ArticleNucleic acids research2018
Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 27 citations in OpenAlex.
- Long-distance RNA-RNA interactions shape dynamic RNA architectures and functional states in plant positive-strand RNA viruses.Frontiers in microbiology · 2026Review
- Selective Degradation of Cucumber Mosaic Virus RNA3 by Nonsense-Mediated Decay Benefits Viral Early Infection.Molecular plant pathology · 2025Article
- Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA.Biophysical journal · 2024Article
- Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus.Viruses · 2024Review
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Foliar Infiltration of Virus-Derived Small Hairpin RNAs Triggers the RNAi Mechanism against the Cucumber Mosaic Virus.International journal of molecular sciences · 2022Article
- A Mathematical Analysis of HDV Genotypes: From Molecules to Cells.Mathematics (Basel, Switzerland) · 2021Article
- Geographically distant isolates of the persistent southern tomato virus (STV) show very low genetic diversity in the putative coat protein gene.Virus genes · 2020Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- Variation Profile of the Orthotospovirus Genome.Pathogens (Basel, Switzerland) · 2020Article
- Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution.Frontiers in plant science · 2020Review
- Physical and Functional Analysis of Viral RNA Genomes by SHAPE.Annual review of virology · 2019Review
- A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation.Nucleic acids research · 2019Article
- In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs.Nucleic acids research · 2019Article
- Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts.mSphere · 2019Article
- dStruct: identifying differentially reactive regions from RNA structurome profiling data.Genome biology · 2019Article
- Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences.Open biology · 2018Review
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3' untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.