ArticleMethods in enzymology2009
High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly.
Article in Methods in enzymology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 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
59 citing papers in PubMed, 77 citations in OpenAlex.
- MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals.PLoS biology · 2024Article
- Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments.Viruses · 2024Article
- Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging.RNA (New York, N.Y.) · 2023Article
- SHAPE to Probe RNA Structure and RNA-Protein Interactions In Vitro.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.Molecular cell · 2020Article
- Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES.Nucleic acids research · 2020Article
- Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing.Nucleic acids research · 2020Article
- Transcriptional and translational S-box riboswitches differ in ligand-binding properties.The Journal of biological chemistry · 2020Article
- Article
- Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS.Molecular microbiology · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome.Cold Spring Harbor perspectives in biology · 2018Review
- A guide to large-scale RNA sample preparation.Analytical and bioanalytical chemistry · 2018Review
- Visible Light-Induced Radical Mediated DNA Damage.Photochemistry and photobiology · 2018Article
- Synergistic SHAPE/Single-Molecule Deconvolution of RNA Conformation under Physiological Conditions.Biophysical journal · 2018Article
- New tRNA contacts facilitate ligand binding in aProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Light-activated chemical probing of nucleobase solvent accessibility inside cells.Nature chemical biology · 2018Article
- SHAPE analysis of theRNA (New York, N.Y.) · 2017Article
- A structural map of oncomiR-1 at single-nucleotide resolution.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA folds to form complex structures vital to many cellular functions. Proteins facilitate RNA folding at both the secondary and tertiary structure levels. An absolute prerequisite for understanding RNA folding and ribonucleoprotein (RNP) assembly reactions is a complete understanding of the RNA structure at each stage of the folding or assembly process. Here we provide a guide for comprehensive and high-throughput analysis of RNA secondary and tertiary structure using SHAPE and hydroxyl radical footprinting. As an example of the strong and sometimes surprising conclusions that can emerge from high-throughput analysis of RNA folding and RNP assembly, we summarize the structure of the bI3 group I intron RNA in four distinct states. Dramatic structural rearrangements occur in both secondary and tertiary structure as the RNA folds from the free state to the active, six-component, RNP complex. As high-throughput and high-resolution approaches are applied broadly to large protein-RNA complexes, other proteins previously viewed as making simple contributions to RNA folding are also likely to be found to exert multifaceted, long-range, cooperative, and nonadditive effects on RNA folding. These protein-induced contributions add another level of control, and potential regulatory function, in RNP complexes.
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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.