ArticleJournal of virology2013
Long-distance RNA-RNA interactions in the coronavirus genome form high-order structures promoting discontinuous RNA synthesis during transcription.
Article in Journal of virology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed.
- A potential RNA-RNA distal interaction competing with a functional pseudoknot in the 3'-untranslated region of SARS-like coronaviruses.Nucleic acids research · 2026Article
- Naturally occurring mutations in replication proteins of a small RNA virus that alter the number, sizes, and relative abundances of subgenomic RNAs.PLoS pathogens · 2026Article
- Extra gene coding capacity of SARS-CoV-2 provides a virus engineering platform for in vitro and in vivo applications.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A stable subgenomic reporter coronavirus enables transcriptional profiling of bystander cells.The Journal of general virology · 2026Article
- Review
- A fusion ORF3a-E subgenomic RNA involved in SARS-CoV-2 infection efficacy by influencing cellular protein synthesis.Frontiers in immunology · 2025Article
- Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion.PLoS biology · 2025Article
- Identification and Characterization of Novel Serpentoviruses in Viperid and Elapid Snakes.Viruses · 2024Article
- Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2.International journal of molecular sciences · 2024Article
- Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations.Virology journal · 2023Article
- Classification, replication, and transcription ofFrontiers in microbiology · 2023Review
- Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing.Frontiers in genetics · 2023Article
- Subgenomic RNAs and Their Encoded Proteins Contribute to the Rapid Duplication of SARS-CoV-2 and COVID-19 Progression.Biomolecules · 2022Review
- In vivo structure and dynamics of the SARS-CoV-2 RNA genome.Nature communications · 2021Article
- Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.Science advances · 2021Article
- The Recombination Potential between SARS-CoV-2 and MERS-CoV from Cross-Species Spill-over Infections.Journal of epidemiology and global health · 2021Article
- Article
- The SARS-CoV-2 subgenome landscape and its novel regulatory features.Molecular cell · 2021Article
- Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection.Cell reports · 2021Article
- Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Coronavirus (CoV) transcription requires a high-frequency recombination process that links newly synthesized minus-strand subgenomic RNA copies to the leader region, which is present only once, at the 5' end of the genome. This discontinuous RNA synthesis step is based on the complementarity between the transcription-regulating sequences (TRSs) at the leader region and those preceding each gene in the nascent minus-strand RNA. Furthermore, the template switch requires the physical proximity of RNA genome domains located between 20,000 and 30,000 nucleotides apart. In this report, it is shown that the efficacy of this recombination step is promoted by novel additional long-distance RNA-RNA interactions between RNA motifs located close to the TRSs controlling the expression of each gene and their complementary sequences mapping close to the 5' end of the genome. These interactions would bring together the motifs involved in the recombination process. This finding indicates that the formation of high-order RNA structures in the CoV genome is necessary to control the expression of at least the viral N gene. The requirement of these long-distance interactions for transcription was shown by the engineering of CoV replicons in which the complementarity between the newly identified sequences was disrupted. Furthermore, disruption of complementarity in mutant viruses led to mutations that restored complementarity, wild-type transcription levels, and viral titers by passage in cell cultures. The relevance of these high-order structures for virus transcription is reinforced by the phylogenetic conservation of the involved RNA motifs in CoVs.
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