A Comprehensive Analysis of cis-Acting RNA Elements in the SARS-CoV-2 Genome by a Bioinformatics Approach

Abstract

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.

To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

“…2). Besides pseudoknots 3_6 and 3_3, three-way junction 3_5, and stem-loop 2_2, alternatives may include two 3_8 pseudoknots, 23,28 a different 3_3 pseudoknot (with Stem 2 formed by Stem 3 loop and 3′ end), 23 and a two-stem 2_1 24,25 (Table 2 and Fig. S13).…”

“…Here we focus on better understanding of this FSE conformational landscape using a combination of complementary graph-based modeling and chemical reactivity experiments. Already, several groups have explored FSE structure by modeling, [21][22][23][24][25] in vivo Selective 2 -Hydroxyl Acylation by Primer Extension (SHAPE) 26,27 and DMS structure probing experiments, 20,[28][29][30][31][32][33][34] NMR, 35 Cryo-EM, 29,36 and other biophysical mutational profiling and scanning experiments. 15,37,38 Many have characterized the FSE as a 3-stem H-type pseudoknot with colinear Stems 1 and 2 intertwined via a pseudoknot and perpendicular Stem 3.…”

In Vitro Inhibitory Analysis of Rationally Designed siRNAs against MERS-CoV Replication in Huh7 Cells

“…The secondary structure of a given viral RNA can be predicted and designed rationally using multiple techniques. Many bioinformatics tools for prediction and designing have been designed, developed and are being successfully used to identify new biological insights pertaining to RNA structures [ 50 ]. siRNAs can silence an unknown number of unintended genes due to the promiscuous entry of siRNAs into endogenous miRNA machinery and the recognition of complementarity to seed regions [ 51 ].…”

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

“…However, depending on the modeling software and experimental technique, alternative secondary structures have been offered for SARS-CoV-2, both pseudoknotted and unknotted (see below). 20 , 23 − 25 , 28 − 34 …”