PXD056493

PXD056493 is an original dataset announced via ProteomeXchange.

Title	Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome maintenance
Description	Linkage-specific ubiquitin (Ub) chains dictate the functional outcome of many critical Ub-dependent signaling processes. However, the functions and targets of several poly-Ub topologies remain poorly understood due to a lack of tools for their specific detection and manipulation. To remedy this knowledge gap, we applied a cell-based Ub replacement strategy enabling specific, conditional abrogation of each of the seven lysine-based Ub chain types in human cells to comprehensively profile global ubiquitylation changes resulting from disabling formation of individual Ub chain types. Focusing on K29-linked ubiquitylation, we found that this linkage type is enriched among chromatin-associated proteins, and that the H3K9me3 methyltransferase SUV39H1 is a prominent cellular target of this modification. We demonstrate that K29-linked ubiquitylation is essential for the proteasomal degradation of SUV39H1 despite its extensive modification by K48-linked ubiquitylation, and that K29-linked ubiquitylation of SUV39H1 is catalyzed and reversed by TRIP12 and TRABID, respectively. Importantly, preventing K29-linked ubiquitylation of SUV39H1 markedly increases H3K9me3 levels, but not other histone marks. Collectively, our Ub replacement cell line panel and datasets provide valuable resources for illuminating cellular functions of linkage-specific ubiquitylation processes and reveal a key role for K29-linked ubiquitylation in epigenome maintenance.
HostingRepository	PRIDE
AnnounceDate	2025-09-19
AnnouncementXML	Submission_2025-09-18_19:34:32.964.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petra Beli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature dipeptidyl lysine; iodoacetamide derivatized residue
Instrument	Orbitrap Astral; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-03 23:31:44	ID requested
⏵ 1	2025-09-18 19:34:33	announced

Dataset with its publication pending

submitter keyword: Ubiquitin

ubiquitin-proteasome system

K29-linked ubiquitylation

chromatin

epigenome

Prof. Dr. Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
lab head
Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.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/2025/09/PXD056493

PRIDE project URI

• PRIDE
  1. PXD056493
     1. Label: PRIDE project
     2. Name: Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome maintenance