ArticleeLife2015
Consistent global structures of complex RNA states through multidimensional chemical mapping.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 74 citations in OpenAlex.
- FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing.bioRxiv : the preprint server for biology · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Black-box data: a new paradigm for biomedicine in the AI era.Chemical science · 2026Review
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- FRET-guided modeling of nucleic acids.Nucleic acids research · 2024Article
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- Chemical crosslinking and ligation methods for in vivo analysis of RNA structures and interactions.Methods in enzymology · 2023Article
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.Nature communications · 2022Article
- Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.Nature communications · 2022Article
- Review
- Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.Biochemistry · 2021Article
- Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.bioRxiv : the preprint server for biology · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Cooperativity and Allostery in RNA Systems.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments.Molecular cell · 2020Article
- Small molecule-RNA targeting: starting with the fundamentals.Chemical communications (Cambridge, England) · 2020Article
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.
Indexed as
Identifiers
What OpenQuestion holds
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.