ArticleNature2015
Structural imprints in vivo decode RNA regulatory mechanisms.
Article in Nature, 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 467 papers.
What it found
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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
467 citing papers in PubMed.
- Structure-driven function of plant lncRNAs: conserved RNA architectures in transcriptional and post-transcriptional regulation.RNA biology · 2026Review
- Multiomic proximity labeling in vivo by D-amino-acid-activated peroxidase reaction.Nature chemical biology · 2026Article
- FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing.bioRxiv : the preprint server for biology · 2026Article
- Glutathione-Responsive Acyl-Modifications for Targeted RNA Decaging and Prolonged Protein Synthesis.Angewandte Chemie (International ed. in English) · 2026Article
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.Nature communications · 2026Article
- A nucleic acid labeling chemistry reveals surface DNA on exosomes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- mNature communications · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Long Noncoding RNA Isoform Specificity and Chemical Modification on tRNA-Derived Fragments Leading to Divergent Functions.The American journal of pathology · 2026Review
- NAP-seq for full-length noncapped RNA sequencing.Nature protocols · 2026Review
- RNA Aptamers and Epitranscriptomics: Charting Unexplored Territories in RNA Biology.Molecular diagnosis & therapy · 2026Review
- Dynamic m⁶A methylation during bovine preadipocyte differentiation and functional implication of the m⁶A writer METTL14.BMC genomics · 2026Article
- A comprehensive analysis of the use of nucleoside analogues in RNA therapeutics.Journal of translational medicine · 2026Review
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Systematic identification of variant-specific RNA structure-small molecule interactions exemplified by RNA G-quadruplexes.Nature communications · 2026Article
- Optimized tRNA structure-seq reveals robust tRNA secondary structures inbioRxiv : the preprint server for biology · 2026Article
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
407 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
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- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
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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.