PXD014483

PXD014483 is an original dataset announced via ProteomeXchange.

Title	ChromID reveals the proteome composition of key chromatin states in murine stem cells
Description	Chromatin modifications instruct genome function through spatiotemporal recruitment of regulatory factors to the genome. However, how these modifications define the proteome composition at distinct chromatin states remains to be fully characterized. Here, we made use of natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for histone and DNA modifications. By stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomicdistribution and histone-PTM-binding preference, we first demonstrate their applicability as selective chromatin binders in living cells. Finally, we exploit the binding specificity of eCRs to establish ChromID, a new method for chromatin-dependent proteome identification based on proximity biotinylation. We use ChromID to reveal the proteome at distinct chromatin states in mouse stem cells, and by using a synthetic dual-modification reader, we furthermore uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the applicability of ChromID as novel method to obtaina detailed view of the protein interaction network determined by the chemical language on chromatin.
HostingRepository	PRIDE
AnnounceDate	2020-04-30
AnnouncementXML	Submission_2020-04-29_22:02:40.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tuncay Baubec
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-04 03:48:52	ID requested
⏵ 1	2020-04-29 22:02:41	announced

Villase, ñ, or R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T, ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol, 38(6):728-736(2020) [pubmed]

curator keyword: Biological

submitter keyword: Chromatin, Epigenetics, Synthetic Biology, Systems Biology, Chromatin Proteomics

Tuncay Baubec
contact affiliation	SNF Professor - Principal Investigator Systems Biology of Gene Regulation University of Zurich Campus Irchel Winterthurerstrasse 190 CH-8057 Zurich Switzerland
contact email	tuncay.baubec@uzh.ch
lab head
Tuncay Baubec
contact affiliation	University of Zurich
contact email	tuncay.baubec@uzh.ch
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/2020/04/PXD014483

PRIDE project URI

• PRIDE
  1. PXD014483
     1. Label: PRIDE project
     2. Name: ChromID reveals the proteome composition of key chromatin states in murine stem cells