ArticlePLoS computational biology2013
Evolutionary evidence for alternative structure in RNA sequence co-variation.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.Nucleic acids research · 2026Article
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
- LinearAlifold: Linear-time consensus structure prediction for RNA alignments.Journal of molecular biology · 2024Article
- RNA structure in alternative splicing regulation: from mechanism to therapy.Acta biochimica et biophysica Sinica · 2024Review
- RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical journal · 2023Article
- Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map.Journal of the Royal Society, Interface · 2022Article
- Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition.Methods and protocols · 2022Article
- Graph deep learning locates magnesium ions in RNA.QRB discovery · 2022Article
- LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- LinearTurboFold: Linear-Time Global Prediction of Conserved Structures for RNA Homologs with Applications to SARS-CoV-2.bioRxiv : the preprint server for biology · 2021Article
- Evolutionary conservation of RNA sequence and structure.Wiley interdisciplinary reviews. RNA · 2021Review
- Variation Profile of the Orthotospovirus Genome.Pathogens (Basel, Switzerland) · 2020Article
- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination.ACS omega · 2019Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
- Article
- Challenges and approaches to predicting RNA with multiple functional structures.RNA (New York, N.Y.) · 2018Review
- Structural divergence creates new functional features in alphavirus genomes.Nucleic acids research · 2018Article
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3 authors.
Funding
Abstract
Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. We set out to characterize the evolutionary co-variation supporting alternative conformations in riboswitches to determine the extent to which alternative secondary structures are conserved. We found strong co-variation support for the terminator, P1, and anti-terminator stems in the purine riboswitch by extending alignments to include terminator sequences. When we performed Boltzmann suboptimal sampling on purine riboswitch sequences with terminators we found that these sequences appear to have evolved to favor specific alternative conformations. We extended our analysis of co-variation to classic alignments of group I/II introns, tRNA, and other classes of riboswitches. In a majority of these RNAs, we found evolutionary evidence for alternative conformations that are compatible with the Boltzmann suboptimal ensemble. Our analyses suggest that alternative conformations are selected for and thus likely play functional roles in even the most structured of RNAs.
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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.