PXD029508

PXD029508 is an original dataset announced via ProteomeXchange.

Title	Identification and profiling of dynamic changes of site-specific histone acylations in HEK293T cells under metabolites treatment
Description	1. Systematic survey of PTM site and stoichiometry on histone proteins has been lagged behind due to the lack of efficient quantitative peptide comparison methodology on histone proteins. Our quantitative mass spectrometry-based proteomics approach, Site-Profiling, used SILAC-based peptide ratio analysis on histone acylations with and without SCFA-derived metabolic treatment to directly compare the same peptide with the same modification and the same chain length. Different from the published methods that isotopically labeled metabolites, which might cause false-positive results and information lost, we only labelled all the lysines and arginines in histones and thus the same modification under native conditions would be kept, resulting that all modification peptides were comparable in parallel before and after metabolites stimulation. By a comprehensive analysis of all peptides containing the same histone marks, Site-Map can compare the abundance of each site-specific modification upon the treatment of the corresponding metabolite. 2. To reveal the site dependency of histone Kbhb distributed at the super enhancer region, we developed a method to isolate the super enhancer condensates by co-immunoprecipitation with coactivators BRD4. Same site-mapping method was utilized for comparasion the site dependency of histone Kbhb enriched with BRD4 or not.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:35:06.437.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fangfei Qin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; 6x(13)C labeled residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-02 06:34:43	ID requested
1	2023-03-05 21:03:05	announced
⏵ 2	2023-11-14 08:35:07	announced	2023-11-14: Updated project metadata.

Qin F, Li B, Wang H, Ma S, Li J, Liu S, Kong L, Zheng H, Zhu R, Han Y, Yang M, Li K, Ji X, Chen PR, Linking chromatin acylation mark-defined proteome and genome in living cells. Cell, 186(5):1066-1085.e36(2023) [pubmed]

submitter keyword: HEK293T, histone acylation, site-specific, LC-MS/MS

Peng R. Chen
contact affiliation	1Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China 2Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China 3Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
contact email	pengchen@pku.edu.cn
lab head
Fangfei Qin
contact affiliation	Peking University
contact email	faqpku@163.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/2023/03/PXD029508

PRIDE project URI

• PRIDE
  1. PXD029508
     1. Label: PRIDE project
     2. Name: Identification and profiling of dynamic changes of site-specific histone acylations in HEK293T cells under metabolites treatment