Ribo-uORF – a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling

Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5′ untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs). Although uORFs are prevalent in eukaryotic mRNAs and modulate the translation of downstream CDSs, a comprehensive resource for uORFs is currently lacking. Researchers at the Guangdong Academy of Agricultural Sciences have developed Ribo-uORF to serve as a comprehensive functional resource for uORF analysis based on ribosome profiling (Ribo-seq) data. Ribo-uORF currently supports six species: human, mouse, rat, zebrafish, fruit fly, and worm. Ribo-uORF includes 501 554 actively translated uORFs and 107 914 upstream translation initiation sites (uTIS), which were identified from 1495 Ribo-seq and 77 quantitative translation initiation sequencing (QTI-seq) datasets, respectively. The researchers also developed mRNAbrowse to visualize items such as uORFs, cis-regulatory elements, genetic variations, eQTLs, GWAS-based associations, RNA modifications, and RNA editing. Ribo-uORF provides a very intuitive web interface for conveniently browsing, searching, and visualizing uORF data. Finally, uORFscan and UTR5var were developed in Ribo-uORF to precisely identify uORFs and analyze the influence of genetic mutations on uORFs using user-uploaded datasets. Ribo-uORF should greatly facilitate studies of uORFs and their roles in mRNA translation and posttranscriptional control of gene expression.

Ribo-uORF workflow overview

Ribo-uORF provides comprehensive information on uORFs (upstream open read frames) generated from 1495 Ribo-seq and 77 QTI-seq datasets. Ribo-uORF integrates an additional 18 related datasets, such as IRES, G-quadruplex secondary structures, eQTL and RNA modification datasets, from sequence annotations and public databases. All results generated by Ribo-uORF are deposited in a MySQL database and are displayed in several convenient modules on web pages. Meanwhile, we developed many convenient tools in Ribo-uORF to facilitate users visualize the data in the database and to identify uORFs from their Ribo-seq data.

Availability – http://rnainformatics.org.cn/RiboUORF