An Investigation of poly(A) site selection loci in estrogen treated breast cancer cells

Download

index.pdf

Date

2019

Author

Bekar, Damla

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

221
views

88
downloads

Alternative polyadenylation (APA) is an mRNA processing step implicated in 3’UTR (Untranslated Region) isoform diversity, which may have significant impacts on protein levels. Nearly 70% of known human genes harbor multiple polyA sites. Proliferative signals, developmental cues and tissue specificity can induce alternative selection of polyA sites, producing transcripts with different 3’UTR lengths. Given that APA generates a vast isoform diversity, there are possible mechanistic explanations emerging on how APA might be regulated. To better understand the APA mechanism in the presence of proliferative signals, we chose a model system where we know APA is induced by Estradiol (E2) in Estrogen positive (ER+) breast cancer cell line. We analyzed existing Chromatin Immunoprecipitation- Sequencing (ChIP- Seq) data for certain histone marks that may overlap with polyA sites in E2 treated cells and performed experiments to confirm usage of these specific polyA sites. Despite the low number of cases we could analyze in this study, our results may suggest a possible link between E2 regulated transcription and APA. Future high throughput experiments will be important to test how widespread these correlations are and what the underlying mechanisms are.

Subject Keywords

Estrogen., APA, Transcription, E2, Poly(A) site selection, Breast Cancer.

URI

http://etd.lib.metu.edu.tr/upload/12624609/index.pdf
https://hdl.handle.net/11511/44360

Collections

Graduate School of Natural and Applied Sciences, Thesis

Suggestions

OpenMETU
Core

An Investigation of HNRNPA1 functions in breast cancer Özgül, İbrahim; Erson Bensan, Ayşe Elif; Department of Molecular Biology and Genetics (2019) Heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) is an RNA-binding protein with a broad range of functions including transcriptional and translational regulation of mRNAs, transport of mRNAs from the nucleus, alternative splicing, telomere maintenance, and miRNA processing. Among all, miRNA related functions of HNRNPA1 are the least understood. Hence, in this study, we aim to investigate potential miRNAs regulated by HNRNPA1.Using HNRNPA1-silenced MCF7 cells, we identified several notable miRNAs using N...
Design and construction of double promoter systems and their use in pharmaceutical protein production in P. Pastoris Demir, İrem; Çalık, Pınar; Department of Chemical Engineering (2019) Intracellular phenomena such as promoter strength, mRNA secondary structure, translation efficiency and codon preference, 5′-untranslated region processing, and protein turnover, have impacts directly on the expression of heterologous genes. Design of multi-promoter expression systems with constituent strong promoters and engineered promoter variants is a novel metabolic engineering strategy for increasing the promoter strength further, and tuning the expression for recombinant protein (r-protein) productio...
In-silico determination of Pichia pastoris signal peptides for extracellular recombinant protein production Massahi, Aslan; Çalık, Pınar (2015-01-07) In-silico identified novel secretory signal peptides (SPs) are required in vivo to achieve efficient transfer or to prevent other cellular proteins from interfering with the process in extracellular recombinant protein (r-protein) production. 56 endogenous and exogenous secretory SPs, have been used or having the potential to be used in Pichia pastoris for r-protein secretion, were analyzed in-silico using the softwares namely SignalP4.1, Phobius, WolfPsort0.2, ProP1.0, and NetNGlyc1.0. Among the predicted ...
Comparison of XL-MS Software to Identify Protein Interactions Akkulak, Hatice; İnce, H. Kerim; Kabasakal, Burak V; Özcan Kabasakal, Süreyya (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Cross-linking mass spectrometry (XL-MS) is an emerging method in structural biology not only for structural elucidation of protein complexes but also for determination of protein-protein interactions. Thus, it is commonly integrated into conventional structural biology techniques, such as Cryo-EM, NMR, and XRay crystallography. XL-MS could be applied to large and dynamic complexes since it is not restricted by sample preparation requirements, and it could capture proteins from their native environment provi...
Investigating possible involvement of miR-125b in the E2, NF-кB network Yavuz, Esra; Erson Bensan, Ayşe Elif; Department of Biology (2015) MicroRNAs (miRNAs) play important roles in diverse biological processes and are emerging as key regulators of tumorigenesis and tumor progression. Some miRNAs act as tumor suppressors and are downregulated in cancers such as miR-125b in breast cancer cell lines and tumors. Earlier, we developed a miR-125b expression model system and performed a transcriptomics experiment. Among many indirect targets, ALCAM (activated leukocyte antigen molecule) appeared to be very significantly upregulated in MCF7-125b cell...

Citation Formats

D. Bekar, “An Investigation of poly(A) site selection loci in estrogen treated breast cancer cells,” Thesis (M.S.) -- Graduate School of Natural and Applied Sciences. Biology., Middle East Technical University, 2019.