ArticleNature communications2013
Determination of in vivo RNA structure in low-abundance transcripts.
Article in Nature communications, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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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.
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Who cites it
73 citing papers in PubMed, 131 citations in OpenAlex.
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Profiling RNA G-Quadruplexes In vivo.Current protocols · 2025Article
- TDP-43 binds to RNA G-quadruplex structure and regulates mRNA stability and translation.Nucleic acids research · 2025Article
- Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in Arabidopsis thaliana Genes.Molecular biology and evolution · 2025Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Regulation of bacterial gene expression by non-coding RNA: It is all about time!Cell chemical biology · 2024Review
- Late consolidation of rRNA structure during co-transcriptional assembly inbioRxiv : the preprint server for biology · 2024Article
- Article
- Beyond transcription: compelling open questions in plant RNA biology.The Plant cell · 2023Article
- Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association.The Plant cell · 2023Article
- How does precursor RNA structure influence RNA processing and gene expression?Bioscience reports · 2023Review
- RNA independent fragment partition method based on deep learning for RNA secondary structure prediction.Scientific reports · 2023Article
- Genome-wide analysis of theProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Development of RNA G-quadruplex (rG4)-targeting L-RNA aptamers by rG4-SELEX.Nature protocols · 2022Review
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
- The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome.PloS one · 2022Article
- In vivo architecture of the telomerase RNA catalytic core in Trypanosoma brucei.Nucleic acids research · 2021Article
- A noncoding RNA modulator potentiates phenylalanine metabolism in mice.Science (New York, N.Y.) · 2021Article
- Article
- In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.Genome biology · 2021Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA structure plays important roles in diverse biological processes. However, the structures of all but the few most abundant RNAs are presently unknown in vivo. Here we introduce DMS/SHAPE-LMPCR to query the in vivo structures of low-abundance transcripts. DMS/SHAPE-LMPCR achieves attomole sensitivity, a 100,000-fold improvement over conventional methods. We probe the structure of low-abundance U12 small nuclear RNA (snRNA) in Arabidopsis thaliana and provide in vivo evidence supporting our derived phylogenetic structure. Interestingly, in contrast to mammalian U12 snRNAs, the loop of the SLIIb in U12 snRNA is variable among plant species, and DMS/SHAPE-LMPCR determines it to be unstructured. We reveal the effects of proteins on 25S rRNA, 5.8S rRNA and U12 snRNA structure, illustrating the critical importance of mapping RNA structure in vivo. Our universally applicable method opens the door to identifying and exploring the specific structure-function relationships of the multitude of low-abundance RNAs that prevail in living cells.
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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.