PXD010644

PXD010644 is an original dataset announced via ProteomeXchange.

Title	Plasmodium falciparum bromo-domain containing epigenetic protein complexes recruited to modified histone tails as identified by histone peptide pulldown (HPP)-MS/MS and further characterized by GFP-IP-MS/MS and HA-IP-MS/MS
Description	In order to identify epigenetic protein complexes recruited to histone PTMs in the deadly human malaria parasite Plasmodium falciparum, we set out to perform histone peptide pulldowns with various histone peptides. Biotinylated peptides corresponding to P. falciparum histone variant H2A.Z, H2B.Z and H3.3, canonical P. falciparum histone H4 or human histone H4 tail sequences (differing on position 21 from the P. falciparum peptide) bearing multiple histone post-translational modifications (acetylations and/or methylations) as well as the unmodified control peptides were coupled to beads and incubated with native nuclear extract obtained from mixed-stage asexual cultures. Proteins preferentially binding to the modified histone peptide were identified by quantitative proteomics using di-methyl labelling. This yielded 6 out of 7 P. falciparum bromo-domain proteins preferentially binding to the acetylated histone peptides, as well as many putative bromo-domain protein interactors. In addition, a PHD-domain containing protein was found to be recruiting a PfSAGA-like complex to H3K4 di- and tri-methylated peptides. 7 reader-domain containing proteins (BDP1, BDP2, BDP4, TAF1, GCN5, PHD1, PHD2) and 5 putative interactors (PF3D7_0306100, PF3D7_1124300, PF3D7_1128000, PF3D7_1225200, PF3D7_1451200) were endogenously tagged by GFP or HA and used in quantitative GFP-/HA-IP-MS/MS experiments to further characterize epigenetic reader-complex composition. As negative control, GFP- and HA-IPs were performed on native nuclear extract not encoding tagged protein. Most HPP experiment employed a 3-label setup, while few only relied on “light” and “heavy”-label sample pools (labels and conditions listed below). GFP- and HA-IP experiments were using a 2-label “light” and “heavy” di-methyl setup only. For all experiments technical replicates were performed using a label-swap approach (called F (forward) and R (reverse)) and independent biological replicates were performed for each. For GFP- and HA-IP forward reactions are set-up as: GFP-/HA-beads = “heavy” di-methyl label, control-beads = “light” di-methyl label. Reverse reactions are set-up as: GFP-/HA-beads = “light” di-methyl label, control-beads = “heavy” di-methyl label. For GFP-/HA-IP raw files the bait and tag used for fishing are included in the file name.
HostingRepository	PRIDE
AnnounceDate	2019-10-16
AnnouncementXML	Submission_2019-10-15_23:37:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wieteke Hoeijmakers
SpeciesList	scientific name: Plasmodium falciparum; NCBI TaxID: 5833;
ModificationList	L-cysteine methyl disulfide
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-01 03:50:04	ID requested
⏵ 1	2019-10-15 23:37:43	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Plasmodium falciparum, histone peptide pulldown, HPP, histone acetylation, histone methylation, GFP-IP, HA-IP, bromo-domain protein, epigenetic complex, reader complex, interactor, GCN5, TAF1

Dr. Richard Bartfai
contact affiliation	Dr. Richard Bartfai ; Department of Molecular Biology ; Faculty of Science ; Radboud University ; Geert Grooteplein 28 ; 6525GA Nijmegen, The Netherlands; Tel.: +31 (0)24-3610561 ; r.bartfai@science.ru.nl
contact email	r.bartfai@science.ru.nl
lab head
Wieteke Hoeijmakers
contact affiliation	Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen The Netherlands
contact email	w.hoeijmakers@ncmls.ru.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/2019/10/PXD010644

PRIDE project URI

• PRIDE
  1. PXD010644
     1. Label: PRIDE project
     2. Name: Plasmodium falciparum bromo-domain containing epigenetic protein complexes recruited to modified histone tails as identified by histone peptide pulldown (HPP)-MS/MS and further characterized by GFP-IP-MS/MS and HA-IP-MS/MS