PXD029913

PXD029913 is an original dataset announced via ProteomeXchange.

Title	Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation
Description	Partitioning of active gene loci to the nuclear envelope is a key mechanism by which organisms can increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the budding yeast Saccharomyces cerevisiae, adaptation and transcriptional memory induced by nutrient depletion or other stresses, results from relocalization of active gene loci from nucleoplasm to the nuclear envelope, leading to increased transport of mRNAs to the cytosol and their translation. The mechanism by which this translocation occurs remains a mystery. We show here, that for the inositol depletion-responsive gene locus INO1 in yeast, translocation to the nuclear envelope is caused by a local phase transition of the mechanical stiffness of chromatin surrounding activated INO1 that favors phase separation of the active gene locus into low density regions of chromatin proximal to the nuclear envelope. Gene regulatory elements essential to translocation encode binding sites for histone acetyl transferases, which are necessary for chromatin decompaction. INO1 locus partitioning can be explained by a phenomenological model of chromatin decompaction, which reflects stiffening of chromatin and its partitioning into a dilute chromatin phase adjacent to the nuclear envelope, from the dense chromatin found in the nucleoplasmic phase. Recent evidence suggests that this demixing of chromatin could be due to the dissolution of multivalent chromatin interactions mediated by histone post-translational modifications.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:54:24.362.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marlene Oeffinger
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	biotinylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-25 00:00:13	ID requested
1	2023-03-01 13:00:10	announced
⏵ 2	2023-11-14 08:54:25	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: active gene, nuclear envelope,INO1, gene partitioning, chromatin decompaction, active chromatin, phase separation

Marlene Eloise Oeffinger
contact affiliation	Associate Research Professor, Institut de recherches cliniques de Montréal (IRCM) Professeure agrégée, Département de biochimie et médecine moléculaire, Université de Montréal Associate Professor, Division of Experimental Medicine, McGill University
contact email	marlene.oeffinger@ircm.qc.ca
lab head
Marlene Oeffinger
contact affiliation	Institut de recherches cliniques Montreal (IRCM) Universite de Montreal
contact email	marlene.oeffinger@ircm.qc.ca
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/2023/03/PXD029913

PRIDE project URI

• PRIDE
  1. PXD029913
     1. Label: PRIDE project
     2. Name: Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation