-IT1 triggers the activation of apoptosis but the mechanism of its induction of apoptosis is still unknown.
  • Master Thesis
    Investigation of Long Non-Coding Rna and Chromatin Interactions in Hela Cells
    (Izmir Institute of Technology, 2022) Atbinek, Melis; Akgül, Bünyamin
    The DNA in the cells is surrounding histone proteins to form nucleosomes. The structure is packed further into chromatin. The chromatin structure is dynamic and flexible. It is regulated by many factors including long non-coding RNAs (lncRNAs). LncRNAs are a class of non-coding RNAs, transcripts that do not encode protein. They are longer than 200 nucleotides and might contain a polyA tail and a 5’ cap. Thus, they are localized in the nucleus. lncRNAs interact with chromatin in two ways, indirect and direct. Direct interaction occurs via two mechanisms: R-loop and triplex formation. These interactions affect the folding of chromatin inducing gene expression under various cellular conditions. LncRNAs interacting with chromatin regulating genes are found in HEK cells. Thus, it is hypothesized that lncRNA – chromatin interactions may differ in cancerous cells as well. In this study, the iMARGI method is optimized to be used in adenocarcinoma HeLa cells. The chromatin digestion and incubation conditions are adjusted to give optimal results for HeLa cells. iMARGI is a recently developed method employed to investigate such interactions in a genome-wide manner. iMARGI allows the isolation of all lncRNAs interacting with the whole genome. The interacting RNA – DNA molecules are pulled down with streptavidin conjugated beads after linker ligation. The chimeric molecules are amplified with PCR forming lncRNA – chromatin libraries of HeLa cells. In the future, new libraries can be formed after inducing apoptosis in HeLa cells. Identification of lncRNAs involved in chromatin remodeling in apoptotic conditions can facilitate new therapeutic methods for fighting tumor initiation and development.
  • Master Thesis
    Identification of Long Non-Coding Rnas That Regulate Apoptosis in Human
    (Izmir Institute of Technology, 2015) Ahmadov, Ulvi; Akgül, Bünyamin
    Apoptosis is essential for cellular homeostasis and normal development. Aberrant apoptosis (too much or too less) is associated with many important diseases such as autoimmune diseases and cancer. Studies have led to the identification of a number of proteins and microRNAs involved in the regulation of apoptosis. However, the role of long non-coding RNAs (lncRNAs) is still unclear. In this study, two cancer therapeutics drugs, cisplatin and doxorubicin, and two ligands, Fas mAb and TNF-alpha, were used in identification of differentially expressed pathway-drug specific and/or global lncRNAs in apoptotic HeLa cells. Following dose-kinetics experiments the level of apoptosis was measured by Flow Cytometry and was further verified by Fluorescence Microscopy and Western Blotting via measurement of Caspase 3, 8 and 9 protein levels. Three replicates of total RNAs (control and drug/ligand-treated cells) were sent to deepsequencing using the Illumina platform. The resulting reads matched to the human genome greater than 95%. Under our experimental setting, treatments with cisplatin, doxorubicin, Fas mAb and TNF-alpha led to the differential expression of 1644, 506, 584 and 807 lncRNAs, respectively (2-fold or higher, P < 0.01). Two of identified lncRNAs common for all inducers was in antisense position to TRAIL-R2 receptor and FasR associated factor which play directly in apoptosis. Results suggest that many lncRNAs are differentially expressed upon treatment with the indicated agents. Functional characterization of candidates might provide an interesting insight into regulation of apoptosis.
  • Master Thesis
    Genomic Profiling of Micrornas Regulating Translation in Drosophila Melanogaster Embryos
    (Izmir Institute of Technology, 2008) Tüncel, Özge; Akgül, Bünyamin
    Among the small RNAs, microRNAs are a particular class of 21 to 23 nucleotide RNAs that negatively regulate translation and play a pivotal role in posttranscriptional gene expression. microRNAs are found in many phyla that control such diverse events as metabolism, cell fate, cell death and development.The aim of this study is to investigate molecular mechanism of miRNAmediated translational regulation by profiling developmentally important microRNAs according to their translational status and to identify new microRNAs that have roles in translational regulation during the embryogenesis of Drosophila. Following RNA purification from different embryonal stages the fractionated RNAs were analyzed by microRNA microarray. Preliminary results show that 9 miRNAs were expressed in both stages whereas 60 miRNAs were accumulated in RNA fractions of 8 hour embryos.Also there are 2 miRNAs in all fractions of both stages in Drosophila embryos. It can be concluded that most of them were expressed in late embryonal development and there does not appear to be a switch in microRNA profiles in fractions for different stages of embryos. The preliminary results suggest that microRNAs may suppress protein synthesis at pre-initiation and initiation phases based on the microarray data.Further studies are required to solidify the preliminary findings.