PXD039054-2

PXD039054 is an original dataset announced via ProteomeXchange.

Title	Time-resolved profiling of mRNA-protein interaction through mRNA life cycle
Description	From synthesis to decay, mRNA changes its protein partners, yet previous studies were limited in that they profiled only the mixed pools of RNA-binding proteins (RBPs) without temporal resolution. Here, we provide time-resolved profiles of human mRNA interactome by combining pulse metabolic labeling, photoactivatable ribonucleoside crosslinking, poly(A) RNA isolation, and mass spectrometry. We captured stage-specific RBPs across 10 time points and quantified over 700 RBPs. The chronological orders of mRNA binding are generally consistent with the known functions and localizations of RBPs: pre-mRNA processing factors are detected as “early binders” while decay factors appear as “late binders”. Notably, stress granule proteins are enriched in “aged” mRNPs, suggesting their roles in the final stage of mRNA life cycle. Many late binders also interact with viral transcripts, implying their regulatory activities on viruses. Furthermore, we built a computational model to systematically identify RBPs with unexpected binding dynamics, which indicates their unknown functions. Our study reveals a dynamic landscape of mRNP remodeling, offering new functional insights into RNA-protein interaction during mRNA life cycle.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:31:33.688.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yeon Choi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-22 02:12:01	ID requested
1	2024-02-23 09:35:34	announced
⏵ 2	2024-10-22 06:31:34	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: mRNA-interactome, HeLa, temporal, RNA-interactome,mRNA, RNA, stage, RBP, age, chronology

V. Narry Kim
contact affiliation	Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
contact email	narrykim@snu.ac.kr
lab head
Yeon Choi
contact affiliation	Seoul National University
contact email	kitechoi9599@gmail.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/2024/02/PXD039054

PRIDE project URI

• PRIDE
  1. PXD039054
     1. Label: PRIDE project
     2. Name: Time-resolved profiling of mRNA-protein interaction through mRNA life cycle