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A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation [dataset2]

ABSTRACT: Various SARS-CoV-2 viruses have caused the COVID-19 pandemic world-wide. As the viruses evolve different mutations along their genomes, these mutations can impact virus RNA structures and their phenotypes. Here we probe the RNA structures across Wuhan, alpha, beta, delta and omnicron strains of the SARS-CoV-2 viruses. We observe that while the mutations impact RNA structures, it is not the main source of RNA structure changes (RBPs?). Structurally conserved structures are enriched for both long and short RNA pair-wise interactions. We identified a conserved 17kb long range interaction that decreases the virus fitness when mutated. Additionally, this interaction binds to ADAR1 to alter editing levels on the virus. These studies reveal the importance of RNA structures along virus genomes to facilitate virus infectivity.

ORGANISM(S): Chlorocebus

PROVIDER: GSE302215 | GEO | 2025/08/01

REPOSITORIES: GEO

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A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation [dataset1]

Project description:Various SARS-CoV-2 viruses have caused the COVID-19 pandemic world-wide. As the viruses evolve different mutations along their genomes, these mutations can impact virus RNA structures and their phenotypes. Here we probe the RNA structures across Wuhan, alpha, beta, delta and omnicron strains of the SARS-CoV-2 viruses. We observe that while the mutations impact RNA structures, it is not the main source of RNA structure changes (RBPs?). Structurally conserved structures are enriched for both long and short RNA pair-wise interactions. We identified a conserved 17kb long range interaction that decreases the virus fitness when mutated. Additionally, this interaction binds to ADAR1 to alter editing levels on the virus. These studies reveal the importance of RNA structures along virus genomes to facilitate virus infectivity.

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A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation [SPLASH]

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A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation

Project description:Long-range RNA-RNA pairing impacts the genome structure and function of SARS-CoV-2 variants. To understand structure and function relationships of different SARS-CoV-2 variants that have emerged during the COVID-19 pandemic, we performed high throughput structure probing and modelling of the genomic structures of the wildtype (WT), Alpha, Beta, Delta and Omicron variants of the SARS-CoV-2. We observed that genomes of SARS-CoV-2 variants are generally structurally conserved, and that single nucleotide variations (SNVs) and interactions with RNA binding proteins (RBPs) can impact RNA structures across the viruses. Importantly, using proximity ligation sequencing, we identified many conserved ultra-long-range RNA-RNA interactions, including one that spans more than 17kb in both the WT virus and Omicron variant. We showed that mutations that disrupt this 17kb long-range interacting structure reduce virus fitness at late stages of its infection cycle, while compensatory mutations partially restore virus fitness. Additionally, we showed that this ultra-long-range RNA-RNA interaction binds directly to ADAR1 to alter the RNA editing levels on the viral genome. These studies deepen our understanding of RNA structures in SARS-CoV-2 genome and their ability to interact with host factors to facilitate virus infectivity.

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