PXD044625

PXD044625 is an original dataset announced via ProteomeXchange.

Title	Chemoproteomic capture of RNA binding activity in living cells
Description	Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5,500 cysteine sites across ~3,000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:05:53.460.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044625
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Dina Bai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-18 06:25:22	ID requested
1	2023-10-10 12:29:00	announced
⏵ 2	2023-11-14 09:06:01	announced	2023-11-14: Updated project metadata.

10.6019/PXD044625;

Heindel AJ, Brulet JW, Wang X, Founds MW, Libby AH, Bai DL, Lemke MC, Leace DM, Harris TE, Hafner M, Hsu KL, Chemoproteomic capture of RNA binding activity in living cells. Nat Commun, 14(1):6282(2023) [pubmed]

submitter keyword: LC-MSMS,Chemoproteomics, Human, Chemical Biology, RNA-binding protein, RNA interactome

Ku-Lung Hsu
contact affiliation	Department of Chemistry University of Texas at Austin
contact email	ken.hsu@austin.utexas.edu
lab head
Dina Bai
contact affiliation	University of Virginia
contact email	dlb6z@virginia.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/2023/10/PXD044625

PRIDE project URI

• PRIDE
  1. PXD044625
     1. Label: PRIDE project
     2. Name: Chemoproteomic capture of RNA binding activity in living cells