PXD057399

PXD057399 is an original dataset announced via ProteomeXchange.

Title	Segmental X-chromosome monosomies are compensated by transcriptional upregulation.
Description	XX mice undergo both X-chromosome inactivation (XCI) and X-chromosome upregulation (XCU) to balance X-linked gene dosage with autosomes and XY mice. XCU has also been reported in XY cells, as well as cells with a single copy of the X-chromosome (XO). The two dosage compensation processes have been shown to occur simultaneously; as one X-chromosome is inactivated, the remaining active X-chromosome becomes upregulated. However, it remains unknown if cells sense and adapt gene dosage at the chromosomal level, or on a gene-by-gene basis. Here, we demonstrate that mouse embryonic stem cells can compensate gene dosage by XCU when specific regions or genes are deleted. Compensation occurs at both the transcriptional and protein levels, and on a gene-by-gene basis. Moreover, we provide evidence for autosomal gene dosage compensation in trans. Overall, our results demonstrate that mammalian cells can sense when specific chromosome regions or genes are heterozygously deleted or inactivated, and can compensate at the transcriptional or protein level with gene specificity. Our results have important implications for our understanding of the evolution of gene dosage compensation, health, and disease.
HostingRepository	PRIDE
AnnounceDate	2025-06-19
AnnouncementXML	Submission_2025-06-19_05:15:58.727.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeroen Demmers
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	2024-10-31 07:46:21	ID requested
⏵ 1	2025-06-19 05:15:59	announced

Dataset with its publication pending

submitter keyword: X-chromosome upregulation (XCU), transcription,X-chromosome, X-chromosome inactivation (XCI)

Jeroen Demmers
contact affiliation	Proteomics Center
contact email	j.demmers@erasmusmc.nl
lab head
Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
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/2025/06/PXD057399

PRIDE project URI

• PRIDE
  1. PXD057399
     1. Label: PRIDE project
     2. Name: Segmental X-chromosome monosomies are compensated by transcriptional upregulation.