ArticleBiochemistry2021
Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.
Article in Biochemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 36 citations in OpenAlex.
- Optimized tRNA structure-seq reveals robust tRNA secondary structures inbioRxiv : the preprint server for biology · 2026Article
- Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RAP-RNA: A Methodological Approach to Study Base-Pairing Between Endogenous RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.Nucleic acids research · 2025Article
- Template switching enables chemical probing of native RNA structures.RNA (New York, N.Y.) · 2024Article
- KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions.Nature biotechnology · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.Biophysical journal · 2024Article
- RNAvigate: efficient exploration of RNA chemical probing datasets.Nucleic acids research · 2024Article
- Single-cell probing of RNA structure.Nature methods · 2024Article
- 2'-OH as a universal handle for studying intracellular RNAs.Cell chemical biology · 2024Review
- Aqueous Activation of RNA 2'-OH for Conjugation with Amines and Thiols.Bioconjugate chemistry · 2024Article
- A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.Nucleic acids research · 2023Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- Probing the dynamic RNA structurome and its functions.Nature reviews. Genetics · 2023Review
- Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications.JACS Au · 2023Review
- Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Dissecting Functional Biological Interactions Using Modular RNA Nanoparticles.Molecules (Basel, Switzerland) · 2022Review
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Higher-order structure governs function for many RNAs. However, discerning this structure for large RNA molecules in solution is an unresolved challenge. Here, we present SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions. A bifunctional small molecule is used to chemically link proximal nucleotides in an RNA structure. The RNA cross-link site is then encoded into complementary DNA (cDNA) in a single, direct step using an engineered reverse transcriptase that "jumps" across cross-linked nucleotides. The resulting cDNAs contain a deletion relative to the native RNA sequence, which can be detected by sequencing, that indicates the sites of cross-linked nucleotides. SHAPE-JuMP measures RNA tertiary structure proximity concisely across large RNA molecules at nanometer resolution. SHAPE-JuMP is especially effective at measuring interactions in multihelix junctions and loop-to-helix packing, enables modeling of the global fold for RNAs up to several hundred nucleotides in length, facilitates ranking of structural models by consistency with through-space restraints, and is poised to enable solution-phase structural interrogation and modeling of complex RNAs.
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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.