ArticleBMC genomics2012
Evaluating our ability to predict the structural disruption of RNA by SNPs.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed, 58 citations in OpenAlex.
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- A spotter's guide to SNPtic exons: The common splice variants underlying some SNP-phenotype correlations.Molecular genetics & genomic medicine · 2022Article
- Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry.Genome biology · 2021Article
- Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka.Viruses · 2021Article
- Secondary Structural Model of MALAT1 Becomes Unstructured in Chronic Myeloid Leukemia and Undergoes Structural Rearrangement in Cervical Cancer.Non-coding RNA · 2021Article
- Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB.NAR genomics and bioinformatics · 2020Article
- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- Resistance to paclitaxel is associated with a variant of the gene BCL2 in multiple tumor types.NPJ precision oncology · 2019Article
- A Functional riboSNitch in the 3' Untranslated Region ofThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2018Article
- Genetic variants in mRNA untranslated regions.Wiley interdisciplinary reviews. RNA · 2018Review
- Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure.RNA (New York, N.Y.) · 2018Article
- Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.BMC bioinformatics · 2018Article
- Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.Biophysical journal · 2017Article
- Effects of Pathogenic Variations in the Human Rhodopsin Gene (hRHO) on the Predicted Accessibility for a Lead Candidate Ribozyme.Investigative ophthalmology & visual science · 2017Article
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The structure of RiboNucleic Acid (RNA) has the potential to be altered by a Single Nucleotide Polymorphism (SNP). Disease-associated SNPs mapping to non-coding regions of the genome that are transcribed into RiboNucleic Acid (RNA) can potentially affect cellular regulation (and cause disease) by altering the structure of the transcript. We performed a large-scale meta-analysis of Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) data, which probes the structure of RNA. We found that several single point mutations exist that significantly disrupt RNA secondary structure in the five transcripts we analyzed. Thus, every RNA that is transcribed has the potential to be a "RiboSNitch;" where a SNP causes a large conformational change that alters regulatory function. Predicting the SNPs that will have the largest effect on RNA structure remains a contemporary computational challenge. We therefore benchmarked the most popular RNA structure prediction algorithms for their ability to identify mutations that maximally affect structure. We also evaluated metrics for rank ordering the extent of the structural change. Although no single algorithm/metric combination dramatically outperformed the others, small differences in AUC (Area Under the Curve) values reveal that certain approaches do provide better agreement with experiment. The experimental data we analyzed nonetheless show that multiple single point mutations exist in all RNA transcripts that significantly disrupt structure in agreement with the predictions.
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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.