Global assessment of combinatorial post-translational modification of core histones in yeast using contemporary mass spectrometry

A global view of all core histones in yeast is provided by tandem mass spectrometry of intact histones H2A, H2B, H4, and H3. This allowed detailed characterization of > 50 distinct histone forms and their semiquantitative assessment in the deletion mutants gcn5 Delta, spt7 Delta, ahc1 Delta, and rtg2 Delta, affecting the chromatin remodeling complexes SAGA, SLIK, and ADA. The "top down" mass spectrometry approach detected dramatic decreases in acetylation on H3 and H2B in gcn5 Delta cells versus wild type. For H3 in wild type cells, tandem mass spectrometry revealed a direct correlation between increases of Lys(4) trimethylation and the 0, 1, 2, and 3 acetylation states of histone H3. The results show a wide swing from 10 to 80% Lys(4) trimethylation levels on those H3 tails harboring 0 or 3 acetylations, respectively. Reciprocity between these chromatin marks was apparent, since gcn5 Delta cells showed a 30% decrease in trimethylation levels on Lys(4) in addition to a decrease of acetylation levels on H3 in bulk chromatin. Deletion of Set1, the Lys(4) methyltransferase, was associated with the linked disappearance of both Lys(4) methylation and Lys(14) and Lys(18) or Lys(23) acetylation on H3. In sum, we have defined the "basis set" of histone forms present in yeast chromatin using a current mass spectrometric approach that both quickly profiles global changes and directly probes the connectivity of modifications on the same histone.