PXD062203

PXD062203 is an original dataset announced via ProteomeXchange.

Title	PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow.
Description	Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which are costly reagents that often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), which enables, in the same workflow, to identify the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions across the genome or to specifically detect proteins which are ubiquitin(-like) modified. After a short biotin pulse, DNA-protein crosslinks are induced by formaldehyde and the interactors of a protein of interest, together with their associated DNA sequences, are purified simultaneously and identified by mass spectrometry-based proteomics and Next Generation Sequencing, respectively. To validate PLAMseq, we performed the proteo-genomic characterization of two proteins which genomic loci are very well characterized, namely, RNA polymerase II and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize Histone H1 SUMOylation, a histone post-translational modification which study has remained elusive due to the lack of specific reagents. We found that SETDB1 binds to SUMOylated histone H1.2 and H1.4 and, accordingly, SUMOylated histone H1 colocalizes with H3K9me3 at repetitive regions of the genome.
HostingRepository	PRIDE
AnnounceDate	2025-10-29
AnnouncementXML	Submission_2025-10-28_17:21:00.752.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Román González-Prieto
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-25 04:14:46	ID requested
⏵ 1	2025-10-28 17:21:01	announced

10.1126/SCIADV.ADY4151;

submitter keyword: None

Román González-Prieto
contact affiliation	CABIMER
contact email	roman.gonzalez@cabimer.es
lab head
Román González-Prieto
contact affiliation	Andalusian Center for Regenerative Medicine and Cell Biology, CABIMER, University of Seville
contact email	roman.gonzalez@cabimer.es
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/2025/10/PXD062203

PRIDE project URI

• PRIDE
  1. PXD062203
     1. Label: PRIDE project
     2. Name: PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow.