Bioinformatic and Proteomic Analysis of Bulk Histones Reveals PTM Crosstalk and Chromatin Features

Systems
analysis of chromatin has been constrained by complex patterns
and dynamics of histone post-translational modifications (PTMs), which
represent major challenges for both mass spectrometry (MS) and immuno-based
approaches (e.g., chromatin immuno-precipitation, ChIP). Here we present
a proof-of-concept study demonstrating that crosstalk among PTMs and
their functional significance can be revealed via systematic bioinformatic
and proteomic analysis of steady-state histone PTM levels from cells
under various perturbations. Using high resolution tandem MS, we quantified
53 modification states from all core histones and their conserved
variants in the unicellular eukaryotic model organism Tetrahymena. By correlating histone PTM patterns across 15 different conditions,
including various physiological states and mutations of key histone
modifying enzymes, we identified 5 specific chromatin states with
characteristic covarying histone PTMs and associated them with distinctive
functions in replication, transcription, and DNA repair. In addition
to providing a detailed picture on histone PTM crosstalk at global
levels, this work has established a novel bioinformatic and proteomic
approach, which can be adapted to other organisms and readily scaled
up to allow increased resolution of chromatin states.