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PXD013407 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSystems biology decodes herpes simplex virus 1
DescriptionSince the genome of herpes simplex virus 1 (HSV-1) was first sequenced more than 30 years ago, the 84 genes it was thought to encode have been intensively studied. Here, we unravel the full complement of viral transcription and translation during lytic infection with base-pair resolution by computational integration of multi-omics data. This includes a total of 201 viral transcripts and 296 open reading frames (ORFs), comprising all known large ORFs, 55 large novel ORFs including a novel spliced ORF in the ICP0 locus that initiates from a non-AUG start codon and a novel strongly translated ORF in the ICP34.5 locus as well as multiple short ORFs. By defining viral gene modules, we link translation of ORFs to the expression of transcript isoforms. This explained translation of the vast majority of viral ORFs as well as N-terminal extensions and truncations thereof. We show that N-terminal extensions initiating from non-AUG start codons govern subcellular protein localization and packaging of key viral regulators and structural proteins. This work has great implications for future functional studies, vaccine design and novel oncolytic therapies.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterGuido Mastrobuoni
SpeciesList scientific name: Herpes simplex virus unknown type; NCBI TaxID: 126283; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-04-08 08:14:18ID requested
12020-05-21 23:59:49announced
Publication List
Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L, Integrative functional genomics decodes herpes simplex virus 1. Nat Commun, 11(1):2038(2020) [pubmed]
Keyword List
submitter keyword: genome annotation, systems biology, shotgun proteomics
Contact List
Stefan Kempa
contact affiliationBerlin Institute for Medical System Biology @ Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association Hannoversche Str. 28, 10115 Berlin Germanyt
contact emailstefan.kempa@mdc-berlin.de
lab head
Guido Mastrobuoni
contact affiliationBerlin Institute for Medical Systems Biology at the Max Delbrueck Centrum for Molecular Medicine
contact emailguido.mastrobuoni@mdc-berlin.de
dataset submitter
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