PXD058937

PXD058937 is an original dataset announced via ProteomeXchange.

Title	H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development
Description	Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. Here, we provide evidence that in Xenopus laevis, H3K4 methylation contributes to epigenetic memory of active chromatin states, which is required for faithful zygotic genome activation and successful embryonic development. We find that chromatin configurations of promoters displaying high H3K4me3 intensity and breadth, alongside DNA hypomethylation and increased GC content, are maintained from the gametes to the embryo across multiple cell divisions and a transcriptionally quiescent phase in early development. We show that this maintenance of H3K4 methylation is essential for precise zygotic genome activation. Finally, we demonstrate that Kmt2b and Cxxc1 facilitate transcription-independent maintenance of H3K4me3 and proper zygotic gene expression. In summary, our study establishes a role for H3K4 methylation for memory of active chromatin states in embryos and reveals its importance for successful embryonic development.
HostingRepository	PRIDE
AnnounceDate	2025-11-25
AnnouncementXML	Submission_2025-11-25_04:41:06.609.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ignasi Forne
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: NEWT:8355;
ModificationList	monomethylated residue; trimethylated residue; acetylated residue; dimethylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-17 04:14:20	ID requested
⏵ 1	2025-11-25 04:41:07	announced

Dataset with its publication pending

submitter keyword: H3K4me3

zygotic genome activation (ZGA)

epigenetic memory

chromatin

transcriptional memory

transcription

early development

Xenopus

Dr. Eva Hörmanseder
contact affiliation	Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Marchioninistrasse 25, D-81377 München, Germany and Wellcome Trust – CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge CB2 1QN, United Kingdom
contact email	eva.hoermanseder@helmholtz-munich.de
lab head
Ignasi Forne
contact affiliation	Biomedical Center-LMU
contact email	ignasi.forne@lrz.uni-muenchen.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/2025/11/PXD058937

PRIDE project URI

• PRIDE
  1. PXD058937
     1. Label: PRIDE project
     2. Name: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development