What Can Ribo-seq and Proteomics Tell Us About the Non-canonical Proteome?

Overview

Journal bioRxiv

Date 2023 Jun 9

PMID 37292611

Authors

John R Prensner

Jennifer G Abelin

Leron W Kok

Karl R Clauser

Jonathan M Mudge

Jorge Ruiz-Orera

Michal Bassani-Sternberg

Eric W Deutsch

Sebastiaan van Heesch

Affiliations

Soon will be listed here.

Abstract

In Brief: The human genome encodes thousands of non-canonical open reading frames (ORFs) in addition to protein-coding genes. As a nascent field, many questions remain regarding non-canonical ORFs. How many exist? Do they encode proteins? What level of evidence is needed for their verification? Central to these debates has been the advent of ribosome profiling (Ribo-seq) as a method to discern genome-wide ribosome occupancy, and immunopeptidomics as a method to detect peptides that are processed and presented by MHC molecules and not observed in traditional proteomics experiments. This article provides a synthesis of the current state of non-canonical ORF research and proposes standards for their future investigation and reporting.

Highlights: Combined use of Ribo-seq and proteomics-based methods enables optimal confidence in detecting non-canonical ORFs and their protein products.Ribo-seq can provide more sensitive detection of non-canonical ORFs, but data quality and analytical pipelines will impact results.Non-canonical ORF catalogs are diverse and span both high-stringency and low-stringency ORF nominations.A framework for standardized non-canonical ORF evidence will advance the research field.

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