PXD053371-1

PXD053371 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Histone H3.3 lysine 9 and 27 control repressive chromatin states at cryptic cis-regulatory elements and bivalent promoters in mouse embryonic stem cells
Description	Histone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutated histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleashed cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupted deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal level of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states at cis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.
HostingRepository	MassIVE
AnnounceDate	2024-09-01
AnnouncementXML	Submission_2024-09-01_09:05:11.685.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matteo Trovato
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Acetyl; Methyl; Dimethyl; Trimethyl
Instrument	Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-24 13:03:51	ID requested
⏵ 1	2024-09-01 09:05:12	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: H3.3, histone modifications, chromatin, transcriptional regulation, endogenous retroviruses, mouse embryonic stem cells

submitter keyword: H3.3, histone modifications, chromatin, transcriptional regulation, endogenous retroviruses, mouse embryonic stem cells

Contact List

Matteo Trovato
contact affiliation	European Molecular Biology Laboratory (EMBL)
contact email	matteo.trovato@embl.de
lab head
Kyung-Min Noh
contact affiliation	European Molecular Biology Laboratory (EMBL)
contact email	kyung.min.noh@embl.de
lab head
Matteo Trovato
contact affiliation	EMBL
contact email	matteo.trovato@embl.de
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive.ucsd.edu/v08/MSV000095134/