PMID- 37808651
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231009
DP  - 2023 Sep 28
TI  - Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling.
LID - 2023.09.26.559641 [pii]
LID - 10.1101/2023.09.26.559641 [doi]
AB  - Unveiling the complete proteome of viruses is crucial to our understanding of the 
      viral life cycle and interaction with the host. We developed Massively Parallel 
      Ribosome Profiling (MPRP) to experimentally determine open reading frames (ORFs) 
      in 20,170 designed oligonucleotides across 679 human-associated viral genomes. We 
      identified 5,381 ORFs, including 4,208 non-canonical ORFs, and show successful 
      detection of both annotated coding sequences (CDSs) and reported non-canonical 
      ORFs. By examining immunopeptidome datasets of infected cells, we found class I 
      human leukocyte antigen (HLA-I) peptides originating from non-canonical ORFs 
      identified through MPRP. By inspecting ribosome occupancies on the 5'UTR and CDS 
      regions of annotated viral genes, we identified hundreds of upstream ORFs (uORFs) 
      that negatively regulate the synthesis of canonical viral proteins. The 
      unprecedented source of viral ORFs across a wide range of viral families, 
      including highly pathogenic viruses, expands the repertoire of vaccine targets 
      and exposes new cis-regulatory sequences in viral genomes.
FAU - Weingarten-Gabbay, Shira
AU  - Weingarten-Gabbay S
FAU - Bauer, Matthew R
AU  - Bauer MR
FAU - Stanton, Alexandra C
AU  - Stanton AC
FAU - Klaeger, Susan
AU  - Klaeger S
AUID- ORCID: 0000-0002-0074-5163
FAU - Verzani, Eva K
AU  - Verzani EK
FAU - Lopez, Daniel
AU  - Lopez D
FAU - Clauser, Karl R
AU  - Clauser KR
FAU - Carr, Steven A
AU  - Carr SA
FAU - Abelin, Jennifer G
AU  - Abelin JG
FAU - Rice, Charles M
AU  - Rice CM
AUID- ORCID: 0000-0003-3087-8079
FAU - Sabeti, Pardis C
AU  - Sabeti PC
LA  - eng
PT  - Preprint
DEP - 20230928
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
PMC - PMC10557741
EDAT- 2023/10/09 06:42
MHDA- 2023/10/09 06:43
PMCR- 2023/10/06
CRDT- 2023/10/09 05:42
PHST- 2023/10/09 06:43 [medline]
PHST- 2023/10/09 06:42 [pubmed]
PHST- 2023/10/09 05:42 [entrez]
PHST- 2023/10/06 00:00 [pmc-release]
AID - 2023.09.26.559641 [pii]
AID - 10.1101/2023.09.26.559641 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2023 Sep 28:2023.09.26.559641. doi: 
      10.1101/2023.09.26.559641.