PXD061212

PXD061212 is an original dataset announced via ProteomeXchange.

Title	Proteomic discovery of DEK and NUMA1 as new players in UV-induced DNA damage repair mechanisms
Description	Ultraviolet (UV)-induced DNA lesions threaten genomic stability and are associated with skin carcinogenesis. These lesions are primarily repaired by the nucleotide excision repair (NER) pathway. However, alternative repair mechanisms and regulators are emerging as critical contributors to managing UV lesions. Here, we used a click chemistry-based proteomic approach to identify DEK and NUMA1 as novel regulators of UV-induced DNA lesion repair. Depletion of DEK or NUMA1 resulted in delayed UV lesion repair and increased cellular UV sensitivity. This was accompanied by delayed recruitment of XPF to UV-damaged sites. Notably, abnormal accumulation of proliferating cell nuclear antigen (PCNA) at UV lesions was observed in DEK- or NUMA1-depleted cells. This PCNA accumulation was not entirely dependent on NER, as it also involved contributions from apurinic/apyrimidinic endonuclease 1 (APE1), a key protein in base excision repair (BER). Co-depletion experiments revealed an epistatic relationship between DEK or NUMA1 and APE1, but not with XPA, suggesting an impaired BER in DEK- or NUMA1-depleted cells, possibly due to excessive PCNA accumulation. Our findings strongly suggest that DEK and NUMA1 facilitate efficient UV lesion removal by promoting proper NER activity and regulating APE1-mediated long-patch BER, highlighting the collaborative roles of NER and BER in UV lesion repair.
HostingRepository	PRIDE
AnnounceDate	2025-12-01
AnnouncementXML	Submission_2025-11-30_16:11:21.291.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD061212
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Byung-gyu kim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-25 23:31:51	ID requested
⏵ 1	2025-11-30 16:11:23	announced

10.6019/PXD061212;

10.1038/s41420-025-02823-z;

Kim N, Kim M, Jeong E, Yeo JE, Kim BG, Myung K, Sch, ä, rer OD, Lee KY, Proteomic discovery of DEK and NUMA1 as new players in UV-induced DNA damage repair mechanisms. Cell Death Discov, 11(1):547(2025) [pubmed]

submitter keyword: UV, UV, DEK, NUMA1, DNA damage

Kyoo-young Lee
contact affiliation	6Department of Biochemistry, College of Medicine, Hallym University, Chuncheon 24252, Gangwon-do, Republic of Korea
contact email	kylee@hallym.ac.kr
lab head
Byung-gyu kim
contact affiliation	Center for genomic integrity (CGI), Institute of basic science (IBS), UNIST, Ulsan, 44919, Republic of Korea
contact email	goldenlion@ibs.re.kr
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/2025/12/PXD061212

PRIDE project URI

• PRIDE
  1. PXD061212
     1. Label: PRIDE project
     2. Name: Proteomic discovery of DEK and NUMA1 as new players in UV-induced DNA damage repair mechanisms