PXD069064-1

PXD069064 is an original dataset announced via ProteomeXchange.

Title	JMJD2 regulates enhancer-promoter interactions via biocondensate formation
Description	Enhancer-promoter (E-P) interactions regulate transcription for cell fate determination. However, the regulatory mechanisms of E-P interactions remain elusive. Here, a chromatin interaction-based proteomics approach, LoopID, was developed to profile the proteins at certain E-P anchors, which were termed looposome. Histone demethylase JMJD2, a key looposome component, can regulate E-P interactions and looposome in a catalytic-independent manner through forming biomolecular condensates. Furthermore, a system to engineer E-P interactions was introduced by assembling JMJD2 condensates at certain genomic loci, enabling the construction of cell-type specific E-P interactions to promote cellular reprogramming into pluripotent or 2-cell-like cells. Our findings reveal a non-canonical function of histone demethylase in regulating chromatin organization and provide a strategy for regulating cell fate transitions through E-P interactions.
HostingRepository	PRIDE
AnnounceDate	2026-03-16
AnnouncementXML	Submission_2026-03-16_09:02:29.589.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xinyi Liu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-01 17:47:11	ID requested
⏵ 1	2026-03-16 09:02:30	announced

10.1038/s41588-025-02415-8;

Jiang S, Liu X, Zhang Z, Yang M, Zhu X, Ma L, Zhao L, Ling X, Zhou Z, Wu Z, Qu J, Li H, Liang J, Deng Z, Tian Q, Huang X, Huang X, Tan J, Sun J, Wang J, Guallar D, Das PP, Pinello L, Wang L, Wu H, Huang DF, Wang J, Lin H, Bai J, Fan L, Chi W, Xiao X, Ding J, JMJD2 regulates enhancer-promoter interactions via biomolecular condensate formation. Nat Genet, 58(3):593-606(2026) [pubmed]

submitter keyword: Enhancer-promoter interactions, proximity ligation, LoopID, biocondensates, proteome

Junjun Ding
contact affiliation	Sun Yat-Sen University
contact email	dingjunj@mail.sysu.edu.cn
lab head
Xinyi Liu
contact affiliation	Sun Yat-Sen University
contact email	tuzi671@outlook.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/2026/03/PXD069064

PRIDE project URI

• PRIDE
  1. PXD069064
     1. Label: PRIDE project
     2. Name: JMJD2 regulates enhancer-promoter interactions via biocondensate formation