PXD002062

PXD002062 is an original dataset announced via ProteomeXchange.

Title	Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics
Description	Cellular reprogramming remodels the gene expression program by re-setting the epigenome of somatic cells into an embryonic-like state. Post-translational modifications of histones play an important role in this process. We previously used ChIP-seq to profile the distribution of specific histone H3 marks during the entire reprogramming process and found widespread loss of H3K27me3 in the initial stages[1]. Here, using an unbiased middle-down proteomics approach we have identified 74 unique isoforms of histone H4 and quantified them across nine stages of reprogramming. Our data showed substantial differences between the precursor cells and late-phase reprogramming cells. Also, ESCs and iPSCs displayed higher levels of H4 acetylation and tri-methylation concomitantly with lower levels of mono- and di-methylation when compared to cells undergoing reprogramming. These results suggest that during reprogramming, the histone H4 “PTM code” experiences dynamic changes in multiple waves, with a final reset taking place during the transition to an ESC-like state, in perfect agreement with the in-parallel generated multi-omics data[1]. Together, these data represent an invaluable resource to study PTMs of H4 and their potential cross-talk and extend our knowledge on the epigenetic mechanisms involved in acquisition of induced pluripotency.
HostingRepository	PRIDE
AnnounceDate	2015-08-17
AnnouncementXML	Submission_2015-08-17_03:47:29.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marco Benevento
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; phosphorylated residue; trimethylated residue; monomethylated residue; dimethylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-04-13 08:38:46	ID requested
⏵ 1	2015-08-17 03:47:30	announced

Benevento M, Tonge PD, Puri MC, Nagy A, Heck AJ, Munoz J, Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics. Proteomics, 15(18):3219-31(2015) [pubmed]

curator keyword: Biological, Technical

submitter keyword: Middle-down, proteomics, Histone H4, cellular reprogramming, Post translational modifications

Javier Muñoz
contact affiliation	Spanish National Cancer Research Centre (CNIO) ProteoRed-ISCIII Melchor Férnandez Almagro, 3 28029 Madrid. SPAIN
contact email	jmunozpe@cnio.es
lab head
Marco Benevento
contact affiliation	Faculty of Sciences
contact email	m.benevento@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/2015/08/PXD002062

PRIDE project URI

• PRIDE
  1. PXD002062
     1. Label: PRIDE project
     2. Name: Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics