PXD039213

PXD039213 is an original dataset announced via ProteomeXchange.

Title	Spic a specific marker of ground state pluripotency that regulates one carbon metabolism
Description	Understanding mechanisms of epigenetic regulation in embryonic stem cells (ESCs) is of fundamental importance for stem cell and developmental biology. Here we identify Spic, a member of the ETS family of transcription factors, as a specific marker of ground state pluripotency. We show that Spic is rapidly induced in ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL), and in response to MEK/ERK inhibition. ChIP-seq analysis demonstrated that Spic binds to enhancer elements that are associated with pluripotency genes. Interaction proteomics and genomic profiling confirmed that SPIC interacts with NANOG and stabilizes its binding to chromatin in 2iL-ESCs. Additional gain of function and loss of function experiments revealed that Spic controls genes involved in one carbon (1C) metabolism, Bhmt, Bhmt2, and Dmgdh, and the flux of SAM-to-SAH in 2iL-ESCs. By maintaining low levels of SAM, Spic controls the level of H3K4me3 and H3R17me2 histone methylation in ground state ESCs. Our data highlight the role of uncharacterized axillary transcription factors that link cellular metabolism to epigenetic regulation in ground state pluripotency.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_09:15:40.666.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yaser Atlasi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-03 01:00:26	ID requested
⏵ 1	2025-05-06 09:15:41	announced

10.1126/sciadv.adg7997;

Mirzadeh Azad F, Struys EA, Wingert V, Hannibal L, Mills K, Jansen JH, Longley DB, Stunnenberg HG, Atlasi Y, regulates one-carbon metabolism and histone methylation in ground-state pluripotency. Sci Adv, 9(33):eadg7997(2023) [pubmed]

submitter keyword: Spic, SAM, embryonic stem, 2iL, one carbone metabolism, epigenetic, ground state, BHMT

Yaser Atlasi
contact affiliation	Queen's University Belfast
contact email	y.atlasi@qub.ac.uk
lab head
Yaser Atlasi
contact affiliation	Queen's University Belfast
contact email	yaseratlasi@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/2025/05/PXD039213

PRIDE project URI

• PRIDE
  1. PXD039213
     1. Label: PRIDE project
     2. Name: Spic a specific marker of ground state pluripotency that regulates one carbon metabolism