ArticleProceedings of the National Academy of Sciences of the United States of America2011
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 235 papers, 1 of them a synthesis that pooled it.
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Who cites it
235 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops.Briefings in bioinformatics · 2022Pooled it
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- Reply to Chi et al.: DefiningProceedings of the National Academy of Sciences of the United States of America · 2026Article
- MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.Genomics, proteomics & bioinformatics · 2026Article
- mNature communications · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- NAP-seq for full-length noncapped RNA sequencing.Nature protocols · 2026Review
- Optimized tRNA structure-seq reveals robust tRNA secondary structures inbioRxiv : the preprint server for biology · 2026Article
- Targeting the UPR with Small Molecules: Emerging Strategies for Immune Regulation.Molecules (Basel, Switzerland) · 2026Review
- Interplay between RNA-protein interactions and RNA structures in gene regulation.FEBS open bio · 2026Review
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- SEISMICgraph: a web-based tool for RNA structure data visualization.Nucleic acids research · 2025Article
- Article
- Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress.bioRxiv : the preprint server for biology · 2025Article
- A comparative analysis of mRNA enrichment strategies and guidance for improving their efficiency.Scientific reports · 2025Article
- Article
- Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.Nucleic acids research · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- SINEUP RNA rescues molecular phenotypes associated with CHD8 suppression in autism spectrum disorder model systems.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
175 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within complex RNA populations. We have developed a high-throughput technique, SHAPE-Seq, that can simultaneously measure quantitative, single nucleotide-resolution secondary and tertiary structural information for hundreds of RNA molecules of arbitrary sequence. SHAPE-Seq combines selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry with multiplexed paired-end deep sequencing of primer extension products. This generates millions of sequencing reads, which are then analyzed using a fully automated data analysis pipeline, based on a rigorous maximum likelihood model of the SHAPE-Seq experiment. We demonstrate the ability of SHAPE-Seq to accurately infer secondary and tertiary structural information, detect subtle conformational changes due to single nucleotide point mutations, and simultaneously measure the structures of a complex pool of different RNA molecules. SHAPE-Seq thus represents a powerful step toward making the study of RNA secondary and tertiary structures high throughput and accessible to a wide array of scientific pursuits, from fundamental biological investigations to engineering RNA for synthetic biological systems.
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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.