Quantitative Chemical Proteomics Approach To Identify Post-translational Modification-Mediated Protein–Protein Interactions

Post-translational modifications (PTMs) (e.g., acetylation,
methylation,
and phosphorylation) play crucial roles in regulating the diverse
protein–protein interactions involved in essentially every
cellular process. While significant progress has been made to detect
PTMs, profiling protein–protein interactions mediated by these
PTMs remains a challenge. Here, we report a method that combines a
photo-cross-linking strategy with stable isotope labeling in cell
culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent
protein–protein interactions. To develop and apply this approach,
we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me3), a PTM linked to actively transcribed
gene promoters. Our approach identified proteins previously known
to recognize this modification and MORC3 as a new protein that binds
H3M4Me3. This study indicates that our cross-linking-assisted
and SILAC-based protein identification (CLASPI) approach can be used to profile
protein–protein interactions mediated by PTMs, such as lysine
methylation.