Exploring the Dynamic Relationship Between Cellular Metabolism and Chromatin Structure Using SILAC-Mass Spec and ChIP-Sequencing

Metabolic state and chromatin structure are tightly linked, enabling adaptation of gene expression to changing environment and metabolism. The bioenergetic pathways and enzymes that provide metabolic cofactors for histone modification have recently emerged as central regulators of chromatin. Current research therefore focuses on the dynamic interface of cellular metabolism and chromatin structure. Here, we provide an adaptable approach to examine broadly in changing physiological states, how chromatin structure is dynamically modulated by metabolic activity. We employ two complementary methods: high-throughput sequencing to establish the location of epigenetic changes, and stable isotope tracing using mass spectrometry to evaluate chromatin modification dynamics. Our two-pronged approach is of particular advantage when interrogating how metabolic and oncogenic mutations influence the dynamic relationship between metabolism, nutritional environment, and chromatin regulation.