ArticleBiochemistry2014
Standardization of RNA chemical mapping experiments.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing.bioRxiv : the preprint server for biology · 2026Article
- A conserved class of viral RNA structures regulates translation reinitiation through dynamic ribosome interactions.Cell reports · 2025Article
- Minimization of the E. coli ribosome, aided and optimized by community science.Nucleic acids research · 2024Article
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Retron reverse transcriptase termination and phage defense are dependent on host RNase H1.Nucleic acids research · 2022Article
- Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.Nature communications · 2022Article
- An expanded class of histidine-accepting viral tRNA-like structures.RNA (New York, N.Y.) · 2021Article
- Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity.Science advances · 2021Article
- Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.bioRxiv : the preprint server for biology · 2021Article
- Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses.RNA (New York, N.Y.) · 2021Article
- Folding heterogeneity in the essential human telomerase RNA three-way junction.RNA (New York, N.Y.) · 2020Article
- Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.Biochemistry · 2020Article
- An RNA pseudoknot stimulates HTLV-1RNA (New York, N.Y.) · 2020Article
- Automated Design of Diverse Stand-Alone Riboswitches.ACS synthetic biology · 2019Article
- RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.Bioinformatics (Oxford, England) · 2018Article
- Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels.Nature communications · 2018Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Blind prediction of noncanonical RNA structure at atomic accuracy.Science advances · 2018Article
- Hidden Structural Modules in a Cooperative RNA Folding Transition.Cell reports · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Chemical mapping experiments offer powerful information about RNA structure but currently involve ad hoc assumptions in data processing. We show that simple dilutions, referencing standards (GAGUA hairpins), and HiTRACE/MAPseeker analysis allow rigorous overmodification correction, background subtraction, and normalization for electrophoretic data and a ligation bias correction needed for accurate deep sequencing data. Comparisons across six noncoding RNAs stringently test the proposed standardization of dimethyl sulfate (DMS), 2'-OH acylation (SHAPE), and carbodiimide measurements. Identification of new signatures for extrahelical bulges and DMS "hot spot" pockets (including tRNA A58, methylated in vivo) illustrates the utility and necessity of standardization for quantitative RNA mapping.
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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.