A Method for Systematic Mapping of Protein Lysine Methylation Identifies Functions for HP1β in DNA Damage Response

• DOI: 10.1016/j.molcel.2013.04.025
• Publication Date: 2013-05-23T15:48:29Z
• Authors: Huadong Liu; Marek Galka; Eiichiro Mori; Xuguang Liu; Yu-fen Lin; Ran Wei; Paula Pittock; Courtney Voss; Gurpreet Dhami; Xing Li; Masaaki Miyaji; Gilles Lajoie; Benjamin Chen; Shawn Shun-Cheng Li
• Keywords: 0301 basic medicine; Chromosomal Proteins, Non-Histone; Lysine; Proteins; Reproducibility of Results; Cell Biology; DNA-Activated Protein Kinase; Methylation; High-Throughput Screening Assays; 03 medical and health sciences; Chromobox Protein Homolog 5; Catalytic Domain; Mutation; Humans; DNA Breaks, Double-Stranded; Molecular Biology; Protein Processing, Post-Translational; DNA Damage

Lysine methylation occurs on both histone and nonhistone proteins. However, our knowledge on the prevalence and function of nonhistone protein methylation is poor. We describe an approach that combines peptide array, bioinformatics, and mass spectrometry to systematically identify lysine methylation sites and map methyllysine-driven protein-protein interactions. Using this approach, we identified a high-confidence and high-resolution interactome of the heterochromatin protein 1β (HP1β) and uncovered, simultaneously, numerous methyllysine sites on nonhistone proteins. We found that HP1β binds to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and regulates its localization to double-strand breaks (DSBs) during DNA damage response (DDR). Mutation of the methylation sites in DNA-PKcs or depletion of HP1β in cells caused defects in DDR. Furthermore, we showed that the methylation of DNA-PKcs and many other proteins in the HP1β interactome undergoes large changes in response to DNA damage, indicating that Lys methylation is a highly dynamic posttranslational modification.