Dataset Information

In silico identification of conserved cis-acting RNA elements in the SARS-CoV-2 genome.

ABSTRACT: Aim:The aim of this study was to computationally predict conserved RNA sequences and structures known as cis-acting RNA elements (CREs) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Materials & methods:Bioinformatics tools were used to analyze and predict CREs by obtaining viral sequences from available databases. Results:Computational analysis revealed the presence of RNA stem-loop structures within the 3' end of the ORF1ab region analogous to previously identified SARS-CoV genomic packaging signals. Alignment-based RNA secondary structure predictions of the 5' end of the SARS-CoV-2 genome also identified conserved CREs. Conclusion:These CREs may be potential vaccine and/or antiviral therapeutic targets; however, further studies are warranted to confirm their roles in the SARS-CoV-2 life cycle.

SUBMITTER: Alhatlani BY

PROVIDER: S-EPMC7507811 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

<i>In silico</i> identification of conserved <i>cis</i>-acting RNA elements in the SARS-CoV-2 genome.

Alhatlani Bader Y BY

Future virology 20200701 7

<h4>Aim</h4>The aim of this study was to computationally predict conserved RNA sequences and structures known as <i>cis</i>-acting RNA elements (CREs) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome.<h4>Materials & methods</h4>Bioinformatics tools were used to analyze and predict CREs by obtaining viral sequences from available databases.<h4>Results</h4>Computational analysis revealed the presence of RNA stem-loop structures within the 3' end of the ORF1ab region analo ...[more]

PMID: 33005212

Similar Datasets

Project description:The emergence of a new coronavirus (CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for severe respiratory disease in humans termed coronavirus disease of 2019 (COVID-19), became a new global threat for health and the economy. The SARS-CoV-2 genome is about a 29,800-nucleotide-long plus-strand RNA that can form functionally important secondary and higher-order structures called cis-acting RNA elements. These elements can interact with viral proteins, host proteins, or other RNAs and be involved in regulating translation and replication processes of the viral genome and encapsidation of the virus. However, the cis-acting RNA elements and their biological roles in SARS-CoV-2 as well as their comparative analysis in the closely related viral genome have not been well explored, which is very important to understand the molecular mechanism of viral infection and pathogenies. In this study, we used a bioinformatics approach to identify the cis-acting RNA elements in the SARS-CoV-2 genome. Initially, we aligned the full genomic sequence of six different CoVs, and a phylogenetic analysis was performed to understand their evolutionary relationship. Next, we predicted the cis-acting RNA elements in the SARS-CoV-2 genome using the structRNAfinder tool. Then, we annotated the location of these cis-acting RNA elements in different genomic regions of SARS-CoV-2. After that, we analyzed the sequence conservation patterns of each cis-acting RNA element among the six CoVs. Finally, the presence of cis-acting RNA elements across different CoV genomes and their comparative analysis was performed. Our study identified 12 important cis-acting RNA elements in the SARS-CoV-2 genome; among them, Corona_FSE, Corona_pk3, and s2m are highly conserved across most of the studied CoVs, and Thr_leader, MAT2A_D, and MS2 are uniquely present in SARS-CoV-2. These RNA structure elements can be involved in viral translation, replication, and encapsidation and, therefore, can be potential targets for better treatment of COVID-19. It is imperative to further characterize these cis-acting RNA elements experimentally for a better mechanistic understanding of SARS-CoV-2 infection and therapeutic intervention.

Dataset Information

In silico identification of conserved cis-acting RNA elements in the SARS-CoV-2 genome.

Publications

<i>In silico</i> identification of conserved <i>cis</i>-acting RNA elements in the SARS-CoV-2 genome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets