PXD053208

PXD053208 is an original dataset announced via ProteomeXchange.

Title	Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels
Description	The human cell nucleus is comprised of proteins, chromatin and RNA, yet how they interact to form supramolecular structures and drive key biological processes remains unknown. Conflicting models have proposed either a fluid-like or solid-like nature for the intranuclear microenvironment. To reconcile this discrepancy, we investigated the 3D structure and properties of the nuclear interior using experiments and computer simulations. We reveal a novel mechanism where newly synthesized RNA interacts with SAF-A (scaffold attachment factor A, or HNRNPU), forming interconnected microgels degraded by the exonuclease XRN2, leading to dynamic cycles of gelation and fluidization. This emergent microgel network depends on transcription, and is disrupted by SAF- A depletion. It also decreases protein mobility and regulates chromatin compaction by modulating microphase separation, thereby opening transcriptionally active regions. This tunable intranuclear network exhibits scale-dependent fluid- and solid-like features, that we suggest may regulate transcription by controlling access to regulatory proteins and polymerases.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:46:08.942.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nick Gilbert
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-18 09:48:54	ID requested
1	2024-06-18 10:53:46	announced
⏵ 2	2024-10-22 06:46:09	announced	2024-10-22: Updated project metadata.

10.1101/2024.06.16.599208;

submitter keyword: nuclear architecture,Chromatin, transcription, HNRNPU, XRN2, SAF-A, RNA, microphase separation, bridging-induced attraction

Nick Gilbert
contact affiliation	MRC Human Genetics Unit, University of Edinburgh
contact email	nick.gilbert@ed.ac.uk
lab head
Nick Gilbert
contact affiliation	The University of Edinburgh
contact email	nick.gilbert@ed.ac.uk
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/2024/06/PXD053208

PRIDE project URI

• PRIDE
  1. PXD053208
     1. Label: PRIDE project
     2. Name: Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels