ArticleNature methods2014
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 445 papers.
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Who cites it
445 citing papers in PubMed, 696 citations in OpenAlex.
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- FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing.bioRxiv : the preprint server for biology · 2026Article
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- Modtector: ultra-fast modification signal mining on mapped sequencing reads.Bioinformatics (Oxford, England) · 2026Article
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- When circular RNAs meet the genome: CiR-loops as chromatin regulators and disease drivers.Nucleic acids research · 2026Review
- Mechanism underlying the high regulatory performance of the doxycycline riboswitch G12.Nature communications · 2026Article
- RNA regulation in plants.Science China. Life sciences · 2026Review
- Pnky lncRNA secondary structure maps identify functional regions that control neurogenesis in neural stem cells.Cell reports · 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
- Fine-scale structural information substantially improves mRNA therapeutic stability prediction.Molecular therapy. Nucleic acids · 2026Article
- Robust mammalian RNA localization elements are complex and multipartite.bioRxiv : the preprint server for biology · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Divergent RNA structures support accurate splicing of the SF3B1-sensitivebioRxiv : the preprint server for biology · 2026Article
- Conserved structural features of the lncRNA HOTAIR in breast cancer cells.bioRxiv : the preprint server for biology · 2026Article
385 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Many biological processes are RNA-mediated, but higher-order structures for most RNAs are unknown, which makes it difficult to understand how RNA structure governs function. Here we describe selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) that makes possible de novo and large-scale identification of RNA functional motifs. Sites of 2'-hydroxyl acylation by SHAPE are encoded as noncomplementary nucleotides during cDNA synthesis, as measured by massively parallel sequencing. SHAPE-MaP-guided modeling identified greater than 90% of accepted base pairs in complex RNAs of known structure, and we used it to define a new model for the HIV-1 RNA genome. The HIV-1 model contains all known structured motifs and previously unknown elements, including experimentally validated pseudoknots. SHAPE-MaP yields accurate and high-resolution secondary-structure models, enables analysis of low-abundance RNAs, disentangles sequence polymorphisms in single experiments and will ultimately democratize RNA-structure analysis.
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Registered trials
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.