PXD002452

PXD002452 is an original dataset announced via ProteomeXchange.

Title	Characterisation of two distinct Nucleosome Remodelling and Deacetylase Complex (NuRD) assemblies in embryonic stem cells.
Description	Pluripotency and self-renewal, the defining properties of embryonic stem cells, are brought about by transcriptional programs involving an intricate network of transcription factors and chromatin remodelling complexes. The Nucleosome Remodelling and Deacetylase (NuRD) complex plays a crucial and dynamic role in the regulation of stemness and differentiation. Several NuRD-associated factors have been reported but how they are organised has not been investigated in detail. Here, we have combined affinity purification and blue native polyacrylamide gel electrophoresis followed by protein identification by mass spectrometry and protein correlation profiling to characterise the topology of the NuRD complex. Our data show that in mouse embryonic stem cells the NuRD complex is present as two distinct assemblies of differing topology with different binding partners. Cell cycle regulator Cdk2ap1 and transcription factor Sall4 associate only with the higher mass NuRD assembly. We further establish that only isoform Sall4A, and not Sall4B, associates with NuRD. By contrast, Suz12, a component of the PRC2 Polycomb repressor complex, associates with the lower mass entity. In addition, we identify and validate a novel NuRD-associated protein, Wdr5, a regulatory subunit of the MLL histone methyltransferase complex, which associates with both NuRD entities. Bioinformatic analyses of published target gene sets of these chromatin binding proteins are in agreement with these structural observations. In summary, this study provides an interesting insight into mechanistic aspects of NuRD function in stem cell biology. The relevance of our work has broader implications because of the ubiquitous nature of the NuRD complex. The strategy described here can be more broadly applicable to investigate the topology of the multiple complexes an individual protein can participate in.
HostingRepository	PRIDE
AnnounceDate	2016-01-05
AnnouncementXML	Submission_2016-01-05_14:23:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Wright
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-30 04:51:33	ID requested
⏵ 1	2016-01-05 14:23:37	announced

Bode D, Yu L, Tate P, Pardo M, Choudhary J, Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells. Mol Cell Proteomics, 15(3):878-91(2016) [pubmed]

curator keyword: Biological

submitter keyword: Nucleosome Remodelling, Deacetylase Complex, LC-MS/MS, NURD, Blue Native, Mouse, Embryonic Stem Cells, Affinty Purification

Jytoi Choudhary
contact affiliation	Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
contact email	jc4@sanger.ac.uk
lab head
James Wright
contact affiliation	Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute
contact email	jw13@sanger.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/2016/01/PXD002452

PRIDE project URI

• PRIDE
  1. PXD002452
     1. Label: PRIDE project
     2. Name: Characterisation of two distinct Nucleosome Remodelling and Deacetylase Complex (NuRD) assemblies in embryonic stem cells.