Integrative functional genomics decodes herpes simplex virus 1

Nat Commun. 2020 Apr 27;11(1):2038. doi: 10.1038/s41467-020-15992-5.

Abstract

The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biological Products / pharmacology
  • Chlorocebus aethiops
  • Computational Biology
  • Cricetinae
  • Fibroblasts / metabolism
  • Gene Expression Regulation, Viral / drug effects
  • Genes, Viral
  • Genome, Viral*
  • Genomics
  • Herpesvirus 1, Human / drug effects
  • Herpesvirus 1, Human / genetics*
  • Humans
  • Open Reading Frames
  • Protein Domains
  • Protein Isoforms
  • Ribosomes / metabolism
  • Transcriptome
  • Vero Cells

Substances

  • Biological Products
  • Protein Isoforms
  • talimogene laherparepvec