PXD050381

PXD050381 is an original dataset announced via ProteomeXchange.

Title	Improved detection of DNA replication fork-associated proteins via iPOND2-DRIPPER
Description	Innovative methods to retrieve proteins associated with actively replicating DNA have provided a glimpse into the molecular dynamics of replication fork stalling. We report that a combination of density-based replisome enrichment by isolating proteins on nascent DNA (iPOND2) and label-free quantitative mass spectrometry (iPOND2-DRIPPER) substantially increases both replication factor yields and the dynamic range of protein quantification. Replication protein abundance in retrieved nascent DNA is elevated up to 300-fold over post-replicative controls and recruitment of replication stress factors upon fork stalling is observed at similar levels. The increased sensitivity of iPOND2-DRIPPER permits direct measurement of ubiquitination events without intervening retrieval of di-glycine tryptic fragments of ubiquitin. Using this approach, we find that stalled replisomes stimulate the recruitment of a diverse cohort of DNA repair factors, including those associated with poly-K63-ubiquitination. Finally, we uncover the temporally controlled association of stalled replisomes with nuclear pore complex components, and nuclear cytoskeleton networks.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_13:38:44.794.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD050381
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ya-Chu Chang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	ubiquitination signature dipeptidyl lysine; sumoylated lysine; acetylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-05 15:11:33	ID requested
⏵ 1	2025-05-06 13:38:45	announced

Rivard RS, Chang YC, Ragland RL, Thu YM, Kassab M, Mandal RS, Van Riper SK, Kulej K, Higgins L, Markowski TM, Shang D, Hedberg J, Erber L, Garcia B, Chen Y, Bielinsky AK, Brown EJ, Improved detection of DNA replication fork-associated proteins. Cell Rep, 43(5):114178(2024) [pubmed]

10.6019/PXD050381;

10.1016/j.celrep.2024.114178;

submitter keyword: quantitative proteomics,Mouse embryonic fibroblasts, replisome

Anja Katrin Bielinsky
contact affiliation	Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903
contact email	azu3jn@virginia.edu
lab head
Ya-Chu Chang
contact affiliation	University of Minnesota
contact email	chan1285@umn.edu
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/2025/05/PXD050381

PRIDE project URI

• PRIDE
  1. PXD050381
     1. Label: PRIDE project
     2. Name: Improved detection of DNA replication fork-associated proteins via iPOND2-DRIPPER