ArticleNature protocols2016
Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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Who cites it
111 citing papers in PubMed.
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
- Multiomic proximity labeling in vivo by D-amino-acid-activated peroxidase reaction.Nature chemical biology · 2026Article
- Nitro Reduction-Based RNA Control and Ultrafast Release.Angewandte Chemie (International ed. in English) · 2026Article
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
- Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.Nature communications · 2026Article
- APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.Nature protocols · 2026Review
- MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.Genomics, proteomics & bioinformatics · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Accessibility in proteins and RNAs interactions prediction with machine learning: are we overlooking non-experts?Briefings in bioinformatics · 2026Review
- Three-dimensional structure of the palbociclib-HIV TAR complex.Nucleic acids research · 2026Article
- The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.Nucleic acids research · 2026Article
- The efficacy of oligonucleotide-based gene therapeutics in gene silencing.Theranostics · 2026Review
- DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.RNA biology · 2025Article
- SHAPE-Based Chemical Probes for Studying preQACS chemical biology · 2025Article
- diPaRIS: Dynamic and Interpretable Protein-RNA Interactions Prediction With U-Shaped Network and Novel Structure Encoding.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Decoding the interactions and functions of non-coding RNA with artificial intelligence.Nature reviews. Molecular cell biology · 2025Review
- PaRPI predicts RNA-Protein interactions from cross-protocol and cross-batch RNA-binding protein datasets.Communications biology · 2025Article
- A circularly permuted CasRx platform for efficient, site-specific RNA editing.Nature biotechnology · 2025Article
- Article
51 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3-modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ∼5 d, and the sequencing and bioinformatics data analysis take an additional 4-5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models.
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