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The energy-spectrum of bicompatible sequences.
Fenix W Huang1, Christopher L Barrett1,2, Christian M Reidys3,4
1Biocomplexity Institute & Initiative, University of Virginia, 995 Research Park Blvd., Suite 400, Charlottesville, VA, 22911, USA.
Algorithms for Molecular Biology : AMB
|June 2, 2021
Summary
Bicompatible RNA sequences enable phenotypic transitions, crucial for evolution. This study introduces a sampler to identify sequences with specific structural properties, revealing a distinct signature in riboswitches.
Area of Science:
- Computational Biology
- Bioinformatics
- Molecular Biology
Background:
- RNA secondary structures define sequence phenotypes, influencing neutral evolution.
- Bicompatible sequences, compatible with two structures, are key to RNA phenotypic transitions.
- RNA riboswitches exemplify bicompatible sequences in biological systems.
Purpose of the Study:
- To develop a computational tool for sampling bicompatible RNA sequences.
- To analyze the structural properties facilitating RNA phenotypic transitions.
- To investigate the sequence signatures of biologically relevant bicompatible sequences, such as those in riboswitches.
Main Methods:
- A dynamic programming-based Boltzmann sampler for bicompatible sequences.
- A novel topological framework to understand sequence sampler complexity.
- Algorithm development for sampling sequences with minimized topological parameters.
Main Results:
- A polynomial-time sequence sampler for bicompatible sequences, dependent on topological parameters.
- Identification of a novel topological framework for analyzing loop relations.
- Application of the sampler to study established riboswitches.
Conclusions:
- Pairs of RNA structures must possess specific properties to enable phenotypic transitions.
- Randomly paired structures are unlikely to support such transitions.
- Riboswitch sequences exhibit a unique signature, offering a new criterion for identifying sequences under evolutionary pressure.
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