Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Author: search.filters.author.Akgül, BünyaminPublisher: search.filters.publisher.Elsevier Ltd.

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  • Data Paper
    Citation - WoS: 3
    Citation - Scopus: 3
    Small Rna Data Set That Includes Trna-Derived Fragments From Jurkat Cells Treated With Camptothecin
    (Elsevier Ltd., 2018) Coşacak, Mehmet İlyas; Erdoğan, İpek; Nalbant, Ayten; Akgül, Bünyamin
    In this article, we report a small RNA data set obtained from human T cell acute leukemia Jurkat cells, which were treated with the universal apoptotic agent camptothecin. Based on the Annexin-V labeling pattern, we sorted two Jurkat subpopulations in treated cells: one that is sensitive to the drug and the other being relatively more resistant. We report new original data that include the frequency of tRNA-derived fragments (tRF) in drug-sensitive and resistant cells. We also present partially analyzed data to show the origin of reads on tRNAs as well as the borders of the fragments. We believe that this data can benefit the science community working in the field of tRF and/or apoptosis.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Regulation of Mrna Stability Through a Pentobarbital-Responsive Element
    (Elsevier Ltd., 2007) Akgül, Bünyamin; Tu, Chen-Pei D.
    Pentobarbital, a general anesthetic and non-genotoxic carcinogen, can induce gene expression by activating transcription. In the Drosophila glutathione S-transferase D21 (gstD21) gene, pentobarbital's regulatory influence extends to the level of mRNA turnover. Transcribed from an intronless gene, gstD21 mRNA is intrinsically very labile. But exposure to pentobarbital renders it stabilized beyond what can be attributed to transcriptional activation. We aim here to identify cis-acting element(s) of gstD21 mRNA as contributors to the molecule's pentobarbital-mediated stabilization. In the context of hsp70 5′UTR and the 3′UTR of act5C, gstD21 mRNA, minus its native UTRs, is stable. Maintaining the same context of heterologous UTRs, we can reconstitute using the full-length gstD21 sequence the inherent instability of gstD21 mRNA and its stabilization by pentobarbital. Transgenic flies that express these chimeric gstD21 mRNA exhibit decay intermediates lacking 3′UTR, which are not stabilized by PB treatment. The 3′UTR sequence, when inserted downstream from a reporter transcript, stabilizes it 1.6-fold under PB treatment. The analysis of the decay intermediates suggests a polysome-associated decay pattern. We propose a regulatory model that features a 59-nucleotide pentobarbital-responsive element (PBRE) in the 3′UTR of gstD21 mRNA.