PXD053638

PXD053638 is an original dataset announced via ProteomeXchange.

Title	DNMT3L safeguards the epigenome and developmental potential of naive human pluripotent stem cells and blastoids
Description	Studies of the catalytically inactive DNA methyltransferase Dnmt3l have mainly been limited to mice where Dnmt3l was shown to be essential for fertility, de novo DNA methylation in early embryos and maintenance of DNA methylation patterns in mouse pluripotent stem cells. In humans, recent work revealed that DNMT3L is the most highly enriched chromatin factor in naive pluripotent stem cells (hPSCs) compared with primed hPSCs. Naive hPSCs and stem cell-based human embryo models provide a unique opportunity to functionally the role of DNMT3L in human naive pluripotency and development. Here we use naive hPSCs and human blastoids, 3D blastocyst models, to investigate the functional impact of DNMT3L on human naive pluripotency and preimplantation development. We demonstrate an essential role of DNMT3L in maintenance of DNA methylation patterns and chromatin states in naive hPSCs, and in trophectoderm cell fate induction and blastoid lineage identity. We further show that DNMT3L promotes reprogramming to naive pluripotency, and has integrated a hominoid-specific naive human pluripotency gene regulatory program involving evolutionarily recent transposable elements. Our work provides crucial insights into the molecular basis of human naive pluripotency and sheds light on human preimplantation development.
HostingRepository	PRIDE
AnnounceDate	2026-08-31
AnnouncementXML	Submission_2026-08-31_09:51:44.015.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD053638
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monomethylated residue; acetylated residue; formylated residue; deamidated residue
Instrument	ZenoTOF 7600

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-04 02:00:03	ID requested
⏵ 1	2026-08-31 09:51:44	announced

10.6019/PXD053638;

submitter keyword: DNMT3L

naive PSCs

blastoids

histones

PTMs

protein interactions

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
contact email	maarten.dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@ugent.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053638
     1. Label: PRIDE project
     2. Name: DNMT3L safeguards the epigenome and developmental potential of naive human pluripotent stem cells and blastoids