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Updated: Jun 23, 2026
08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
Sarah E Calvo1, David J Pagliarini, Vamsi K Mootha
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Summary
Upstream open reading frames (uORFs) significantly reduce protein expression, impacting thousands of mammalian genes. Variations in uORFs can also influence human disease and phenotype.
Area of Science:
- Molecular Biology
- Genetics
- Gene Regulation
Background:
- Upstream open reading frames (uORFs) are common mRNA elements found in the 5' untranslated region (UTR).
- Their global impact on protein expression has not been previously investigated.
- uORFs are present in approximately half of human and mouse transcripts.
Purpose of the Study:
- To investigate the global impact of uORFs on protein expression.
- To quantify the effect of uORFs on downstream open reading frame (ORF) protein levels.
- To identify genetic variations affecting uORFs and their potential role in human disease.
Main Methods:
- Analysis of 11,649 matched mRNA and protein measurements from four mammalian studies.
- Reporter construct experiments to test the function of 25 selected uORFs.
- Identification of polymorphisms altering uORF presence in human genes.
Main Results:
- uORFs significantly correlate with reduced protein expression of downstream ORFs (30-80% reduction).
- uORFs have a modest impact on mRNA levels.
- Polymorphisms altering uORF presence were identified in 509 human genes.
- Five uORF-altering mutations in disease-associated genes were found to dramatically silence protein expression.
Conclusions:
- uORFs are a widespread regulatory mechanism influencing protein output for thousands of mammalian genes.
- Variation in uORFs can significantly impact protein levels and potentially contribute to human phenotype and disease.
- uORFs represent a critical layer of gene expression regulation with implications for human health.
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