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

Abstract

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. We developed Ribo-uORF (http://rnainformatics.org.cn/RiboUORF) 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. We 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.

Translational regulation by uORFs and start codon selection stringency

“…Not all uORFs are regulatory. A vast number of translated uORFs have been identified in ribosome profiling experiments (for example, see Ingolia et al 2009 , 2011 ; Chew et al 2016 ; Johnstone et al 2016 ; Zhang et al 2018 ; Takahashi et al 2020 ; Chothani et al 2022 ; Liu et al 2023 ); however, it is likely that many of these uORFs simply reduce the number of ribosomes that translate the mORF but do not alter translation of the mORF in response to changing conditions. Here, we focus on several well-characterized examples of regulatory uORFs and describe the varied ways by which they control mORF translation.…”

Treatability of the KMT2-Associated Neurodevelopmental Disorders Using Antisense Oligonucleotide-Based Treatments

“…Although no ASO based on this strategy has yet been approved as a drug, this approach has already been tested for several genes in vitro and in vivo [76,106]. To date, KMT2C, KMT2D, KMT2E, and ASH1L have been reported to contain uORFs [91,92] (Table 3). Regulation of these elements using steric blocking ASOs could be employed to increase the levels of the WT protein of the respective disorder and improve the phenotype (Figure 5(a)).…”

“…: alternative splicing; PE: poison exon; UTR: untranslated region; NATs: naturally occurring antisense transcripts; GoF: gain of function. The additional symbols indicate in which publications the features have been reported: ǂ, Felker et al[89]; * , Lim et al[90]; ⊢, Liu et al[91]; and ¶, Mittal et al[92].…”

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

“…The third, LncBook ( 14 ), a curated database of human lncRNAs, reports improved multi-omics annotations including, for the first time, any experimentally-supported small proteins that they encode. Two further databases focus on uORFs: uORFDB ( 15 ) returns and expands on its original literature focus to now cover, sequences and sequence variants across 13 eukaryotes, while the new Ribo_uORF ( 16 ) provides rich annotations of uORFs identified by ribosome profiling across six animal species. Elsewhere, popular returning databases include AnimalTFDB which doubles its content to cover 183 animals ( 17 ); mirDIP, the aggregative database of microRNA–target interactions ( 18 ) and UTRdb, the database of richly annotated 5′ and 3′ untranslated regions of mRNA ( 19 ).…”