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Insertions and deletions in the RNA sequence-structure map.

Nora S Martin1,2, Sebastian E Ahnert3,4

  • 1Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.

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|October 5, 2021
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Summary
This summary is machine-generated.

This study expands RNA sequence-structure maps to include insertions and deletions, revealing similar robustness and mutation patterns across all genetic changes. These findings impact understanding of evolutionary rates.

Keywords:
RNA secondary structuregenotype–phenotype maprobustnesssequence–structure map

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Area of Science:

  • Evolutionary biology
  • Computational biology
  • RNA structure prediction

Background:

  • Genotype-phenotype maps are crucial for evolutionary models, linking genetic changes to fitness effects.
  • The RNA sequence-to-structure map is vital for functional RNA evolution, but existing models often neglect insertions and deletions.
  • Understanding the impact of insertions and deletions on RNA structure is essential for comprehensive evolutionary modeling.

Purpose of the Study:

  • To extend the RNA sequence-structure map to incorporate single nucleotide insertions and deletions.
  • To quantify the structural effects of insertions and deletions by generalizing robustness and mutation probability definitions.
  • To investigate the similarities and differences in structural effects between substitutions, insertions, and deletions in RNA.

Main Methods:

  • Utilized the RNAshapes concept to model RNA secondary structures.
  • Generalized existing definitions for robustness and non-neutral mutation probabilities to include insertions and deletions.
  • Analyzed correlations between robustness to substitutions, insertions, and deletions.
  • Examined the frequency of structural changes following different types of mutations.

Main Results:

  • Found striking similarities in robustness and mutation probabilities between substitutions, insertions, and deletions.
  • Robustness to substitutions is correlated with robustness to insertions and, in most cases, deletions.
  • Frequent structural changes after substitutions were also common for insertions and deletions, consistent with suboptimal folding leading to transitions.
  • Observed similarities in both genotypic (individual sequences) and phenotypic (structure averages) robustness and mutation probabilities.

Conclusions:

  • The inclusion of insertions and deletions reveals conserved patterns in RNA sequence-structure relationships across mutation types.
  • The findings suggest that RNA evolution dynamics may be more unified than previously thought, irrespective of mutation type.
  • These results have implications for understanding the rates of neutral and non-neutral evolution in RNA populations.