PXD016729

PXD016729 is an original dataset announced via ProteomeXchange.

Title	Identification of X-linked genes that drive sex differences in murine embryonic stem cells
Description	Dosage imbalance of X-chromosomal genes contributes to sex differences, in particular during early development, when both X chromosomes are active in females. X-encoded inhibitors of the differentiation-promoting MAP kinase (MAPK) signalling pathway slow down development, increase levels of naive pluripotency factors and decrease MAPK target gene expression. Through a hierarchical CRISPR screening approach in murine embryonic stem cells (mESC) we have comprehensively identified X-linked genes that modulate MAPK signalling, pluripotency factor expression and differentiation. We show that multiple genes act in concert to drive sex differences in mESC. Dusp9, a known negative regulator of the MAPK pathway alters phosphorylation of MAPK pathway intermediates in female cells, while Klhl13 underlies differences in pluripotency factor expression and differentiation by targeting differentiation-promoting factors for degradation. Klhl13 is a member of the Cullin 3 E3 ubiquitin ligase complex, where it acts as a substrate adaptor to target proteins for proteasomal degradation (Dhanoa et al., 2013). We reasoned that the Klhl13-mediated sex differences we have identified might be due to reduced protein abundance of Klhl13 substrate proteins in female compared to male cells, which affect pluripotency factors, differentiation and MAPK target gene expression. To identify Klhl13 substrates in mESCs, we comprehensively profiled Klhl13 interaction partners and then selected those with increased protein levels in K13-HOM mutant cells. To identify interaction partners, we ectopically expressed either full-length Klhl13 or the substrate-binding Kelch domain, tagged with a green fluorescent protein (GFP), and identified binding partners by Immunoprecipitation-Mass Spectrometry (IP-MS) using a GFP-specific antibody. These experiments were performed in female mESCs with a homozygous Klhl13 deletion. By using this approach, we identify Scml2 and Alg13 as Klhl13 substrates.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:20:09.755.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Meierhofer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-12 08:09:00	ID requested
1	2021-03-18 06:59:01	announced
⏵ 2	2024-10-22 05:20:10	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Klhl13, sex differences, pluripotency, differentiation, MAPK,mouse embryonic stem cells

Edda G. Schulz
contact affiliation	max Planck Institute for Molecular Genetics
contact email	edda.schulz@molgen.mpg.de
lab head
David Meierhofer
contact affiliation	Mass Spectrometry Facility MPIMG
contact email	meierhof@molgen.mpg.de
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/2021/03/PXD016729

PRIDE project URI

• PRIDE
  1. PXD016729
     1. Label: PRIDE project
     2. Name: Identification of X-linked genes that drive sex differences in murine embryonic stem cells