ArticlePLoS biology2010
mRNA secondary structures fold sequentially but exchange rapidly in vivo.
Article in PLoS biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
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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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Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
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- A roadmap for rRNA folding and assembly during transcription.Trends in biochemical sciences · 2021Review
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- Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency.Molecules (Basel, Switzerland) · 2019Article
- Challenges and approaches to predicting RNA with multiple functional structures.RNA (New York, N.Y.) · 2018Review
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs.Nature communications · 2018Article
- Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure.RNA (New York, N.Y.) · 2018Article
- Genetic Polymorphism of miR-196a-2 is Associated with Bone Mineral Density (BMD).International journal of molecular sciences · 2017Article
- RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing.Genomics, proteomics & bioinformatics · 2017Review
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- The 5΄ UTR of the type I toxin ZorO can both inhibit and enhance translation.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
RNAs adopt defined structures to perform biological activities, and conformational transitions among alternative structures are critical to virtually all RNA-mediated processes ranging from metabolite-activation of bacterial riboswitches to pre-mRNA splicing and viral replication in eukaryotes. Mechanistic analysis of an RNA folding reaction in a biological context is challenging because many steps usually intervene between assembly of a functional RNA structure and execution of a biological function. We developed a system to probe mechanisms of secondary structure folding and exchange directly in vivo using self-cleavage to monitor competition between mutually exclusive structures that promote or inhibit ribozyme assembly. In previous work, upstream structures were more effective than downstream structures in blocking ribozyme assembly during transcription in vitro, consistent with a sequential folding mechanism. However, upstream and downstream structures blocked ribozyme assembly equally well in vivo, suggesting that intracellular folding outcomes reflect thermodynamic equilibration or that annealing of contiguous sequences is favored kinetically. We have extended these studies to learn when, if ever, thermodynamic stability becomes an impediment to rapid equilibration among alternative RNA structures in vivo. We find that a narrow thermodynamic threshold determines whether kinetics or thermodynamics govern RNA folding outcomes in vivo. mRNA secondary structures fold sequentially in vivo, but exchange between adjacent secondary structures is much faster in vivo than it is in vitro. Previous work showed that simple base-paired RNA helices dissociate at similar rates in vivo and in vitro so exchange between adjacent structures must occur through a different mechanism, one that likely involves facilitation of branch migration by proteins associated with nascent transcripts.
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What OpenQuestion 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 OpenQuestion graph.