PXD007513

PXD007513 is an original dataset announced via ProteomeXchange.

Title	Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei
Description	Cells organize their actions partly through tightly controlled protein-protein interactions – collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the interactome of intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links connecting distinct proteins. From this data we constructed an overview of the nuclear interactome. We observed that the histone proteins on the nucleosomes expose well-defined crosslinking hot-spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build models of their binding mode to the nucleosome. For HMGN2 the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS and modeling. Excitingly, several isoform-specific interactors seem to exist for distinct histone H1 variants and the analysis of crosslinks carrying post-translational modifications allowed us to extract how specific modifications influence the nucleosome interactome. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.
HostingRepository	PRIDE
AnnounceDate	2018-07-23
AnnouncementXML	Submission_2018-07-23_07:31:46.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Domenico Fasci
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-18 00:19:08	ID requested
⏵ 1	2018-07-23 07:31:47	announced

Fasci D, van Ingen H, Scheltema RA, Heck AJR, Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Mol Cell Proteomics, 17(10):2018-2033(2018) [pubmed]

curator keyword: Biological

submitter keyword: Nuclear interactome, Crosslinking Mass Spectrometry, Nuclear protein-protein interactions, Histone interaction network – PTM interplay, Histone variant specific interactions

Albert J.R. Heck
contact affiliation	Utrecht University
contact email	A.J.R.Heck@uu.nl
lab head
Domenico Fasci
contact affiliation	Utrecht University
contact email	d.fasci@uu.nl
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/2018/07/PXD007513

PRIDE project URI

• PRIDE
  1. PXD007513
     1. Label: PRIDE project
     2. Name: Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei