PXD045745-1

PXD045745 is an original dataset announced via ProteomeXchange.

Title	Molecular basis for the interaction of intrinsically disordered proteins with nuclear PIP2 compartments
Description	Phosphatidylinositol 4,5 bisphosphate (PIP2) is the most abundant eukaryotic nuclear phosphoinositide. PIP2 is found in the nuclear speckles (NS), nucleoli (NL), and nuclear lipid islets (NLIs) and participates in the RNA polymerase II (Pol2) transcription. The formation of phase-separated nuclear sub-compartments, such as NS and NL, as well as PIP2 localization, depends on RNA. Thus, we studied if the PIP2 and RNA cooperate in the establishment of nuclear architecture. We identified the RNA-dependent PIP2-associated (RDPA) nuclear proteome in human cells. RDPA proteome participates in all steps of gene expression, and typical RDPA protein possesses RNA binding and phase separation capacity. RDPA proteins associate with PIP2 by electrostatic interactions, which depend on intact RNA and the phase separation capacity of the participating proteins. Moreover, we identified that intrinsically disordered regions (IDRs) with polybasic PIP2-binding K/R-motifs are common structural features of RDPA proteins and confirmed that manipulation of the PIP2 level changes the nuclear localization of RDPA proteins. We showed that PIP2 spatiotemporally orchestrates nuclear processes through association with RNA and RDPA proteins and their capacity to phase separate, which is the first evidence that PIP2 is crucial for establishment of functional nuclear architecture competent for gene expression.
HostingRepository	PRIDE
AnnounceDate	2024-09-30
AnnouncementXML	Submission_2024-09-30_08:50:45.433.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbora Salovska
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-27 13:48:42	ID requested
⏵ 1	2024-09-30 08:50:45	announced
2	2024-10-22 07:00:08	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: AP-MS,PIP2

Martin Sztacho
contact affiliation	Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
contact email	martin.sztacho@img.cas.cz
lab head
Barbora Salovska
contact affiliation	Yale Cancer Biology Institute
contact email	salovska.b@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/2024/09/PXD045745

PRIDE project URI

• PRIDE
  1. PXD045745
     1. Label: PRIDE project
     2. Name: Molecular basis for the interaction of intrinsically disordered proteins with nuclear PIP2 compartments