Profiling of Putative Androgen Response Elements in Endoplasmic Reticulum Protein Quality Control Mechanism Members

Yıl 2021, Cilt: 12 Sayı: 1, 86 - 94, 30.04.2021

Yalçın Erzurumlu

Öz

Aim: In our study, we aimed to in silico analyze the putative androgen response element regions in the promoter sequences of endoplasmic reticulum protein-quality control mechanism related genes by using bioinformatics tools. In this way, it is aimed to define the possible regulation with androgens of protein-quality control mechanism in the ER and to understand its role in prostate cancer. Material and Method: Promoter sequences of 29 target genes associated with the Endoplasmic Reticulum protein-quality control mechanism were determined using University of California, Santa Cruz ve Eukaryotic Promotor Databases. These sequences were transferred to the matinspector bioinformatics tool, and the putative androgen response element motifs that enable the selective transcription process by mediating the interaction of DNA with the androgen receptor, which works as a selective transcription factor, were analyzed. In silico analyzes was carried out using the V$GREF similarity matrix. Results: Our in silico analysis results showed that there were putative androgen response element regions of the 29 genes we examined in relation to endoplasmic reticulum protein-quality control mechanism components near the promoter and promoter region. Conclusion: Our results suggest that proteins that play a role in the endoplasmic reticulum protein-quality control mechanism might be selectively regulated by the androgen signaling mechanism. This possible regulation will be a guide to understanding the processes related to pathologies such as prostate cancer where androgen signal transduction is highly critical. Although putative androgen response element regions have been defined in bioinformatic analyzes, further analysis of the functionality of these regions is needed.

Endoplazmik Retikulum Protein Kalite Kontrol Mekanizması Üyelerinde Varsayılan Androjen Cevap Elementlerinin Profillemesi

Öz

Amaç: Çalışmamızda endoplazmik retikulum protein-kalite kontrol mekanizması ile ilişkili genlerin promotor dizilerindeki varsayılan androjen cevap elementi bölgelerinin biyoinformatik araçlardan faydalanılarak in silico olarak analiz edilmesi amaçlanmıştır. Bu yol ile ER’deki protein-kalite kontrol mekanizmasının androjenler ile gerçekleşebilecek olası regülasyonunun tanımlanması ve prostat kanserindeki rolünün anlaşılması hedeflenmiştir. Materyal ve Metot: Endoplazmik Retikulum protein-kalite kontrol mekanizmasına ile ilişkili 29 hedef genin promotor dizileri University of California, Santa Cruz ve Eukaryotic Promotor Database veri tabanları kullanılarak belirlenmiştir. Tanımlanan bu diziler matinspector biyoinformatik aracına aktarılarak selektif transkripsiyon faktörü olarak çalışan androjen reseptörü ile DNA’nın etkileşimine aracılık ederek seçici transkripsiyon sürecine olanak sağlayan varsayılan androjen cevap elementi motifleri analiz adildi. İn silico analizler V$GREF benzeşim matrixi kullanılarak sürdürüldü. Bulgular: İn silico analiz sonuçlarımız Endoplazmik Retikulum protein kalite kontrol mekanizması ile ilişkili olarak incelediğimiz 29 adet genin promotor ve promotor bölge yakınında varsayılan androjen cevap elementi bölgelerinin bulunduğunu göstermiştir. Sonuç: Sonuçlarımız Endoplazmik Retikulum protein-kalite kontrol mekanizmasında yer alan proteinlerin androjen sinyal mekanizması aracılığıyla selektif olarak düzenlenebileceğini önermektedir. Olası bu regülasyon prostat kanseri gibi androjen sinyal iletiminin son derece kritik öneme sahip olduğu patolojilere ilişkin süreçlerin anlaşılabilmesine yol gösterici olacaktır. Her ne kadar biyoinformatik analizlerde varsayılan androjen cevap elementi bölgeleri tanımlanmış olsa da bu bölgelerin fonksiyonelliğine ilişkin ileri analizlerin gerçekleştirilmesine ihtiyaç duyulmaktadır.

Anahtar Kelimeler

Endoplazmik Retikulum, Protein kalite kontrol mekanizması, Androjen Cevap Elementi, Prostat Kanseri, İn silico analiz

Kaynakça

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• Web Sayfaları Genomatix Software, MatInspector, Munich, Germany. Available from: http://www.genomatix.de/cgi-bin/eldorado/main.pl?s=8a065286baae1e0945d3d9294f299d6d;SELECTION=reg (Last accessed: October 2020)