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Related Experiment Video

Updated: Jan 2, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Accurate annotation of human protein-coding small open reading frames.

Thomas F Martinez¹, Qian Chu², Cynthia Donaldson²

¹Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA. tmartinez@salk.edu.

Nature Chemical Biology

|December 11, 2019

Summary

This summary is machine-generated.

Researchers identified thousands of functional human small open reading frames (smORFs) using an improved workflow. These smORFs encode microproteins and can serve as antigens, expanding our understanding of the human genome.

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Last Updated: Jan 2, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Area of Science:

Genomics
Proteomics
Molecular Biology

Background:

Small open reading frames (smORFs) are increasingly recognized as functional genes.
Current proteogenomic and Ribo-seq methods have limitations in comprehensively identifying translated smORFs.
Accurate annotation of smORFs is crucial for understanding their role in human biology.

Purpose of the Study:

To develop and validate an improved workflow for confident annotation of translated human smORFs.
To assess the functional potential and biological relevance of newly identified smORFs.
To explore smORFs as a source of human antigens.

Main Methods:

Integration of de novo transcriptome assembly with enhanced Ribo-seq strategies.
Implementation of additional validation steps for smORF annotation.
Evolutionary conservation analysis and detection of smORF-derived peptides on human leukocyte antigen (HLA) complexes.

Main Results:

Thousands of previously unannotated translated smORFs were confidently identified.
Hundreds of smORF-encoded microproteins show evidence of evolutionary conservation, suggesting functionality.
smORFs are regulated during cellular stress and their peptides are presented on HLA molecules.

Conclusions:

The developed workflow significantly enhances the accuracy and comprehensiveness of smORF annotation.
A substantial number of functional human smORFs and their encoded microproteins have been discovered.
These findings reveal smORFs as a vital source of functional genes and potential antigens, opening new avenues for research.