Figure 4. Stable isotope labeling by amino acids in cell culture nucleosome affinity purification.

First, chemically modified histones are prepared, assembled into nucleosomes with biotinylated DNA and finally immobilized on streptavidin beads. The recombinant nucleosomes containing methylated or unmethylated DNA are treated with nuclear extracts from metabolically labeled cells. The beads are washed and combined, and the bound proteins are eluted and mixed in a 1:1 ratio, resolved with SDS-PAGE gel, in-gel digested and analyzed by MS.

LC–MS: Liquid chromotography–mass spectrometry; MS: Mass spectrometry.