PXD041712
PXD041712 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | The TDG interactome connects active DNA demethylation with chromatin and RNA biology |
| Description | Controlled gene expression requires the crosstalk of different chromatin-targeted mechanisms to regulate the accessibility and configuration of the genome for transcription. Dynamic DNA methylation is of them, but its role in chromatin organization is poorly understood. We set out to explore the functional space of the DNA glycosylase and demethylase TDG in mouse embryonic stem cells (mESCs). Taking advantage of the unbiased proximity ligation method (BIOID2), we discovered a series of novel TDG interacting partners relating to functions beyond DNA bases excision repair. We identified proteins functionally involved in chromatin remodeling, such as RUVBL2 and SMARCA4, and also with HCFC1, which has been shown to tether the histone methyltransferase MLL complex to important regulatory sites. Moreover, we could discover a new role of TDG with RNA-binding proteins and demonstrate that TDG is associated with the paraspeckle components, including the noncoding RNA Neat1. Its ability to associate with several noncoding RNAs and process DNA in R-loops suggests a function of such structures in regulating active DNA demethylation. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-11-26 |
| AnnouncementXML | Submission_2025-11-26_01:19:27.184.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Katarzyna Buczak |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | LTQ Orbitrap Elite |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-04-21 02:05:25 | ID requested | |
| ⏵ 1 | 2025-11-26 01:19:28 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Active DNA demethylation, TDG, chromatin and epigenetics, RNA biology, BIOID2 method, mouse embryonic stem cells |
Contact List
| Alexander Schmidt | |
|---|---|
| contact affiliation | Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland |
| contact email | alex.schmidt@unibas.ch |
| lab head | |
| Katarzyna Buczak | |
| contact affiliation | Biozentrum, University of Basel |
| contact email | katarzyna.buczak@unibas.ch |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive-ftp.ucsd.edu/v05/MSV000091764/ |
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