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

Abstract

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 <i>N</i>-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 <u>c</u>ross-<u>l</u>inking-<u>a</u>ssisted and <u>S</u>ILAC-based <u>p</u>rotein <u>i</u>dentification (CLASPI) approach can be used to profile protein–protein interactions mediated by PTMs, such as lysine methylation