@Article{Whisnant2020,
  author          = {Whisnant, Adam W. and Jürges, Christopher S. and Hennig, Thomas and Wyler, Emanuel and Prusty, Bhupesh and Rutkowski, Andrzej J. and L'hernault, Anne and Djakovic, Lara and Göbel, Margarete and Döring, Kristina and Menegatti, Jennifer and Antrobus, Robin and Matheson, Nicholas J. and Künzig, Florian W. H. and Mastrobuoni, Guido and Bielow, Chris and Kempa, Stefan and Liang, Chunguang and Dandekar, Thomas and Zimmer, Ralf and Landthaler, Markus and Grässer, Friedrich and Lehner, Paul J. and Friedel, Caroline C. and Erhard, Florian and Dölken, Lars},
  journal         = {Nature communications},
  title           = {Integrative functional genomics decodes herpes simplex virus 1.},
  year            = {2020},
  issn            = {2041-1723},
  month           = apr,
  pages           = {2038},
  volume          = {11},
  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.},
  chemicals       = {Biological Products, Protein Isoforms, talimogene laherparepvec},
  citation-subset = {IM},
  completed       = {2020-08-10},
  country         = {England},
  doi             = {10.1038/s41467-020-15992-5},
  issn-linking    = {2041-1723},
  issue           = {1},
  keywords        = {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, genetics; Humans; Open Reading Frames; Protein Domains; Protein Isoforms; Ribosomes, metabolism; Transcriptome; Vero Cells},
  nlm-id          = {101528555},
  owner           = {NLM},
  pii             = {10.1038/s41467-020-15992-5},
  pmc             = {PMC7184758},
  pmid            = {32341360},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2021-04-27},
}