<<< Full experiment listing


PXD020290 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAnalysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
DescriptionProtein–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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLuisa Welp
SpeciesList scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: 8355; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue; monohydroxylated residue; acetylated residue
InstrumentQ Exactive HF; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-07-09 18:17:11ID requested
12020-10-20 01:51:07announced
Publication List
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]
Keyword List
submitter keyword: UV-Cross-Linking, Protein-DNA Interactions, Mass Spectrometry
Contact List
Henning Urlaub
contact affiliationMax-Planck-Institute for Biophysical Chemistry
contact emailhenning.urlaub@mpibpc.mpg.de
lab head
Luisa Welp
contact affiliationMax-Planck-Institute for Biophysical Chemistry
contact emaillwelp@gwdg.de
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/2020/10/PXD020290
PRIDE project URI
Repository Record List
[ + ]