<<< Full experiment listing

PXD028063

PXD028063 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDefining proximity proteomics of Histone modifications by antibody-mediated protein A-APEX2 labeling
DescriptionProximity 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:53:45.212.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterzhao wenjuan
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListmethylated lysine; acetylated residue; monohydroxylated residue; N6,N6,N6-trimethyl-L-lysine; iodoacetamide derivatized residue; N6,N6-dimethyl-L-lysine
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-08-23 06:36:48ID requested
12024-10-07 13:42:13announced
22024-10-22 05:53:45announced2024-10-22: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Proximity labeling
Post-translationally
AMAPEX
Modified histones
Contact List
Li Nan
contact affiliationShenzhen 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 emailnan.li@siat.ac.cn
lab head
zhao wenjuan
contact affiliationInstitute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences
contact emailwj.zhao1@siat.ac.cn
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]