PXD030181

PXD030181 is an original dataset announced via ProteomeXchange.

Title	A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development
Description	Histone post-translational modifications (PTMs) are frequently co-occurring on the same chromatin domains or even the same molecule. It is now established that these ‘histone codes’ are the result of cross-talk between enzymes that catalyse multiple PTMs with univocal readout as compared to these PTMs in isolation. Here, we performed a comprehensive identification and quantification of histone codes of the malaria parasite, Plasmodium falciparum. We used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 72 PTMs on H3 and H3.3, of which 30 newly identified. Several co-existing PTMs with unique stage distinction was identified, indicating that many of these combinatorial PTMs are associated to specific stages of the parasite life cycle. We focused on the code H3R17me2K18acK23ac for its unique presence in mature gametocytes; chromatin proteomics identified a gametocyte-specific SAGA-like effector complex including the transcription factor AP2-G2 which we associated to this specific histone code, as involved in regulating gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with co-existing partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher order gene regulation for distinct proliferation and differentiation processes.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:43:43.988.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simone Sidoli
SpeciesList	scientific name: Plasmodium falciparum V1; NCBI TaxID: 5847;
ModificationList	monomethylated residue; phosphorylated residue; acetylated residue; N6,N6,N6-trimethyl-L-lysine (from L-lysinium residue); N6,N6-dimethyl-L-lysine
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-05 04:35:03	ID requested
⏵ 1	2024-10-07 13:43:44	announced

von Gr, ü, ning H, Coradin M, Mendoza MR, Reader J, Sidoli S, Garcia BA, Birkholtz LM, A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development. Mol Cell Proteomics, 21(3):100199(2022) [pubmed]

10.1016/j.mcpro.2022.100199;

submitter keyword: malaria, middle-down mass spectrometry proteomics, post-translational modification, parasite, PTM,Gametocyte, histone code, Plasmodium falciparum

Simone Sidoli
contact affiliation	Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
contact email	simone.sidoli@einsteinmed.org
lab head
Simone Sidoli
contact affiliation	Albert Einstein College of Medicine
contact email	simone.sidoli@gmail.com
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/2022/05/PXD030181

PRIDE project URI

• PRIDE
  1. PXD030181
     1. Label: PRIDE project
     2. Name: A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development