Pan-viral ORFs discovery using massively parallel ribosome profiling
Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively parallel ribosome profiling (MPRP) to determine open reading frames (ORFs) across tens of thousands of designed oligonucleotides. MPRP identified 4208 unannotated ORFs in 679 human-associated viral genomes. We found viral peptides originating from detected noncanonical ORFs presented on class-I human leukocyte antigen in infected cells and hundreds of upstream ORFs that likely modulate translation initiation of viral proteins. The discovery of viral ORFs across a wide range of viral families-including highly pathogenic viruses-expands the repertoire of vaccine targets and reveals potential cis-regulatory sequences.
Authors
- Karl R. Clauser (ORCID: https://orcid.org/0000-0002-1052-9456)
- Matthew R. Bauer (ORCID: https://orcid.org/0000-0001-6309-3548)
- Charles M. Rice (ORCID: https://orcid.org/0000-0003-3087-8079)
- Jennifer G. Abelin (ORCID: https://orcid.org/0000-0001-5262-7241)
- Yingpu Yu (ORCID: https://orcid.org/0000-0003-4837-5744)
- Daniel López (ORCID: https://orcid.org/0000-0003-0268-5878)
- Susan Klaeger (ORCID: https://orcid.org/0000-0002-0074-5163)
- Steven A. Carr (ORCID: https://orcid.org/0000-0002-7203-4299)
- Alexandra C. Stanton (ORCID: https://orcid.org/0000-0001-8355-345X)
- Pardis C. Sabeti (ORCID: https://orcid.org/0000-0002-9843-1890)
- Eva K. Verzani (ORCID: https://orcid.org/0009-0004-0846-4878)
- Shira Weingarten-Gabbay (ORCID: https://orcid.org/0000-0001-7579-0236)
- Lisa E. Hensley (ORCID: https://orcid.org/0000-0003-1188-4342)
- Chloe K. Boehm (ORCID: https://orcid.org/0000-0002-6136-3257)
- Catherine A. Freije (ORCID: https://orcid.org/0000-0002-1939-3102)
- Nicole L. Welch (ORCID: https://orcid.org/0000-0002-6225-487X)
Institutions
- Broad Institute (US)
- United States Department of Agriculture (US)
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Instituto de Salud Carlos III (ES)
- Concord Consortium (US)
- Centro Nacional de Microbiologia (ES)
- Rockefeller University (US)
Publication Details
- Journal
- Science
- Published
- 2025-06-12
- DOI
- https://doi.org/10.1126/science.ado6670
- Citations
- 1
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 0.81