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

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.

SUBMITTER: Makowski MM

PROVIDER: S-EPMC5916898 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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

Makowski Matthew M MM Gräwe Cathrin C Foster Benjamin M BM Nguyen Nhuong V NV Bartke Till T Vermeulen Michiel M

Nature communications 20180425 1

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 m ...[more]

PMID: 29695722

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

Project description: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.

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