ArticleRNA (New York, N.Y.)2011
Correlating SHAPE signatures with three-dimensional RNA structures.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.Molecular cell · 2021Article
- Predicting RNA SHAPE scores with deep learning.RNA biology · 2020Article
- Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.Nucleic acids research · 2020Article
- DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.Bioinformatics (Oxford, England) · 2019Article
- reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction.BMC bioinformatics · 2019Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.The journal of physical chemistry letters · 2018Article
- Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer.Biochemistry · 2017Article
- Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.Nucleic acids research · 2017Article
- Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution.Wiley interdisciplinary reviews. RNA · 2017Review
- Cotranscriptional folding of a riboswitch at nucleotide resolution.Nature structural & molecular biology · 2016Article
- Data-directed RNA secondary structure prediction using probabilistic modeling.RNA (New York, N.Y.) · 2016Article
- Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).Methods (San Diego, Calif.) · 2016Article
- Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.Nucleic acids research · 2016Article
- Article
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8 authors.
Funding
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structural properties of the respective nucleotide, such as different types of base-pairing, stacking, and phosphate-backbone interactions. We find that the RNA SHAPE signal is strongly correlated with cis-Watson-Crick/Watson-Crick base-pairing and is to a remarkable degree not dependent on other structural properties with the exception of stacking. We subsequently generated probabilistic models that estimate the likelihood that a residue with a given SHAPE score participates in base-pairing. We show that several models that take SHAPE scores of adjacent residues into account perform better in predicting base-pairing compared with individual SHAPE scores. This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification.
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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.