Virally-Encoded Long and Short Non-Coding RNAs

Year 2023, , 2209 - 2224, 24.10.2023

Mehmet Kara

https://doi.org/10.29130/dubited.1212643

Abstract

Recent advances in RNA sequencing methods have elucidated that over the last decade, regions in the mammalian genome, which was previously described as ‘junk DNA’, is actively converted to RNA. Through bioinformatic and proteomic analyses, it was shown that the majority of these transcripts do not code for protein. Identified as long non-coding RNAs, these genes exceed the number of known protein-coding genes. It is required to investigate how these RNA molecules are generated and how they function, in order to understand how the genome works at a fundamental level and to design therapies against diseases and biosensors for early prognosis. Viruses, as organisms to utilize their hosts’ mechanisms, encode for these RNA molecules which do not induce immune system-like proteins, and exploit ncRNAs to manipulate cellular pathways for their life cycles. In addition to understanding viral pathogenesis at a molecular level, it has become increasingly important to study virally encoded ncRNA function since viruses are used as vectors for gene therapy and vaccines. In this work, certain viral non-coding RNAs excluding the miRNAs and circular RNAs have been reviewed. Additionally, the methods and techniques for identification, characterization, and functional analyses for the lncRNA studies have been summarized. Understanding the key roles of these small molecules, which viruses utilize for infecting the host, is important for us to realize how commonly RNA is utilized for regulatory purposes.

Keywords

Virus, herpesvirus, long non-coding RNA, RNA-protein interactions, RNA omics technologies

Virüslerin Kodladığı Uzun ve Kısa Kodlamayan RNA’lar

Abstract

Yeni geliştirilen RNA dizileme teknolojileri ile yaklaşık son on yıldır, memeli genomlarının önceden çöp, ‘junk’ DNA olarak görülen kısımlarının aslında aktif olarak RNA’ya dönüştükleri gözlemlenmektedir. Yapılan biyoinformatik analizler ve proteomik çalışmalar, bu RNA ürünlerinin çok büyük bir kısmının proteine dönüşmediğini göstermektedir. Uzun kodlamayan RNA olarak adlandırılan bu sınıftaki genlerin, günümüzde, bilinen genlerden sayıca daha fazla olduğu ortaya çıkarılmıştır. Bu RNA moleküllerinin nasıl üretildikleri ve ne yaptıklarını incelemek, hem genomun nasıl çalıştığını temel bilim düzeyinde anlamak hem de hastalıklara karşı tedavi geliştirmek ve erken teşhiste biyosensör olarak kullanmak için elzemdir. Virüsler, konak canlının mekanizmalarını kullanan organizmalar olarak, bu tür RNA’ları kendi genomlarında barındırır ve proteinler gibi immün sistem gözetimi altında kalmadan görev yapan RNA moleküllerini, hücrenin yolaklarını kendi lehlerine manipüle etmede kullanırlar. Viral hastalıkları moleküler düzeyde anlamanın yanı sıra, virüslerin aşı geliştirmede ve gen terapide vektör olarak kullanılmalarından dolayı viral kökenli RNA’ların fonksiyonlarını araştırmak giderek önem kazanmaktadır. Bu derlemede viral mikroRNA’lar ve halkasal circRNA’lar hariç tutularak, başlıca virüslerin ürettiği kodlamayan RNA’lardan ve hücredeki etki mekanizmalarından bahsedilmiştir. Ayrıca bu tür RNA’ların keşfi, yapısının belirlenmesi, karakterizasyonu ve fonksiyonunun anlaşılması için kullanılan yöntemlere değinilmiştir. Virüslerin konak hücreyi enfekte ederken kullandıkları bu küçük moleküllerin görevlerini ve etkilerini anlamak, bize RNA moleküllerinin düzenleyici ajanlar olarak ne kadar yaygın biçimde kullanıldığını göstermesi açısından önemlidir.

Keywords

Virüs, Herpesvirüs, Uzun kodlamayan RNA, RNA protein etkileşimi, RNA omik teknikleri

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