PXD050777

PXD050777 is an original dataset announced via ProteomeXchange.

Title	Identification of DNA methylation reader proteins of Arabidopsis thaliana by DNA-affinity pull-down MS and their characterization by IP-MS.
Description	In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (GbM). GbM is correlated with ubiquitously expressed genes, however its function, or absence thereof, is highly debated. The different output that mC can have raises questions as to how it is interpreted - or read - differently in these sequence and genomic contexts. To screen for potential mC binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date were found to preferentially bind to the methylated probes, along with a range of new mC binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to GbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodelling processes in plants.
HostingRepository	PRIDE
AnnounceDate	2025-06-09
AnnouncementXML	Submission_2025-06-08_16:08:43.156.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Owen Duncan
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-19 12:21:57	ID requested
⏵ 1	2025-06-08 16:08:44	announced

10.1101/gr.279379.124;

Cahn J, Lloyd JPB, Karemaker ID, Jansen PWTC, Pflueger J, Duncan O, Petereit J, Bogdanovic O, Millar AH, Vermeulen M, Lister R, . Genome Res, 34(12):2229-2243(2024) [pubmed]

submitter keyword: MBD, Arabidopsis, Plants, DNA affinity pull-down,DNA methylation, Epigenetics, SUVH, AP, LC-MS/MS

Ryan Lister
contact affiliation	ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Australia and Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
contact email	ryan.lister@uwa.edu.au
lab head
Owen Duncan
contact affiliation	UWA
contact email	owen.duncan@uwa.edu.au
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/2025/06/PXD050777

PRIDE project URI

• PRIDE
  1. PXD050777
     1. Label: PRIDE project
     2. Name: Identification of DNA methylation reader proteins of Arabidopsis thaliana by DNA-affinity pull-down MS and their characterization by IP-MS.