Yılmaz, Utku Cem
Alternative polyadenylation is a widespread mRNA processing event affecting the length of the 3’UTR of mRNAs. Alternative use of polyadenylation sites sometimes occurs in terminal exons, proximal exons, or proximal introns, affecting the coding 3’UTR length and even the coding sequence of the mRNA. To identify estrogen (E2) related polyadenylation changes by a 3’-seq experiment, we detected an early intronic polyadenylation site for IGFBP4 (insulin-like growth factor binding protein 4). In this thesis, I present data to confirm the existence of an intronic transcript that is robustly upregulated in response to E2 exposure in estrogen receptor-positive breast cancer cell lines. The expression pattern for this isoform follows an opposite pattern to that of the full-length isoform. Hence, we focused on the initial characterization of this isoform. I confirmed the 3’-end of the transcript with an intronic novel poly(A) signal. I performed reporter assays to suggest the functionality of the candidate poly(A) signal compared to the poly(A) signal found at the 3’UTR of the canonical isoform. I provide additional insight into the characterization of the intronicly polyadenylated isoform including mRNA stability and coding potential. While the functional role of this isoform is still not clear, these results highlight the need to detect and investigate different isoforms that may originate from a gene locus.


Use of an intronic polyadenylation site in breast cancer
Köksal Bıçakcı, Gözd; Erson Bensan, Ayşe Elif; Department of Molecular Biology and Genetics (2020)
Alternative polyadenylation is an important mRNA processing step in which the length and/or the sequence of 3’UTR of mRNAs are altered. This change in 3’UTRs may have significant effects on mRNA stability, localization and translational efficiency. One of the APA types, called intronic polyadenylation (IPA), occurs on intronic sites rather than 3’UTRs. Recent evidence shows that almost 20% of human genes have a poly(A) site in at least one intron. In fact, some introns even may have more than one poly(A) si...
Characterization of microRNA-125b expression in MCF7 breast cancer cells by ATR-FTIR spectroscopy
OZEK, Nihal Simsek; TUNA, Serkan; Erson Bensan, Ayşe Elif; Severcan, FERİDE (2010-01-01)
MicroRNAs (miRNAs), are similar to 22 nucleotides long, non-coding RNAs that control gene expression post-transcriptionally by binding to their target mRNA's 3'UTRs (untranslated regions). Due to their roles in various important regulatory processes and pathways, miRNAs have been implicated in disease mechanisms such as tumorigenesis when their expression is deregulated. To date, a significant number of miRNAs and their target messenger RNAs (mRNAs) have been identified and verified. It is generally accepte...
Identification of electron acceptor properties of Penicillium camemberti used for effective treatment of chlorinated organic compounds
Taseli, BK; Gökçay, Celal Ferdi (2005-01-01)
Two methods described in this paper use respirometric monitoring of the accumulated oxygen uptake rate, following the addition of bleachery effluents to a reactor containing Penicillium camemberti and detection of inorganic chloride removal by a chloride electrode for electron acceptor identification. In the case of respirometric studies, adsorbable organic halogens (AOX) removal was retarded at high acetate concentrations and the metabolism shifted towards aerobic respiration. Contrary to this, aerobic res...
Synthesis and enhanced photocatalytic activity of nitrogen-doped triphasic TiO2 nanoparticles
Erdogan, Nursev; Bouziani, Asmae; PARK, JONGEE; Micusik, Matej; Kim, Soo Young; Majkova, Eva; Omastova, Maria; Öztürk, Abdullah (Elsevier BV, 2019-05-15)
TiO2 nanoparticles of the single anatase phase, binary anatase-brookite phases, and ternary anatase-brookite-rutile phases were synthesized using an HNO3-catalyzed hydrothermal process. The types and amounts of phases varied depending on the hydrothermal synthesis conditions. The results revealed that N dissolves in different amounts and chemical states, depending on the phases present and their proportions in the nano particles. Brookite and rutile nanoparticles oriented through one direction were found to...
Identification of small-molecule urea derivatives as novel NAMPT inhibitors via pharmacophore-based virtual screening
Ozgencil, Fikriye; EREN, GÖKÇEN; ÖZKAN, YEŞİM; GÜNTEKİN ERGÜN, SEZEN; Atalay, Rengül (Elsevier BV, 2020-01-01)
Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the condensation of nicotinamide (NAM) with 5-phosphoribosyl-1-prophosphate (PRPP) to yield nicotinamide mononucleotide (NMN), a rate limiting enzyme in a mammalian salvage pathway of nicotinamide adenine dinucleotide (NAD(+)) synthesis. Recently, intracellular NAD(+) has received substantial attention due to the recent discovery that several enzymes including poly(ADPribose) polymerases (PARPs), mono(ADP-ribose) transferases (ARTs), and sirtuins (SIR...
Citation Formats
U. C. Yılmaz, “IDENTIFICATION AND CHARACTERIZATION OF AN INTRONIC TRANSCRIPT FOR IGFBP4,” M.S. - Master of Science, Middle East Technical University, 2023.