ArticleNucleic acids research2014
Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- Probing the dynamic RNA structurome and its functions.Nature reviews. Genetics · 2023Review
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
- "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates.Nucleic acids research · 2022Article
- Article
- Review
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Assaying RNA structure with LASER-Seq.Nucleic acids research · 2019Article
- Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays.Current protocols in nucleic acid chemistry · 2018Article
- Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk.Nucleic acids research · 2018Article
- RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing.Genomics, proteomics & bioinformatics · 2017Review
- Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.Nucleic acids research · 2017Article
- Managing the sequence-specificity of antisense oligonucleotides in drug discovery.Nucleic acids research · 2017Review
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
- Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments.Nature methods · 2017Article
- Structural transitions during large ribosomal subunit maturation analyzed by tethered nuclease structure probing in S. cerevisiae.PloS one · 2017Article
- Metrics for rapid quality control in RNA structure probing experiments.Bioinformatics (Oxford, England) · 2016Article
- Data-directed RNA secondary structure prediction using probabilistic modeling.RNA (New York, N.Y.) · 2016Article
- Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.Methods (San Diego, Calif.) · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hydroxyl Radical Footprinting (HRF) is a tried-and-tested method for analysis of the tertiary structure of RNA and for identification of protein footprints on RNA. The hydroxyl radical reaction breaks accessible parts of the RNA backbone, thereby allowing ribose accessibility to be determined by detection of reverse transcriptase termination sites. Current methods for HRF rely on reverse transcription of a single primer and detection by fluorescent fragments by capillary electrophoresis. Here, we describe an accurate and efficient massive parallel-sequencing-based method for probing RNA accessibility with hydroxyl radicals, called HRF-Seq. Using random priming and a novel barcoding scheme, we show that HRF-Seq dramatically increases the throughput of HRF experiments and facilitates the parallel analysis of multiple RNAs or experimental conditions. Moreover, we demonstrate that HRF-Seq data for the Escherichia coli 16S rRNA correlates well with the ribose accessible surface area as determined by X-ray crystallography and have a resolution that readily allows the difference in accessibility caused by exposure of one side of RNA helices to be observed.
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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.