Protocol to define the in situ proteome of endogenous PRC2 bodies in the triple-negative breast cancer cell line BoM-1833 using optoproteomics

Polycomb repressive complex 2 (PRC2) and its catalytic subunit EZH2 regulate transcriptional repression and display subcellular organization patterns important for cell function. Here, we present a protocol that applies image-guided optoproteomics to profile the in situ proteome of endogenous EZH2-containing PRC2 bodies in the triple-negative breast cancer cell line BoM-1833. We describe steps for cell culture, EZH2 immunofluorescence, and Microscoop-based photolabeling. We then detail procedures for protein enrichment and mass spectrometry for profiling chromatin-associated signaling. For complete details on the use and execution of this protocol, please refer to Pelzer et al.1