An effort to identify novel proteins in alternative polyadenylation

Download
2020
Çiçek, Mustafa
Polyadenylation, the addition of a poly (A) tail to a nascent messenger RNA (mRNA), is a tightly regulated process occurring co-transcriptionally. Human pre-mRNA 3’ processing complex is a multi-protein machinery: Core complexes of this machinery can be listed as; i) Cleavage and Polyadenylation Specificity Factor (CPSF), ii) Cleavage Stimulatory Factor (CSTF), and iii) Cleavage Factors Im and IIm (CFIm and CFIIm). Majority of the human genes have multiple poly(A) signals which emphasizes the significance of alternative polyadenylation (APA), which is the regulated selection of alternate polyadenylation signals on mRNAs. APA may change the post-transcriptional fate of a eukaryotic mRNA by affecting its stability, localization and translational activity through altering availability of cis-regulatory elements on mRNA molecule. It is known that proliferative factors alter poly(A) signal selection in normal and cancer cells with a tendency towards increased 3’ UTR shortening. Avoiding negative regulatory trans-factors such as microRNAs, these shortened 3’UTRs have been linked to increased protein levels. These events may explain how certain proteins are upregulated in cancer cells despite the lack of activating mutations. However, it is not yet fully understood how proximal signals are selected in proliferative cells. At this point we hypothesize that, along with core subunits of polyadenylation machinery there may be other proteins which may play a role in selection of poly (A) signals. Aim of this thesis was to identify new proteins that may play a role in APA. For this purpose, we chose proximity-dependent biotin identification coupled with mass spectrometry analysis to identify interacting partners of CSTF2 to better understand how specific poly (A) sites are selected.

Suggestions

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...
Investigating the malleability of RNA aptamers
İlgü, Müslüm; Lamm, Monica H.; Nilsen-Hamilton, Marit (Elsevier BV, 2013-09-15)
Aptamers are short, single-stranded nucleic acids with structures that frequently change upon ligand binding and are sensitive to the ionic environment. To achieve facile application of aptamers in controlling cellular activities, a better understanding is needed of aptamer ligand binding parameters, structures, intramolecular mobilities and how these structures adapt to different ionic environments with consequent effects on their ligand binding characteristics. Here we discuss the integration of biochemic...
Construction of various fusion proteins of recombinant citrate synthase from thermoplasma volcanium
Özdoğan, Seda; Kocabıyık, Semra; Department of Biology (2004)
In this study, a strategy called gene splicing by overlap extension, 3Gene SOEing4, was used for the construction of the fusion proteins with the purpose of increasing the thermostability of mesophilic enzymes by incorporation of stability domain from a thermostable enzyme. Gene SOEing is a PCR-based approach for recombining DNA molecules at precise junctions irrespective of nucleotide sequences at the recombination site and without the use of restriction endonucleases or ligase. In fusion constructs, as th...
Investigating the Interactions of Poly(A)-Coralyne in Crowded Environments and the Effect of DNA Methylation on DDD-Lysine and DDD-Arginine Interactions
Suvacı, Zeynep; Persil Çetinkol, Özgül; Department of Chemistry (2022-1)
Poly(A) tail is an essential determinant of mRNA stability and maturation and is required for translation initiation. Small molecules recognizing poly(A) tails might interfere with mRNA processing. Hence, they have the potential to act as therapeutic agents. Coralyne (COR), a strong poly(A) binder, is shown to induce the formation of a stable, double-stranded poly(A) self-structure under dilute solution conditions. Although studies in dilute solutions are very informative, they do not necessarily reflect DN...
Analysis of motifs in microRNA-transcription factor gene regulatory networks
Sürün, Bilge; Acar, Aybar Can; Purutçuoğlu Gazi, Vilda; Department of Bioinformatics (2014)
MicroRNAs are small non-coding RNA molecules which contain 21-25 nucleotides, and function in post transcriptional regulation by inhibiting the translation of mRNA targets. miRNAs typically affect gene regulation by forming composite feed forward circuits (cFFCs) which also comprise a transcription factor (TF) and a target gene. By analyzing these cFFCs, the contribution of miRNAs in altering TF networks can be revealed. These contributions could either be the de-escalation of the target gene repertoire or ...
Citation Formats
M. Çiçek, “An effort to identify novel proteins in alternative polyadenylation,” Thesis (Ph.D.) -- Graduate School of Natural and Applied Sciences. Biotechnology., Middle East Technical University, 2020.