PXD063191-1

PXD063191 is an original dataset announced via ProteomeXchange.

Title	Label-free LC-MS/MS analysis of proteins associated with specific RNAs in HeLa cells
Description	Proteins co-localizing with RNA targets of interest in HeLa cells were identified using our recently optimized hybridization-proximity labeling approach (HyPro2) combined with label-free mass spectrometry. Briefly, fixed and permeabilized cells were hybridized with digoxigenin-labeled antisense oligonucleotide probes targeting the long noncoding RNA PNCTR or pre-mRNAs encoding ACTB and FUS proteins. A no-probe negative control was also included. The purified HyPro2 enzyme, which contains a digoxigenin-binding domain and a modified ascorbate peroxidase domain, was then recruited to the RNA targets, enabling in vitro biotinylation of target-proximal proteins. Following streptavidin pull-down, biotinylated proteins were fragmented using a Trypsin/Lys-C protease mix and identified by label-free LC-MS/MS analysis. All experiments were performed in triplicate.
HostingRepository	PRIDE
AnnounceDate	2025-08-04
AnnouncementXML	Submission_2025-08-03_16:34:35.166.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD063191
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Steven Lynham
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-22 05:56:34	ID requested
⏵ 1	2025-08-03 16:34:36	announced

Huang WP, Kumar V, Yap K, An H, John SJ, Hodgson RE, Avila AS, Day E, Ellis BCS, Chung TH, Lord J, M, ü, ller-McNicoll M, Makeyev EV, Shelkovnikova TA, M6A-dependent RNA condensation underlies FUS autoregulation and can be harnessed for ALS therapy development. Sci Adv, 11(30):eadx1357(2025) [pubmed]

10.6019/PXD063191;

10.1126/sciadv.adx1357;

submitter keyword: ACTB,RNA-protein interactions, lncRNA, FUS, pre-mRNA, hybridization-proximity labeling, PNCTR.

Eugene Makeyev
contact affiliation	Centre for Developmental Neurobiology, King's College London
contact email	eugene.makeyev@kcl.ac.uk
lab head
Steven Lynham
contact affiliation	King's College London
contact email	steven.lynham@kcl.ac.uk
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/2025/08/PXD063191

PRIDE project URI

• PRIDE
  1. PXD063191
     1. Label: PRIDE project
     2. Name: Label-free LC-MS/MS analysis of proteins associated with specific RNAs in HeLa cells