Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

By Sarah E. Calvo, D. Pagliarini, Vamsi K. Mootha. Proceedings of the National Academy of Sciences of the United States of America, 2009

890 citations recorded by the source corpus.

Upstream ORFs (uORFs) are mRNA elements defined by a start codon in the 5′ UTR that is out-of-frame with the main coding sequence. Although uORFs are present in approximately half of human and mouse transcripts, no study has investigated their global impact on protein expression. Here, we report that uORFs correlate with significantly reduced protein expression of the downstream ORF, based on analysis of 11,649 matched mRNA and protein measurements from 4 published mammalian studies. Using reporter constructs to test 25 selected uORFs, we estimate that uORFs typically reduce protein expression by 30–80%, with a modest impact on mRNA levels. We additionally identify polymorphisms that alter uORF presence in 509 human genes. Finally, we report that 5 uORF-altering mutations, detected within genes previously linked to human diseases, dramatically silence expression of the downstream protein. Together, our results suggest that uORFs influence the protein expression of thousands of mammalian genes and that variation in these elements can influence human phenotype and disease.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/08728000f78195b3763e85aa29e0a5c4f2dcca5c

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Citations in the corpus

Comparative Analysis of Proteome and Transcriptome Variation in Mouse (2011, background): “The importance of these post-transcriptional processes is highlighted by a recent report showing that the presence of genetic variation in some of these post-transcriptional processes is associated with certain human diseases [34].”
Protein Synthesis Initiation in Eukaryotic Cells. (2018, background): “Given the findings that a high percentage of mRNAs contain either bona fide uORFs or uORFs with non-AUG start codons (Calvo et al. 2009), it is highly probable that both nonstandard and reinitiation mechanisms will turn out to be more common than currently thought (Hinnebusch et al.”
THE MECHANISM OF EUKARYOTIC TRANSLATION INITIATION AND PRINCIPLES OF ITS REGULATION (2010, background): “About 45–50% of mammalian genes (but only ∼ 13% of yeast genes) encode mRNAs that have at least one short uORF (typically”
RefSeq: an update on mammalian reference sequences (2013, background): “Although this revised policy will result in annotation of a larger number of predicted alternate proteins, some alternatively spliced transcripts will continue to be represented as noncoding because no ORF meets our quality criteria.”
Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. (2014, background): “The discovery of these surprising RNAs in the transcriptome as well as the existence of short upstream open reading frames (uORFs) in 50 leader regions (often referred to as 50 UTRs; Calvo et al., 2009; Wethmar et al., 2014) highlight the need for comparable direct, experimental maps of translation.”
Peptidomic discovery of short open reading frame-encoded peptides in human cells (2012, neutral): “Short open reading frames (sORFs) in the 5 ′ -untranslated region (5 ′ - UTR) of eukaryotic mRNAs (uORFs) are well studied 4-6 and some have been shown to produce detectable polypeptides 7, 8 .”
Translational regulation of gene expression during conditions of cell stress. (2010, background): “UORFs are present in 50% of protein coding transcripts (Calvo et al., 2009).”
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes (2011, background): “The first uORF in the Atf4 transcript is constitutively translated, and ribosomes then reinitiate at either the second uORF or the CDS (Calvo et al., 2009; Lu et al., 2004; Morris and Geballe, 2000) (Figure 6B).”
Roles for microRNAs in conferring robustness to biological processes. (2012, positive): “For example, AU-rich elements reduce the lifetime of an mRNA, upstream open reading frames and weak noncanonical Kozak sequences reduce the efficiency of translation initiation (Calvo et al., 2009), and rare codons and secondary structures slow translation elongation.”
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line (2010, background): “…and Macmillan Publishers Limited All rights reserved 1744-4292/10 www.molecularsystemsbiology.com & 2010 EMBO and Macmillan Publishers Limited Molecular Systems Biology 2010 1 uORFs can slow down the passage of the ribosome and subsequently reduce translation of the main ORF (Calvo et al, 2009).”
Translational Control in Cancer. (2018, background): “These mRNAs disproportionately encode proteins involved in pathways that allow cancer cells to adapt to their environment (Calvo et al. 2009; Andreev et al. 2015; Young andWek 2016;Wek 2018).”