ArticleNature protocols2015
Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.
Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 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.
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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
55 citing papers in PubMed, 106 citations in OpenAlex.
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Profiling RNA G-Quadruplexes In vivo.Current protocols · 2025Article
- DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via mNature communications · 2024Article
- Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect.Nature communications · 2023Article
- Rock, scissors, paper: How RNA structure informs function.The Plant cell · 2023Article
- In vivo secondary structural analysis of Influenza A virus genomic RNA.Cellular and molecular life sciences : CMLS · 2023Article
- RNA Structure Determination by High-Throughput Structural Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication.Computational and structural biotechnology journal · 2023Article
- Structure-seq of tRNAs and other short RNAs in droplets and in vivo.Methods in enzymology · 2023Article
- Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0.BMC biology · 2022Article
- RNA G-quadruplex structure contributes to cold adaptation in plants.Nature communications · 2022Article
- Web-based platform for analysis of RNA folding from high throughput chemical probing data.Nucleic acids research · 2022Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
- Incorporation of a FRET Pair into a Riboswitch RNA to Measure MgInternational journal of molecular sciences · 2022Article
- The RNA structurome in the asexual blood stages of malaria pathogenRNA biology · 2021Article
- Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry.Genome biology · 2021Article
- Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants.Biochemical Society transactions · 2021Review
- RNA architecture influences plant biology.Journal of experimental botany · 2021Review
- Chemical Approaches To Analyzing RNA Structure Transcriptome-Wide.Chembiochem : a European journal of chemical biology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structure-seq is a high-throughput and quantitative method that provides genome-wide information on RNA structure at single-nucleotide resolution. Structure-seq can be performed both in vivo and in vitro to study RNA structure-function relationships, RNA regulation of gene expression and RNA processing. Structure-seq can be carried out by an experienced molecular biologist with a basic understanding of bioinformatics. Structure-seq begins with chemical RNA structure probing under single-hit kinetics conditions. Certain chemical modifications, e.g., methylation of the Watson-Crick face of unpaired adenine and cytosine residues by dimethyl sulfate, result in a stop in reverse transcription. Modified RNA is then subjected to reverse transcription using random hexamer primers, which minimizes 3' end bias; reverse transcription proceeds until it is blocked by a chemically modified residue. Resultant cDNAs are amplified by adapter-based PCR and subjected to high-throughput sequencing, subsequently allowing retrieval of the structural information on a genome-wide scale. In contrast to classical methods that provide information only on individual transcripts, a single structure-seq experiment provides information on tens of thousands of RNA structures in ∼1 month. Although the procedure described here is for Arabidopsis thaliana seedlings in vivo, structure-seq is widely applicable, thereby opening new avenues to explore RNA structure-function relationships in living organisms.
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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 Socratic graph.