Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

Matthew M. Makowski, Cathrin Gräwe, Benjamin M. Foster, Nhuong V. Nguyen, Till Bartke () and Michiel Vermeulen ()
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Matthew M. Makowski: Radboud University
Cathrin Gräwe: Radboud University
Benjamin M. Foster: Helmholtz Zentrum München
Nhuong V. Nguyen: MRC London Institute of Medical Sciences (LMS)
Till Bartke: Helmholtz Zentrum München
Michiel Vermeulen: Radboud University

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract Interaction proteomics studies have provided fundamental insights into multimeric biomolecular assemblies and cell-scale molecular networks. Significant recent developments in mass spectrometry-based interaction proteomics have been fueled by rapid advances in label-free, isotopic, and isobaric quantitation workflows. Here, we report a quantitative protein–DNA and protein–nucleosome binding assay that uses affinity purifications from nuclear extracts coupled with isobaric chemical labeling and mass spectrometry to quantify apparent binding affinities proteome-wide. We use this assay with a variety of DNA and nucleosome baits to quantify apparent binding affinities of monomeric and multimeric transcription factors and chromatin remodeling complexes.

Date: 2018
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DOI: 10.1038/s41467-018-04084-0

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