ArticleGenetics2000
Comparative sequence analysis and patterns of covariation in RNA secondary structures.
Article in Genetics, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Predicting RNA and Protein:RNA Complexes with AlphaFold: Possibilities, Limitations, and Practical Guidelines.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Identification of conserved RNA secondary structures in human respiratory syncytial virus A (hRSV A).NAR genomics and bioinformatics · 2025Article
- Deep generalizable prediction of RNA secondary structure via base pair motif energy.Nature communications · 2025Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Computational modelling of flavivirus dynamics: The ins and outs.Methods (San Diego, Calif.) · 2021Review
- Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia.Viruses · 2020Article
- Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats.Journal of molecular cell biology · 2019Article
- The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology.PloS one · 2019Article
- Translation: The Universal Structural Core of Life.Molecular biology and evolution · 2018Article
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
- A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.Molecular cell · 2016Article
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- Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity.Biophysical journal · 2014Article
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- Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa.BMC evolutionary biology · 2011Article
- The role of the effective population size in compensatory evolution.Genome biology and evolution · 2011Article
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- Accurate and efficient reconstruction of deep phylogenies from structured RNAs.Nucleic acids research · 2009Article
- Compensatory evolution in RNA secondary structures increases substitution rate variation among sites.Molecular biology and evolution · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.
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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.