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  Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Stützer, A., Welp, L., Raabe, M., Sachsenberg, T., Kappert, C., Wulf, A., et al. (2020). Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications, 11: 5250. doi:10.1038/s41467-020-19047-7.

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 Creators:
Stützer, A.1, Author              
Welp, L.2, Author              
Raabe, Monika1, Author              
Sachsenberg, T., Author
Kappert, C., Author
Wulf, A.2, Author              
Lau, A. M., Author
David, S.-S., Author
Chernev, A.2, Author              
Kramer, K., Author
Politis, A., Author
Kohlbacher, O., Author
Fischle, W., Author
Urlaub, H.1, Author              
Affiliations:
1Research Group of Bioanalytical Mass Spectrometry, MPI for biophysical chemistry, Max Planck Society, ou_578613              
2Research Group of Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Max Planck Society, ou_578613              

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Free keywords: DNA, DNA-binding proteins, Mass spectrometry, Proteomics, Structural Biology
 Abstract: 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 ultraviolet (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 insights into chromatin and its regulation in the future.

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Language(s): eng - English
 Dates: 2020-10-16
 Publication Status: Published online
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 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41467-020-19047-7
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Title: Nature Communications
Source Genre: Journal
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Pages: 12 Volume / Issue: 11 Sequence Number: 5250 Start / End Page: - Identifier: -