Mass spectrometry-based characterization of histone post-translational modification

Abstract

Histone post-translational modifications (PTMs) play critical roles in regulating chromatin dynamics and gene expression. Increasing evidence demonstrates that the dysregulation of histone PTMs is closely associated with the pathogenesis of various diseases. Traditional methods for detecting histone PTMs, such as western blot (WB) and chromatin immunoprecipitation sequencing (ChIP-seq), are often limited by their dependence on specific antibodies and relatively low analytical throughput. Mass spectrometry (MS)-based proteomics offers a powerful and unbiased approach for comprehensive characterization of histone PTMs. This review focuses on the advanced development of MS-based strategies for characterizing histone PTMs. These strategies include histone extraction, enzymatic digestion, labeling, enrichment, and MS-based detection. These techniques not only enable comprehensive identification and quantitative analysis of classical modifications, such as acetylation and methylation, but also substantially facilitate the discovery of less-characterized histone PTMs, including succinylation, lactylation, crotonylation, and monoaminylation. Consequently, these findings significantly enhance the complexity of histone code. Collectively, MS-based approaches have profoundly advanced our understanding of histone PTM landscapes and their potential epigenetic regulatory mechanisms in both physiology and pathology contexts.