PXD057811

PXD057811 is an original dataset announced via ProteomeXchange.

Title	ncRNA DUBR RAP-MS in HCT116 cells
Description	Non-coding RNAs (ncRNAs) are finely tuned cellular regulators important for human cell growth and cancer progression. DUBR (also known as linc00883) is a nuclear ncRNA first discovered in mice for its role in regulating myoblast differentiation through interactions with chromatin and DNA methyltransferases. High expression levels of this ncRNA are predictive of poor patient outcome in colon adenocarcinoma, suggesting that DUBR may be involved in controlling cancer growth. To elucidate its function, we used RAP-MS and RNA immunoprecipitation techniques which revealed its interaction with epigenetic maintenance proteins in the human colon cancer cell line HCT116. Further, ATAC-seq and RNA-seq were used to address its function in regulating the epigenome and transcriptome of HCT116 cells. Here we report that DUBR is a regulator of human colon cancer cell line HCT116 survival.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_04:56:40.236.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Colleen McHugh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-12 13:17:11	ID requested
⏵ 1	2025-05-07 04:56:41	announced

10.1007/s10142-025-01582-5;

Hall SD, Tran K, Zhu J, Su T, McHugh CA, DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility. Funct Integr Genomics, 25(1):68(2025) [pubmed]

submitter keyword: DUBR, HCT116,ncRNA, RAP-MS

Dr. Colleen Adare McHugh
contact affiliation	Department of Chemistry and Biochemistry, University of California San Diego
contact email	c1mchugh@ucsd.edu
lab head
Colleen McHugh
contact affiliation	University of California San Diego
contact email	c1mchugh@ucsd.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/PXD057811

PRIDE project URI

• PRIDE
  1. PXD057811
     1. Label: PRIDE project
     2. Name: ncRNA DUBR RAP-MS in HCT116 cells