PXD056253

PXD056253 is an original dataset announced via ProteomeXchange.

Title	RNA interactome capture identifies key proteins for herpesviral gene expression
Description	The primary mRNA sequence determines its secondary structure and the repertoire of interacting RNA binding proteins (RBPs). The resulting mRNA ribonucleoprotein complex (mRNP) then influences all stages of the life of an mRNA. Here, we determined the mRNP composition of individual Kaposi Sarcoma Herpesviral (KSHV) mRNAs. In KSHV, the viral RNA regulator ORF57 ensures the translation of viral mRNAs by increasing mRNA stability and nuclear export. By optimizing an LNA/DNA mixmer RNA capture protocol to both transfection and virus replication settings, we identified the RBPome of specific ORF57-dependent viral transcripts. Both capture and eCLIP experiments robustly detected ORF57 as a direct RNA binder to an AU-rich motif, which may enable ORF57 to discriminate viral from cellular RNAs. Furthermore, we identified the RNA processing factor SRSF3 as a key regulator of viral replication. This work facilitates RNA-interactome studies of specific mRNAs and sheds light on how the mRNP composition orchestrates gene expression.
HostingRepository	PRIDE
AnnounceDate	2026-01-23
AnnouncementXML	Submission_2026-01-23_06:53:24.760.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lothar Jaensch
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Human gammaherpesvirus 8; NCBI TaxID: NEWT:37296;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-25 10:40:53	ID requested
⏵ 1	2026-01-23 06:53:25	announced

10.1093/pnasnexus/pgaf225;

Vogt C, van Ham M, Bhowmik R, Argoetti A, Depledge DP, Steinbr, ü, ck L, G, ö, tting J, Henkel C, Cuadra Granados A, Mandel-Gutfreund Y, J, ä, nsch L, Bohne J, RNA-interactome capture identifies SRSF3 as a key protein for herpesviral gene expression. PNAS Nexus, 4(8):pgaf225(2025) [pubmed]

submitter keyword: KSHV, AU-rich sequences, SRSF3,RNA-binding-proteins, RNA interactome capture, RNA stability, codon optimization, herpesviral gene expression, RBPs, lytic transcripts, ORF57

Lothar Jaensch
contact affiliation	Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
contact email	Lothar.Jaensch@Helmholtz-HZI.de
lab head
Lothar Jaensch
contact affiliation	HZI
contact email	lothar.jaensch@helmholtz-hzi.de
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/2026/01/PXD056253

PRIDE project URI

• PRIDE
  1. PXD056253
     1. Label: PRIDE project
     2. Name: RNA interactome capture identifies key proteins for herpesviral gene expression