Application of Mass Spectrometry in Translational Epigenetics

Eukaryotic chromatin is a highly dynamic structure composed of proteins and DNA. Epigenetic regulation, such as DNA methylation and posttranslational modification (PTM) of nucleosome core histone proteins, alters chromatin architecture and regulates gene expression. Mass spectrometry (MS) has been accepted as a powerful technology to study epigenetic mechanisms, understanding the importance of the combinatorial histone codes on the determination of cell phenotypes and in the etiology of diseases. In this chapter, we introduce the principles of mass spectrometry. Then we review recent accomplishments of mass spectrometry-based proteomics in the field of epigenetics, including histone sample preparation, enrichment of low abundant PTMs, different mass-spectrometry-based analytic strategies and bioinformatics tools in identification and quantification of histone PTMs, histone variants and characterization of chromatin interactome. With the demand for both chromatin biology and translational epigenetics, we think mass spectrometry will continue to serve as a key and complementary technology for the analysis of gene regulation networks.