Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions
Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions
In this chapter, we describe the proteomic approach named "Native Chromatin Proteomics" (N-ChroP) that couples a modified Chromatin ImmunoPrecipitation (ChIP) protocol with the mass spectrometry (MS) analysis of immunoprecipitated proteins to study the combinatorial enrichment or exclusion of histone post-translational modifications (PTMs) at specific genomic regions, such as promoters or enhancers. We describe the protocol steps from the digestion of chromatin and nucleosome immunoprecipitation to histone digestion and peptide enrichment prior to MS analysis, up to the MS raw data analysis. We also discuss current challenges and offer suggestions based on the direct hands-on experience acquired during the method setup.
Data Analysis, Proteomics, Chromatin Immunoprecipitation, Chromatin; Chromatin immunoprecipitation; Genomic regions; Histone post-translational modifications; Label-free quantification; Mass spectrometry; Proteomics; Chromatin; Chromatin Immunoprecipitation; Chromatography, Liquid; DNA-Binding Proteins; Data Analysis; Histones; Nucleosomes; Tandem Mass Spectrometry; Genomics; Protein Processing, Post-Translational; Proteomics, Genomics, Chromatin, Nucleosomes, DNA-Binding Proteins, Histones, Tandem Mass Spectrometry, Protein Processing, Post-Translational, Chromatography, Liquid
Data Analysis, Proteomics, Chromatin Immunoprecipitation, Chromatin; Chromatin immunoprecipitation; Genomic regions; Histone post-translational modifications; Label-free quantification; Mass spectrometry; Proteomics; Chromatin; Chromatin Immunoprecipitation; Chromatography, Liquid; DNA-Binding Proteins; Data Analysis; Histones; Nucleosomes; Tandem Mass Spectrometry; Genomics; Protein Processing, Post-Translational; Proteomics, Genomics, Chromatin, Nucleosomes, DNA-Binding Proteins, Histones, Tandem Mass Spectrometry, Protein Processing, Post-Translational, Chromatography, Liquid
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