ArticleMethods (San Diego, Calif.)2016
Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
Article in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Noncoding RNAs and the phytochemical economy: Molecular regulators of secondary metabolism in medicinal plants.Biochemistry and biophysics reports · 2026Review
- Article
- Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.RNA (New York, N.Y.) · 2025Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- Short tandem repeat variants are possibly associated with RNA secondary structure and gene expression.PloS one · 2025Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution.Nature communications · 2024Article
- A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A riboswitch separated from its ribosome-binding site still regulates translation.Nucleic acids research · 2023Article
- The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing.Life (Basel, Switzerland) · 2022Review
- Web-based platform for analysis of RNA folding from high throughput chemical probing data.Nucleic acids research · 2022Article
- An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch.Nature communications · 2022Article
- The RNA structurome in the asexual blood stages of malaria pathogenRNA biology · 2021Article
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
- A noncoding RNA modulator potentiates phenylalanine metabolism in mice.Science (New York, N.Y.) · 2021Article
- An exon-biased biophysical approach and NMR spectroscopy define the secondary structure of a conserved helical element within the HOTAIR long non-coding RNA.Journal of structural biology · 2021Article
- Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.Molecular cell · 2021Article
- Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations.Non-coding RNA · 2021Review
- Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.Nucleic acids research · 2020Article
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5 authors.
Funding
Abstract
RNA molecules adopt a wide variety of structures that perform many cellular functions, including, among others, catalysis, small molecule sensing, and cellular defense. Our ability to characterize, predict, and design RNA structures are key factors for understanding and controlling the biological roles of RNAs. Fortunately, there has been rapid progress in this area, especially with respect to experimental methods that can characterize RNA structures in a high throughput fashion using chemical probing and next-generation sequencing. Here, we describe one such method, selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), which measures nucleotide resolution flexibility information for RNAs in vitro and in vivo. We outline the process of designing and performing a SHAPE-Seq experiment and describe methods for using experimental SHAPE-Seq data to restrain computational folding algorithms to generate more accurate predictions of RNA secondary structure. We also provide a number of examples of SHAPE-Seq reactivity spectra obtained in vitro and in vivo and discuss important considerations for performing SHAPE-Seq experiments, both in terms of collecting and analyzing data. Finally, we discuss improvements and extensions of these experimental and computational techniques that promise to deepen our knowledge of RNA folding and function.
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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 Socratic graph.