PXD020290-2

PXD020290 is an original dataset announced via ProteomeXchange.

Title	Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
Description	Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by UV light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain completely new insights into chromatin and its regulation in the future.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:13:52.371.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luisa Welp
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue
Instrument	Q Exactive HF; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-09 18:17:11	ID requested
1	2020-10-20 01:51:07	announced
⏵ 2	2024-10-22 05:14:00	announced	2024-10-22: Updated project metadata.

10.1038/s41467-020-19047-7;

St, ü, tzer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H, Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nat Commun, 11(1):5250(2020) [pubmed]

submitter keyword: Mass Spectrometry, Protein-DNA Interactions,UV-Cross-Linking

Henning Urlaub
contact affiliation	Max-Planck-Institute for Biophysical Chemistry
contact email	henning.urlaub@mpibpc.mpg.de
lab head
Luisa Welp
contact affiliation	Max-Planck-Institute for Biophysical Chemistry
contact email	lwelp@gwdg.de
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/2020/10/PXD020290

PRIDE project URI

• PRIDE
  1. PXD020290
     1. Label: PRIDE project
     2. Name: Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry