PXD041946

PXD041946 is an original dataset announced via ProteomeXchange.

Title	Changes in replisome composition underlie the rewiring of DNA replication during embryonic stem cell reprogramming
Description	Pluripotent stem cells can give rise to the three embryonic germ layers and the characterization of their properties is crucial to exploit their therapeutic potential. Mouse embryonic stem cells (mESCs) are isolated and usually maintained in vitro in a primed state that resembles the post-implantation epiblast features. Furthermore, primed mESCs can be de-differentiated to a naive state that resembles the pre-implantation inner cell mass (ICM). Cell differentiation or genotoxic stress, among others, can alter DNA replication, which is a flexible process able to adapt to different cellular contexts. Here, we demonstrate that primed-to-naive mESC reprogramming triggers replication fork slowdown, increased fork asymmetry and a compensatory activation of dormant origins. Using iPOND (“isolation of proteins on nascent DNA”) coupled to mass spectrometry we have characterized the changes in replisome composition between naive and primed mESCs. Several DNA repair factors, including MRE11 nuclease, are enriched in naive mESCs forks, while factors involved in ubiquitin-dependent protein metabolism are enriched in primed mESC forks. We report that primed-to-naive mESC de-differentiation promotes recruitment of MRE11 to the forks in response to transcription-replication conflicts, underlying the DNA replication rewiring required for efficient mESC reprogramming.
HostingRepository	PRIDE
AnnounceDate	2024-04-03
AnnouncementXML	Submission_2024-04-03_06:33:14.875.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pilar Ximenez-Embun
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-03 03:48:40	ID requested
⏵ 1	2024-04-03 06:33:15	announced

10.1016/J.CELREP.2024.114024;

submitter keyword: mESCs, iPOND, HF-X mass spectrometer,replisome, primed-to-naive reprogramming

Javier Munoz
contact affiliation	Head of Proteomics Unit Spanish National Cancer Research Centre (CNIO) Melchor Fernández Almagro, 3. 28029 Madrid. SPAIN +34 917 328 000 Ext. 3110
contact email	jmunozpe@cnio.es
lab head
Pilar Ximenez-Embun
contact affiliation	Proteomics Group
contact email	mpximenez@cnio.es
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/2024/04/PXD041946

PRIDE project URI

• PRIDE
  1. PXD041946
     1. Label: PRIDE project
     2. Name: Changes in replisome composition underlie the rewiring of DNA replication during embryonic stem cell reprogramming