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Updated: Jul 30, 2025
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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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uORF4u: a tool for annotation of conserved upstream open reading frames
Artyom A Egorov1, Gemma C Atkinson1
1Department of Experimental Medical Science, Lund University, Sölvegatan 19, Lund, 223 62, Sweden.
Bioinformatics (Oxford, England)
|May 15, 2023
Summary
Identifying functional upstream open reading frames (uORFs) is challenging. This study presents a tool to find conserved uORFs using evolutionary conservation, aiding in the annotation of these regulatory elements.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Upstream open reading frames (uORFs) regulate gene expression in prokaryotes and eukaryotes.
- Identifying functional uORFs is difficult due to their small size (<100 codons).
- Genome-wide sequencing data for uORF identification is not available for most species.
Purpose of the Study:
- To develop a computational tool for annotating conserved uORFs.
- To enable the identification of functional uORFs in species lacking experimental data.
- To leverage evolutionary conservation for predicting novel uORFs.
Main Methods:
- The tool, uORF4u, analyzes 5' upstream sequences for conserved small ORFs.
- It can process user-defined proteins or sets of nucleotide sequences.
- It utilizes evolutionary conservation to predict functional uORFs.
Main Results:
- The tool identifies conserved uORFs within specified sequences.
- It generates publication-quality figures including multiple sequence alignments and sequence logos.
- Predicted conserved uORFs are annotated graphically.
Conclusions:
- Conserved uORF annotation is a viable strategy for discovering functional uORFs.
- The developed tool facilitates the identification of regulatory elements across diverse species.
- This approach aids in understanding gene regulation through conserved uORFs.
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