ArticleNature protocols2013
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 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
62 citing papers in PubMed.
- Direct circRNA-mRNA Binding Controls mRNA Fate: A New Mechanism for circRNAs.Non-coding RNA · 2025Review
- Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.Nucleic acids research · 2025Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Article
- Targeting and engineering long non-coding RNAs for cancer therapy.Nature reviews. Genetics · 2024Review
- Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq.Nucleic acids research · 2024Article
- Alternative splicing and related RNA binding proteins in human health and disease.Signal transduction and targeted therapy · 2024Review
- Blood transcriptome differentiates clinical clusters for asthma.The World Allergy Organization journal · 2024Article
- Probing RNA structural landscapes acrossFrontiers in microbiology · 2024Article
- Survey of the binding preferences of RNA-binding proteins to RNA editing events.Genome biology · 2022Article
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Review
- Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine.Non-coding RNA · 2021Review
- Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments.NAR genomics and bioinformatics · 2021Article
- Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.The Journal of biological chemistry · 2020Article
- Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB.NAR genomics and bioinformatics · 2020Article
- Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions.Nucleic acids research · 2020Article
- Review
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
RNA structure is important for RNA function and regulation, and there is growing interest in determining the RNA structure of many transcripts. Here we provide a detailed protocol for the parallel analysis of RNA structure (PARS) for probing RNA secondary structures genome-wide. In this method, enzymatic footprinting is coupled to high-throughput sequencing to provide secondary structure data for thousands of RNAs simultaneously. The entire experimental protocol takes ∼5 d to complete, and sequencing and data analysis take an additional 6-8 d. PARS was developed using the yeast genome as proof of principle, but its approach should be applicable to probing RNA structures from different transcriptomes and structural dynamics under diverse solution conditions.
Indexed as
Identifiers
23558785What 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.