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Updated: Aug 19, 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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Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling
Qi Liu1,2,3,4, Xin Peng1,2,3,4, Mengyuan Shen1,2,3,4
1Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Nucleic Acids Research
|November 28, 2022
Summary
A new resource, Ribo-uORF, catalogs over 500,000 translated upstream open reading frames (uORFs) and 100,000 upstream translation initiation sites (uTIS) across six species. This tool aids in understanding uORF functions in gene expression regulation.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Upstream open reading frames (uORFs) are regulatory elements in the 5' untranslated region of mRNAs.
- uORFs influence the translation of downstream coding sequences (CDSs).
- A comprehensive functional resource for uORFs was previously unavailable.
Purpose of the Study:
- To develop a comprehensive functional resource for analyzing uORFs.
- To provide a platform for exploring uORF data across multiple species.
- To facilitate research on the role of uORFs in gene expression.
Main Methods:
- Utilized ribosome profiling (Ribo-seq) and quantitative translation initiation sequencing (QTI-seq) data.
- Developed the Ribo-uORF web resource and associated tools (mRNAbrowse, uORFscan, UTR5var).
- Integrated data from 1495 Ribo-seq and 77 QTI-seq datasets.
Main Results:
- Cataloged 501,554 actively translated uORFs and 107,914 upstream translation initiation sites (uTIS).
- The resource supports analysis in human, mouse, rat, zebrafish, fruit fly, and worm.
- Developed visualization tools for uORFs, genetic variations, and regulatory elements.
Conclusions:
- Ribo-uORF serves as a valuable functional resource for uORF research.
- The platform enables precise identification and analysis of uORFs and their associated genetic variations.
- Facilitates studies on mRNA translation and posttranscriptional gene regulation.
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