ArticleNature protocols2015
Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.
Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 299 papers.
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Who cites it
299 citing papers in PubMed.
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- SARS-CoV-2 5'-UTR stem-loops activate the antiviral protein oligoadenylate synthetase 1 (OAS1).The Journal of biological chemistry · 2026Article
- An IRES-like cis-acting element located within the EV-A71 coding region drives translation independent of the 5'-IRES and modulates viral fitness through regulated binding of viral RNA to 3D polymerase.Journal of virology · 2026Article
- Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells.Cell reports · 2026Article
- Sequence and structure of protein binding sites in RNA impact biomolecular condensates.Molecular biology of the cell · 2026Article
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- Mapping the rRNA methylome reveals contributions of methyltransferases to ribosome function and antibiotic sensitivity.bioRxiv : the preprint server for biology · 2026Article
- Mapping RNA structure assembly and remodeling in biomolecular condensates.bioRxiv : the preprint server for biology · 2026Article
239 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs. This protocol describes the experimental steps, implemented over 3 d, that are required to perform SHAPE probing and to construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots and provides useful troubleshooting information. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures and visualize probable and alternative helices, often in under 1 d. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and entire transcriptomes.
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