PXD039633

PXD039633 is an original dataset announced via ProteomeXchange.

Title	USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and non-catalytic activity
Description	USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function to shape the transcriptional network in mouse embryonic stem cells (mESCs) remains poorly understood. Here, we report that USP7 maintains mESCs identity through both catalytic activity-dependent and -independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 level and derepresses lineage differentiation genes thereby compromising mESCs pluripotency. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant Polycomb repressive complex 1 and contributes to Polycomb chromatin-mediated repression of ME lineage genes in a catalytic activity-dependent manner. Importantly, USP7 deficient in its deubiquitination function is able to maintain RYBP binding to chromatin for repressing primitive endoderm-associated genes. Overall, our study demonstrates that USP7 harbors both catalytic and non-catalytic activity to repress different lineage differentiation genes thereby revealing a previously unrecognized role in controlling gene expression for maintaining mESCs identity.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:03:20.574.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tiannan Guo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-24 08:25:54	ID requested
1	2023-07-20 11:22:19	announced
⏵ 2	2023-11-14 09:03:24	announced	2023-11-14: Updated project metadata.

Liu C, Sun L, Tan Y, Wang Q, Luo T, Li C, Yao N, Xie Y, Yi X, Zhu Y, Guo T, Ji J, USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and noncatalytic activities. Sci Adv, 9(20):eade3888(2023) [pubmed]

submitter keyword: Pluripotent stem cells

USP7

Polycomb

Epigenetic regulation

Tiannan Guo
contact affiliation	School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
contact email	guotiannan@westlake.edu.cn
lab head
Tiannan Guo
contact affiliation	Westlake University
contact email	guotiannan@westlake.edu.cn
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/2023/07/PXD039633

PRIDE project URI

• PRIDE
  1. PXD039633
     1. Label: PRIDE project
     2. Name: USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and non-catalytic activity