ArticlePloS one2012
Structural constraints identified with covariation analysis in ribosomal RNA.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Variable Region Sequences Influence 16S rRNA Performance.Microbiology spectrum · 2023Article
- bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.RNA (New York, N.Y.) · 2023Article
- The how and why of lncRNA function: An innate immune perspective.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Principles for targeting RNA with drug-like small molecules.Nature reviews. Drug discovery · 2018Review
- Translation: The Universal Structural Core of Life.Molecular biology and evolution · 2018Article
- COMPASS: the COMPletely Arbitrary Sequence Simulator.Bioinformatics (Oxford, England) · 2017Article
- In-cell SHAPE uncovers dynamic interactions between the untranslated regions of the foot-and-mouth disease virus RNA.Nucleic acids research · 2017Article
- Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes.Scientific reports · 2016Article
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- Article
- Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.Nucleic acids research · 2015Article
- Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.RNA (New York, N.Y.) · 2015Article
- Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.PLoS computational biology · 2015Article
- In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- RNA structural constraints in the evolution of the influenza A virus genome NP segment.RNA biology · 2014Article
- Specificity between lactobacilli and hymenopteran hosts is the exception rather than the rule.Applied and environmental microbiology · 2013Article
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Authors and funding
4 authors.
Funding
Abstract
Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab's new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab's Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair.
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