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Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry.
Stützer, Alexandra; Welp, Luisa M; Raabe, Monika; Sachsenberg, Timo; Kappert, Christin; Wulf, Alexander; Lau, Andy M; David, Stefan-Sebastian; Chernev, Aleksandar; Kramer, Katharina; Politis, Argyris; Kohlbacher, Oliver; Fischle, Wolfgang; Urlaub, Henning.
Afiliación
  • Stützer A; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Welp LM; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Raabe M; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Sachsenberg T; Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.
  • Kappert C; Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany.
  • Wulf A; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Lau AM; Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany.
  • David SS; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Chernev A; Department of Chemistry, King's College London, London, SE1 1DB, UK.
  • Kramer K; Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Politis A; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia.
  • Kohlbacher O; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
  • Fischle W; CSL Behring GmbH, 35041, Marburg, Germany.
  • Urlaub H; Department of Chemistry, King's College London, London, SE1 1DB, UK.
Nat Commun ; 11(1): 5250, 2020 10 16.
Article en En | MEDLINE | ID: mdl-33067435
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.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: ADN / Cromatina / Proteínas Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2020 Tipo del documento: Article País de afiliación: Alemania

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: ADN / Cromatina / Proteínas Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2020 Tipo del documento: Article País de afiliación: Alemania