ArticleJournal of virology2003
Stem-loop III in the 5' untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication.
Article in Journal of virology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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68 citing papers in PubMed, 86 citations in OpenAlex.
- Identification and comparison of RNA structures in 5'- and 3'-terminal genomic regions across four coronavirus genera by SHAPE analysis.Virology journal · 2026Article
- Characterization of the binding features between SARS-CoV-2 5'-proximal transcripts of genomic RNA and nucleocapsid proteins.RNA biology · 2025Review
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- Tiny but mighty: Diverse functions of uORFs that regulate gene expression.Computational and structural biotechnology journal · 2024Review
- Regulation viral RNA transcription and replication by higher-order RNA structures within the nsp1 coding region of MERS coronavirus.Scientific reports · 2024Article
- Targeting the conserved coronavirus octamer motif GGAAGAGC is a strategy for the development of coronavirus vaccine.Virology journal · 2023Article
- High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.Nucleic acids research · 2023Article
- Biological characterization of coronavirus noncanonical transcripts in vitro and in vivo.Virology journal · 2023Article
- Classification, replication, and transcription ofFrontiers in microbiology · 2023Review
- Evolution of naturally arising SARS-CoV-2 defective interfering particles.Communications biology · 2022Article
- Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.Microbiology and molecular biology reviews : MMBR · 2022Review
- Prevention and Control of Porcine Epidemic Diarrhea: The Development of Recombination-Resistant Live Attenuated Vaccines.Viruses · 2022Review
- An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies.Gene reports · 2021Review
- Dengue virus-free defective interfering particles have potent and broad anti-dengue virus activity.Communications biology · 2021Article
- De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures.Nucleic acids research · 2021Article
- Secondary structure of the SARS-CoV-2 5'-UTR.RNA biology · 2021Article
- Article
- Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome.Evolutionary bioinformatics online · 2021Article
- Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2.Virus evolution · 2021Article
- A synthetic defective interfering SARS-CoV-2.PeerJ · 2021Article
8 more citing papers are in PubMed but not listed here.
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4 authors at 1 institution in 1 country.
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Abstract
Higher-order structures in the 5' untranslated region (UTR) of plus-strand RNA viruses are known in many cases to function as cis-acting elements in RNA translation, replication, or transcription. Here we describe evidence supporting the structure and a cis-acting function in defective interfering (DI) RNA replication of stem-loop III, the third of four predicted higher-order structures mapping within the 210-nucleotide (nt) 5' UTR of the 32-kb bovine coronavirus (BCoV) genome. Stem-loop III maps at nt 97 through 116, has a calculated free energy of -9.1 kcal/mol in the positive strand and -3.0 kcal/mol in the negative strand, and has associated with it beginning at nt 100 an open reading frame (ORF) potentially encoding an 8-amino-acid peptide. Stem-loop III is presumed to function in the positive strand, but its strand of action has not been established. Stem-loop III (i) shows phylogenetic conservation among group 2 coronaviruses and appears to have a homolog in coronavirus groups 1 and 3, (ii) has in all coronaviruses for which sequence is known a closely associated short, AUG-initiated intra-5' UTR ORF, (iii) is supported by enzyme structure-probing evidence in BCoV RNA, (iv) must maintain stem integrity for DI RNA replication in BCoV DI RNA, and (v) shows a positive correlation between maintenance of the short ORF and maximal DI RNA accumulation in BCoV DI RNA. These results indicate that stem-loop III in the BCoV 5' UTR is a cis-acting element for DI RNA replication and that its associated intra-5' UTR ORF may function to enhance replication. It is postulated that these two elements function similarly in the virus genome.
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