PXD025262

PXD025262 is an original dataset announced via ProteomeXchange.

Title	The nuclear RNA-interactome of human embryonic stem cells (hESCs)
Description	Here, we performed RNA-interactome capture (RIC) on nuclear fractions from human embryonic stem cells (hESCs). The poly(A)+ RNA-bound proteome was determined by UV light-mediated cross-linking (CL) of RNAs to proteins in living cells, followed by nuclei isolation, oligo(dT) purification of poly(A)-RNA-protein complexes, and mass spectrometry analysis of captured proteins. As a control, we applied a similar strategy to non-cross-linked (non-CL) samples. RIC was performed in four independent biological replicates. This data accompanies the manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells". Abstract: "Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that directly bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during exit from pluripotency and early lineage specification. Moreover, we show that nearly 200 RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly bound by this factor. Intriguingly, over 20 percent of the proteins detected in our study are putative DNA- and RNA-binding proteins (DRBPs), among them key transcription factors (TFs). Using fluorescently labeled RNA and seCLIP (single-end enhanced crosslinking and immunoprecipitation) experiments, we discover that the pluripotency-associated STAT3 and OCT4 TFs interact with RNA in hESCs and confirm the direct binding of STAT3 to the conserved NORAD long-noncoding RNA. Taken together, our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated, reinforcing the importance of post-transcriptional regulation in stem cell biology".
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:32.034.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shlomi Dvir
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-08 06:00:16	ID requested
1	2023-05-04 18:36:02	announced
⏵ 2	2023-11-14 08:45:36	announced	2023-11-14: Updated project metadata.

Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y, Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep, 35(9):109198(2021) [pubmed]

submitter keyword: nuclear RNA interactome, RIC, hESCs, RNA-binding proteome,mass spectrometry, RBPs, RNA-binding proteins, RBPome, human embryonic stem cells, RNA-interactome capture

Yael Mandel-Gutfreund
contact affiliation	1. Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel. 2. Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
contact email	yaelmg@technion.ac.il
lab head
Shlomi Dvir
contact affiliation	Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
contact email	shlomidvir1@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/2023/05/PXD025262

PRIDE project URI

• PRIDE
  1. PXD025262
     1. Label: PRIDE project
     2. Name: The nuclear RNA-interactome of human embryonic stem cells (hESCs)