ArticleJournal of the Royal Society, Interface2021
Insertions and deletions in the RNA sequence-structure map.
Article in Journal of the Royal Society, Interface, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites.Nucleic acids research · 2026Article
- Association of leptin and insulin-like growth factor-1 gene polymorphisms with milk production and reproductive traits in Indonesian Friesian Holstein cattle.Veterinary world · 2026Article
- Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation.Molecular biology and evolution · 2024Article
- Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.PLoS computational biology · 2024Article
- The Boltzmann distributions of molecular structures predict likely changes through random mutations.Biophysical journal · 2023Article
- The non-deterministic genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2023Article
- Maximum mutational robustness in genotype-phenotype maps follows a self-similar blancmange-like curve.Journal of the Royal Society, Interface · 2023Article
- Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts.Life (Basel, Switzerland) · 2023Article
- The structure of genotype-phenotype maps makes fitness landscapes navigable.Nature ecology & evolution · 2022Article
- Life finds a way.Nature ecology & evolution · 2022Article
- Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map.Journal of the Royal Society, Interface · 2022Article
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Authors and funding
2 authors.
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Abstract
Genotype-phenotype maps link genetic changes to their fitness effect and are thus an essential component of evolutionary models. The map between RNA sequences and their secondary structures is a key example and has applications in functional RNA evolution. For this map, the structural effect of substitutions is well understood, but models usually assume a constant sequence length and do not consider insertions or deletions. Here, we expand the sequence-structure map to include single nucleotide insertions and deletions by using the RNAshapes concept. To quantify the structural effect of insertions and deletions, we generalize existing definitions for robustness and non-neutral mutation probabilities. We find striking similarities between substitutions, deletions and insertions: robustness to substitutions is correlated with robustness to insertions and, for most structures, to deletions. In addition, frequent structural changes after substitutions also tend to be common for insertions and deletions. This is consistent with the connection between energetically suboptimal folds and possible structural transitions. The similarities observed hold both for genotypic and phenotypic robustness and mutation probabilities, i.e. for individual sequences and for averages over sequences with the same structure. Our results could have implications for the rate of neutral and non-neutral evolution.
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