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Updated: Mar 21, 2026
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
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FScanR reveals widespread programmed ribosomal frameshifting consistent with neutral evolution in a ciliate model
Juan Yang1, Yuhao Yang2, Ruanlin Wang3
1Marine College, Shandong University, Weihai 264209, China.
European Journal of Protistology
|March 19, 2026
Summary
Programmed ribosomal frameshifting (PRF) is a vital gene expression mechanism. A new tool, FScanR, effectively identifies PRF events, revealing its widespread occurrence and evolutionary dynamics in single-celled eukaryotes.
Area of Science:
- Molecular Biology
- Genomics
- Computational Biology
Background:
- Programmed ribosomal frameshifting (PRF) enables synthesis of multiple proteins from one mRNA.
- Assessing PRF's scope is challenging with traditional genomic/proteomic data.
Purpose of the Study:
- Develop a computational tool, FScanR, to identify PRF events accurately.
- Characterize PRF events and their evolutionary dynamics in eukaryotes.
Main Methods:
- Developed FScanR to compare in-frame and out-of-frame sequences with peptide data.
- Systematically analyzed PRF events across phylogenetically distinct organisms, focusing on euplotid ciliates.
Main Results:
- FScanR detects PRF events in diverse organisms, characterizing surrounding sequence features.
- Euplotid ciliates show widespread PRF, with no bias in flanking GC content or inter-site distance.
- PRF-associated genes are involved in critical processes like phosphorylation and metabolic regulation.
- PRF in euplotids occurs across genes with varied expression and appears under neutral selection.
Conclusions:
- FScanR is valuable for discovering recoding mechanisms.
- PRF is evolutionarily dynamic in single-celled eukaryotes, impacting key physiological processes.
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