PXD056346-1

PXD056346 is an original dataset announced via ProteomeXchange.

Title	Inherited folding programs: SILAC LC-MS of early G1 isolated nuclei formed in the presence or absence of Nup93- or RanGAP1-AID
Description	Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, this chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. The microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis. In our proteomics dataset we identify factors requiring nuclear import to access the genome at the end of mitosis.
HostingRepository	PRIDE
AnnounceDate	2025-11-05
AnnouncementXML	Submission_2025-11-04_22:07:25.995.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Allana Schooley
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	6x(13)C labeled residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-28 13:26:14	ID requested
⏵ 1	2025-11-04 22:07:26	announced

Dataset with its publication pending

submitter keyword: early G1, LC-MS, human, DLD1-RanGAP1-AID, SILAC, DLD1-Nup93-AID, nuclear isolation

Job Dekker
contact affiliation	Department of Systems Biology, University of Massachusetts Chan Medical School, investigator of the Howard Hughes Medical Institute.
contact email	job.dekker@umassmed.edu
lab head
Allana Schooley
contact affiliation	UMass Chan Medical School
contact email	allana.schooley@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD056346
     1. Label: PRIDE project
     2. Name: Inherited folding programs: SILAC LC-MS of early G1 isolated nuclei formed in the presence or absence of Nup93- or RanGAP1-AID