PXD002282

PXD002282 is an original dataset announced via ProteomeXchange.

Title	Reader interactome of epigenetic histone marks in birds
Description	Lysine methylation is part of the posttranscriptional histone code employed to recruit modification specific readers to chromatin. Unbiased, quantitative mass spectrometry approaches combined with peptide pull-downs have been used to study histone methylation-dependent binders in mammalian cells. Here, we extend the study to birds by investigating the interaction partners for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 in chicken (gallus gallus) and zebra finch (taeniopygia guttata) using label free quantitative proteomics. In general, we find very strong overlap in interaction partners for the trimethyl marks in birds compared to mammals, underscoring the known conserved function of these modifications. In agreement with their epigenetic role, we find binding of PHF2 and members of the TFIID, SAGA, SET1 and NURF complex to the activation mark H3K4me3. Our data furthermore supports the existence of a LID complex in vertebrates recruited to the H3K4me3. The repressive marks are bound by the HP1 proteins and the EED subunit of the PRC2 complex as well as by WIZ. Like the screens in mammals, we found ZNF462, ZNF828 and POGZ enriched at H3K9me3. However, we noted some unexpected differences. First, we did not observe the enrichment of CDYL and CDYL2 at the repressive marks. Second N-PAC (also known as GLYR1), an H3K36me3 interactor in mammals, is not binding to this modification in our screen. This suggests that despite strong conservation of the histone tail sequence, species-specific differences in epigenetic readers may have evolved.
HostingRepository	PRIDE
AnnounceDate	2016-01-04
AnnouncementXML	Submission_2016-01-04_07:58:17.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	F Butter
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Taeniopygia guttata (Zebra finch) (Poephila guttata); NCBI TaxID: 59729;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-02 00:37:31	ID requested
⏵ 1	2016-01-04 07:58:18	announced

Bluhm A, Casas-Vila N, Scheibe M, Butter F, Reader interactome of epigenetic histone marks in birds. Proteomics, 16(3):427-36(2016) [pubmed]

curator keyword: Biological

submitter keyword: LC-MSMS, birds, interactome, histone

Falk Butter
contact affiliation	Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
contact email	f.butter@imb.de
lab head
F Butter
contact affiliation	Dept. of Proteomics and Signal Transduction
contact email	f.butter@imb-mainz.de
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/PXD002282

PRIDE project URI

• PRIDE
  1. PXD002282
     1. Label: PRIDE project
     2. Name: Reader interactome of epigenetic histone marks in birds