PXD057926-1

PXD057926 is an original dataset announced via ProteomeXchange.

Title	The epigenetic reader Phf2 is positioned in the genome by cohesin
Description	Eukaryotic genomes are assembled into chromatin by histones and extruded into loops by cohesin. These mechanisms control important genomic functions, but whether histones and cohesin cooperate in genome regulation is poorly understood. Here we identify Phf2, a member of the Jumonji-C family of histone demethylases, as a cohesin-interacting protein. Phf2 binds to H3K4me3 nucleosomes at active transcription start sites (TSSs) but also co-localizes with cohesin. Cohesin depletion reduces Phf2 binding at sites lacking H3K4me3, and depletion of Wapl and CTCF re-positions Phf2 together with cohesin in the genome, resulting in the accumulation of both proteins in vermicelli and cohesin islands. Conversely, Phf2 depletion reduces cohesin binding at TSSs lacking CTCF, decreases the number of short cohesin loops, but increases the length of heterochromatic B compartments. These results suggest that Phf2 is an ‘epigenetic reader’, which is translocated through the genome by cohesin-mediated DNA loop extrusion, and which recruits cohesin to active TSSs and limits the size of B compartments. These findings reveal an unexpected degree of cooperativity between epigenetic and architectural mechanisms of eukaryotic genome regulation.
HostingRepository	PRIDE
AnnounceDate	2024-12-18
AnnouncementXML	Submission_2024-12-18_03:06:18.343.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Otto Hudecz
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue; acetylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-15 03:45:30	ID requested
⏵ 1	2024-12-18 03:06:18	announced

Dataset with its publication pending

submitter keyword: cohesin, genome regulation, Phf2, epigenetic reader

Jan-Michael Peters
contact affiliation	Research Institute of Molecular Pathology (IMP), Austria
contact email	peters@imp.ac.at
lab head
Otto Hudecz
contact affiliation	IMBA
contact email	hudecz@imp.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD057926
     1. Label: PRIDE project
     2. Name: The epigenetic reader Phf2 is positioned in the genome by cohesin