ArticlePLoS computational biology2015
Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.
Article in PLoS computational biology, 2015. 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, 39 citations in OpenAlex.
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 2021Article
- Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets.NAR genomics and bioinformatics · 2021Article
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Machine learning a model for RNA structure prediction.NAR genomics and bioinformatics · 2020Article
- HIV-1 Lethality and Loss of Env Protein Expression Induced by Single Synonymous Substitutions in the Virus Genome Intronic-Splicing Silencer.Journal of virology · 2020Article
- Supersized Ribosomal RNA Expansion Segments in Asgard Archaea.Genome biology and evolution · 2020Article
- IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.Nucleic acids research · 2020Article
- Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.Biochemistry · 2020Article
- SHAPE Probing Reveals Human rRNAs Are Largely Unfolded in Solution.Biochemistry · 2019Article
- Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies.Biochemistry · 2019Article
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Article
- In-cell RNA structure probing with SHAPE-MaP.Nature protocols · 2018Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
- A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs.Frontiers in molecular biosciences · 2018Article
- Article
- Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA.RNA (New York, N.Y.) · 2017Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
Abstract
Discovery and characterization of functional RNA structures remains challenging due to deficiencies in de novo secondary structure modeling. Here we describe a dynamic programming approach for model-free sequence comparison that incorporates high-throughput chemical probing data. Based on SHAPE probing data alone, ribosomal RNAs (rRNAs) from three diverse organisms--the eubacteria E. coli and C. difficile and the archeon H. volcanii--could be aligned with accuracies comparable to alignments based on actual sequence identity. When both base sequence identity and chemical probing reactivities were considered together, accuracies improved further. Derived sequence alignments and chemical probing data from protein-free RNAs were then used as pseudo-free energy constraints to model consensus secondary structures for the 16S and 23S rRNAs. There are critical differences between these experimentally-informed models and currently accepted models, including in the functionally important neck and decoding regions of the 16S rRNA. We infer that the 16S rRNA has evolved to undergo large-scale changes in base pairing as part of ribosome function. As high-quality RNA probing data become widely available, structurally-informed sequence alignment will become broadly useful for de novo motif and function discovery.
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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.