PXD016080-2

PXD016080 is an original dataset announced via ProteomeXchange.

Title	Genomic rewiring of Sox2 chromatin interaction network during differentiation of ESCs to postmitotic neurons
Description	Cellular differentiation requires cells to undergo dramatic but strictly controlled changes in chromatin organization, transcriptional regulation, and protein production and interaction. To understand the regulatory connections between these processes, we applied a multi-omics approach integrating proteomic, transcriptomic, chromatin accessibility, protein occupancy, and protein-chromatin interaction data acquired during differentiation of mouse embryonic stem cells (ESCs) into post-mitotic neurons. We found extensive remodeling of the chromatin that was preceding changes on RNA and protein levels. We found the pluripotency factor Sox2 as regulator of neuron-specific genes and, as a potential mechanism, revealed its genomic redistribution from pluripotency enhancers to neuronal promoters and concomitant change of its protein interaction network upon differentiation. We identified Atrx as a major Sox2 partner in neurons, whose co-localisation correlated with an increase in active enhancer marks and increased expression of nearby genes, and where deletion of a Sox2-Atrx co-bound site resulted in reduced expression of the proximal gene. Collectively, these findings provide key insights into the regulatory transformation of Sox2 during neuronal differentiation and highlight the significance of multi-omic approaches in understanding gene regulation in complex systems.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:06:43.120.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nade Abazova
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-30 02:54:37	ID requested
1	2020-06-04 03:28:54	announced
⏵ 2	2024-10-22 05:06:43	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Differentiation, LC-MSMS,Mouse, Neurons, ESCs

Jeroen Krijgsveld
contact affiliation	German Cancer Research Center (DKFZ)
contact email	j.krijgsveld@dkfz-heidelberg.de
lab head
Nade Abazova
contact affiliation	DKFZ, EMBL
contact email	nade.abazova@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/2020/06/PXD016080

PRIDE project URI

• PRIDE
  1. PXD016080
     1. Label: PRIDE project
     2. Name: Genomic rewiring of Sox2 chromatin interaction network during differentiation of ESCs to postmitotic neurons