Mass Spectrometry and Epigenetics

Abstract

Chromatin is a nucleoprotein complex composed of DNA and histone proteins. The concerted activity of chromatin-associated proteins, histone post-transla-tional modifications, and DNA methylation induces epigenetic variations that regulate most of the physiological processes of eukaryotic cells, ranging from gene expression to DNA replication and repair. Epigenetics has also been shown to be tightly linked to cell metabolism. For instance, histone modifications are highly sensitive to the changes in the microenvironment and the local concentration of specific metabolites. Mass-spectrometry (MS)-based proteomics significantly contributed to the recent advances in the epigenetic field, by allowing the comprehensive analysis of histone post-translational modifications as well as the systematic identification of chromatin constituents. In this chapter, we will provide a general overview of various MS-based experimental strategies developed to boost the epigenetic field, with references to the studies whereby chromatin biology was assessed in relation to cell metabolism. Keywords Mass spectrometry • Histone post-translational modifications • Chromatin • Metabolism • Epigenetics • Stable isotope labeling with amino acids in cell culture • Chromatin-associated proteins •