ArticleJournal of virology2007
An RNA stem-loop within the bovine coronavirus nsp1 coding region is a cis-acting element in defective interfering RNA replication.
Article in Journal of virology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 69 citations in OpenAlex.
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- 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
- In vivo structure and dynamics of the SARS-CoV-2 RNA genome.Nature communications · 2021Article
- An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies.Gene reports · 2021Review
- De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures.Nucleic acids research · 2021Article
- Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies.Biochemical Society transactions · 2021Review
- Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2.Virus evolution · 2021Article
- Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome.Evolutionary bioinformatics online · 2021Article
- A synthetic defective interfering SARS-CoV-2.PeerJ · 2021Article
- SARS-CoV-2: A critical review of its history, pathogenesis, transmission, diagnosis and treatment.Biosafety and health · 2020Review
- Coronavirus Pandemic-Therapy and Vaccines.Biomedicines · 2020Review
- Coronaviruses: An Updated Overview of Their Replication and Pathogenesis.Methods in molecular biology (Clifton, N.J.) · 2020Review
- Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.Genome research · 2019Article
- Interplay between the Poly(A) Tail, Poly(A)-Binding Protein, and Coronavirus Nucleocapsid Protein Regulates Gene Expression of Coronavirus and the Host Cell.Journal of virology · 2018Article
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4 authors at 1 institution in 1 country.
Funding
Abstract
Higher-order cis-acting RNA replication structures have been identified in the 3'- and 5'-terminal untranslated regions (UTRs) of a bovine coronavirus (BCoV) defective interfering (DI) RNA. The UTRs are identical to those in the viral genome, since the 2.2-kb DI RNA is composed of only the two ends of the genome fused between an internal site within the 738-nucleotide (nt) 5'-most coding region (the nsp1, or p28, coding region) and a site just 4 nt upstream of the 3'-most open reading frame (ORF) (the N gene). The joined ends of the viral genome in the DI RNA create a single continuous 1,635-nt ORF, 288 nt of which come from the 738-nt nsp1 coding region. Here, we have analyzed features of the 5'-terminal 288-nt portion of the nsp1 coding region within the continuous ORF that are required for DI RNA replication. We observed that (i) the 5'-terminal 186 nt of the nsp1 coding region are necessary and sufficient for DI RNA replication, (ii) two Mfold-predicted stem-loops within the 186-nt sequence, named SLV (nt 239 to 310) and SLVI (nt 311 to 340), are supported by RNase structure probing and by nucleotide covariation among closely related group 2 coronaviruses, and (iii) SLVI is a required higher-order structure for DI RNA replication based on mutation analyses. The function of SLV has not been evaluated. We conclude that SLVI within the BCoV nsp1 coding region is a higher-order cis-replication element for DI RNA and postulate that it functions similarly in the viral genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.