Simultaneous detection of site-specific histone methylations and acetylation assisted by single template oriented...

Histone post-translational modification (PTM) is a marker for gene transcription and is involved in a range of cancers, such as breast cancer. Most importantly, different modifications of a specific site (e.g., mono-, di- and tri-methylations and acetylation at a lysine residue) are individually enriched in particular regions of the genome, indicating that they may serve distinct functions. How these patterns are built and whether downstream events are dependent on the precise site-specific modification status are still poorly understood. One of the prerequisites is to obtain quantitative information on individual modification forms. Currently, the low abundance of these forms creates a great challenge. In this study, a targeted proteomics assay based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with single template oriented molecularly imprinted polymers (MIPs) was developed to attempt to simultaneously quantify site-specific histone mono-, di- and tri-methylated and acetylated forms. Surrogate peptides, including an unmodified one, were selected as targets in both MIP enrichment and subsequent LC-MS/MS detection. As a consequence, a limit of quantification (LOQ) of ∼0.5 nM was achieved, which was 10-fold more sensitive than without MIPs and much more sensitive than mass spectrometry involving a scanning mode. Finally, the assay was employed to quantitatively analyze the H3K79, H3K122 and H4K31 modification status in human breast cell lines.