PXD028063-1

PXD028063 is an original dataset announced via ProteomeXchange.

Title	Defining proximity proteomics of Histone modifications by antibody-mediated protein A-APEX2 labeling
Description	Proximity labeling catalyzed by promiscuous enzymes, such as APEX2, has emerged as a powerful approach to characterize multiprotein complexes and protein–protein interactions. However, current methods depend on the expression of exogenous fusion proteins and cannot be applied to identify proteins surrounding of post-translationally modified proteins. To address this limitation, we developed a new method to label proximal proteins of interest by antibody-mediated protein A-APEX2 labeling (AMAPEX). In this method, a modified protein is bound in situ by a specific antibody, which then tehers a protein A-APEX2 (pA-APEX2) fusion protein. Activation of APEX2 labels the nearby proteins with biotin; these proteins are then purified using streptavidin beads and are identified by mass spectrometry. We demonstrate the utility of this approach by profiling the binding proteins of histone modifications including H3K27me3, H3K9me3, H3K4me3, H4K5ac and H4K12ac, verified the co-localization of these identified proteins with baits proteins by published ChIP-seq analysis and nucleosome immunoprecipitation. Overall, AMAPEX is an efficient tool to identify proteins that are proximal to modified histones.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_13:42:13.029.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	zhao wenjuan
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	methylated lysine; acetylated residue; monohydroxylated residue; N6,N6,N6-trimethyl-L-lysine; iodoacetamide derivatized residue; N6,N6-dimethyl-L-lysine
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-23 06:36:48	ID requested
⏵ 1	2024-10-07 13:42:13	announced
2	2024-10-22 05:53:45	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Proximity labeling

Post-translationally

AMAPEX

Modified histones

Li Nan
contact affiliation	Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
contact email	nan.li@siat.ac.cn
lab head
zhao wenjuan
contact affiliation	Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences
contact email	wj.zhao1@siat.ac.cn
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/2023/07/PXD028063

PRIDE project URI

• PRIDE
  1. PXD028063
     1. Label: PRIDE project
     2. Name: Defining proximity proteomics of Histone modifications by antibody-mediated protein A-APEX2 labeling