PXD005467

PXD005467 is an original dataset announced via ProteomeXchange.

Title	Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus (HSV-1) Infection
Description	Herpes simplex virus (HSV-1) lytic infection results in global changes to the host cell proteome and the proteins associated with host chromatin. We present a system level characterization of proteome dynamics during infection by performing a multi-dimensional analysis during HSV-1 lytic infection of human foreskin fibroblast (HFF) cells. Our study includes identification and quantification of the host and viral proteomes, phosphoproteomes, chromatin bound proteomes and post-translational modifications (PTMs) on cellular histones during infection. We analyzed proteomes across six time points of virus infection (0, 3, 6, 9, 12 and 15 hours post-infection) and clustered trends in abundance using fuzzy c-means. Globally, we accurately quantified more than 4,000 proteins, 200 differently modified histone peptides and 9,000 phosphorylation sites on cellular proteins. In addition, we identified 67 viral proteins and quantified 571 phosphorylation events (465 with high confidence site localization) on viral proteins, which is currently the most comprehensive map of HSV-1 phosphoproteome. We investigated chromatin bound proteins by proteomic analysis of the high-salt chromatin fraction and identified 510 proteins that were significantly different in abundance during infection. We found 53 histone marks significantly regulated during virus infection, including a steady increase of histone H3 acetylation (H3K9ac and H3K14ac). Our data provide a resource of unprecedented depth for human and viral proteome dynamics during infection. Collectively, our results indicate that the proteome composition of the chromatin of HFF cells is highly affected during HSV-1 infection, and that phosphorylation events are abundant on viral proteins. We propose that our epi-proteomics approach will prove to be important in the characterization of other model infectious systems that involve changes to chromatin composition.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:35:35.354.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simone Sidoli
SpeciesList	scientific name: Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1); NCBI TaxID: 10299; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-30 01:54:38	ID requested
1	2017-02-10 07:15:42	announced
2	2017-02-10 08:48:43	announced	Updated publication reference for PubMed record(s): 28179408.
3	2017-02-14 00:37:17	announced	Updated project metadata.
4	2017-10-24 04:07:16	announced	Updated project metadata.
5	2017-11-13 00:21:19	announced	Updated project metadata.
⏵ 6	2024-10-22 04:35:43	announced	2024-10-22: Updated project metadata.

10.1074/mcp.tir117.000438;

10.1074/mcp.M116.065987;

Weiner AK, Sidoli S, Diskin SJ, Garcia BA, Graphical Interpretation and Analysis of Proteins and their Ontologies (GiaPronto): A One-Click Graph Visualization Software for Proteomics Data Sets. Mol Cell Proteomics, 17(7):1426-1431(2018) [pubmed]

Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD, Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection. Mol Cell Proteomics, 16(4 suppl 1):S92-S107(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: post-translational modifications (PTMs), viral life cycle, chromatin dynamics,Herpes simplex virus (HSV-1) infection, lytic infection, phosphoproteomics, histone modifications

Matthew D. Weitzman
contact affiliation	Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA
contact email	weitzmanm@email.chop.edu
lab head
Simone Sidoli
contact affiliation	Albert Einstein College of Medicine
contact email	simone.sidoli@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005467

PRIDE project URI

• PRIDE
  1. PXD005467
     1. Label: PRIDE project
     2. Name: Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus (HSV-1) Infection