ReviewAccounts of chemical research2021
SHAPE Directed Discovery of New Functions in Large RNAs.
Review in Accounts of chemical research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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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.
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.
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Who cites it
40 citing papers in PubMed, 57 citations in OpenAlex.
- Article
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Article
- Integrative In Silico and In Vitro Screening of Low Molecular Weight Compounds Targeting SARS-CoV-2 RNA Elements.Chembiochem : a European journal of chemical biology · 2025Article
- Mapping of HOCl-oxidized RNA identifies abasic sites as major damage and oxidation product of oxoNature communications · 2025Article
- Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.bioRxiv : the preprint server for biology · 2025Article
- A small cationic probe for accurate, punctate discovery of RNA tertiary structure.bioRxiv : the preprint server for biology · 2025Article
- TheiScience · 2025Article
- Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.RNA (New York, N.Y.) · 2025Article
- Ligand-binding pockets in RNA and where to find them.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Druggable Transcriptome Project: From Chemical Probes to Precision Medicines.Biochemistry · 2025Review
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.Nature communications · 2025Article
- Visualizing RNA structure ensembles by single-molecule correlated chemical probing.Current opinion in structural biology · 2024Review
- Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.Genomics, proteomics & bioinformatics · 2024Article
- Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform fromMicrobiology spectrum · 2024Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.bioRxiv : the preprint server for biology · 2024Article
- RNAvigate: efficient exploration of RNA chemical probing datasets.Nucleic acids research · 2024Article
- Minimization of the E. coli ribosome, aided and optimized by community science.Nucleic acids research · 2024Article
- Small molecule approaches to targeting RNA.Nature reviews. Chemistry · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
RNA lies upstream of nearly all biology and functions as the central conduit of information exchange in all cells. RNA molecules encode information both in their primary sequences and in complex structures that form when an RNA folds back on itself. From the time of discovery of mRNA in the late 1950s until quite recently, we had only a rudimentary understanding of RNA structure across vast regions of most messenger and noncoding RNAs. This deficit is now rapidly being addressed, especially by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, mutational profiling (MaP), and closely related platform technologies that, collectively, create chemical microscopes for RNA. These technologies make it possible to interrogate RNA structure, quantitatively, at nucleotide resolution, and at large scales, for entire mRNAs, noncoding RNAs, and viral RNA genomes. By applying comprehensive structure probing to diverse problems, we and others are showing that control of biological function mediated by RNA structure is ubiquitous across prokaryotic and eukaryotic organisms.Work over the past decade using SHAPE-based analyses has clarified key principles. First, the method of RNA structure probing matters. SHAPE-MaP, with its direct and one-step readout that probes nearly every nucleotide by reaction at the 2'-hydroxyl, gives a more detailed and accurate readout than alternatives. Second, comprehensive chemical probing is essential. Focusing on fragments of large RNAs or using meta-gene or statistical analyses to compensate for sparse data sets misses critical features and often yields structure models with poor predictive power. Finally, every RNA has its own internal
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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.