PXD022369

PXD022369 is an original dataset announced via ProteomeXchange.

Title	DNA damage-induced chromatome analysis in yeast reveals recruitment of Ubiquitin ligases for efficient DNA repairtest1
Description	Eukaryotic cells package their genomes around histone octamers. In response to DNA damage checkpoint kinase-induced core histone degradation leads to a 20-40% reduction in nucleosome density in yeast. To gain insights into this process we report the first comprehensive proteomic analysis of yeast chromatin and the alterations that occur in response to DNA damage. We analyzed the protein content of formaldehyde cross-linked chromatin using tandem mass tag (TMT), multiplexing and high-resolution mass spectrometry (MS), after sucrose gradient enrichment of the chromatin fraction. Quantitative damage-induced changes in the chromatin-bound proteome (called chromatome), were compared among wild-type cells and those defective for the INO80 remodeler (arp8Δ), or high mobility group box proteins (Nhp6a and Nhp6b, nhp6ΔΔ). We find massive changes in the chromatome in response to Zeocin, which are strongly attenuated in cells lacking a functional INO80 remodeler.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:36:50.095.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jan Seebacher
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; ubiquitinylated lysine; N6-methyl-L-lysine; phosphorylated residue; acetylated residue; monohydroxylated residue; N6,N6,N6-trimethyl-L-lysine; N6,N6-dimethyl-L-lysine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-05 01:08:31	ID requested
⏵ 1	2024-10-07 13:36:50	announced

Dataset with its publication pending

submitter keyword: HMGB1/NHP6, DNA dynamics, S. Cerevisiae,tesChromatome, Chromatin proteomics, INO80, Ubiquitin ligases, Proteasome, Zeocin, homologous recombination, DNA damage response, Histone degradation

Susan Gasser
contact affiliation	Friedrich Miescher Institute for Biomedical Research (FMI) Basel, Switzerland
contact email	susan.gasser@fmi.ch
lab head
Jan Seebacher
contact affiliation	FMI Basel
contact email	jan.seebacher@fmi.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/2021/02/PXD022369

PRIDE project URI

• PRIDE
  1. PXD022369
     1. Label: PRIDE project
     2. Name: DNA damage-induced chromatome analysis in yeast reveals recruitment of Ubiquitin ligases for efficient DNA repairtest1