Identification of Small Open Reading Frame-encoded Proteins in the Human Genome

Area of Science:

• Genomics
• Proteomics
• Molecular Biology

Background:

• The human genome project aimed to identify all protein-coding genes, with ~20,500 currently annotated.
• Proteogenomics studies have recently predicted thousands of novel protein-coding regions, including small open reading frame (sORF)-encoded proteins (SEPs), often from untranslated regions.

Purpose of the Study:

• To develop a strategy for identifying reliable novel protein-coding regions and SEPs.
• To expand the current catalog of human protein-coding genes and investigate their potential roles in diseases.

Main Methods:

• An integrated proteogenomics workflow was developed using publicly available ribosome profiling and global proteomics datasets.
• Recurrent observations across multiple samples were used to establish protein-coding evidence.
• Bioinformatics analysis and ribosome footprint data were utilized for predictions.

Main Results:

• Protein translation was predicted from 4008 ORFs based on recurrent ribosome occupancy signals.
• 825 SEPs were identified using proteomics data.
• Some novel protein-coding regions were located in genome-wide association studies (GWAS) loci linked to traits and diseases.
• SEPs peptides are presented by MHC-I complexes, similar to canonical proteins.

Conclusions:

• The study expands the catalog of human protein-coding genes by identifying numerous novel SEPs.
• These findings warrant further experimental studies to elucidate the cellular functions and disease relevance of these newly identified proteins.