The polycomb repressive complex 2 (PRC2) is a histone methyltransferase complex that tri-methylates histone H3 at lysine 27 (H3K27me3), an epigenetic repressive mark that is essential to maintain the repressed state of thousands of genes during development. Interactions between PRC2 core subunits (EZH2, SUZ12, EED, and RBBP4) to its various accessory subunits and RNA provide it with extensive functional diversity. Mapping the domains and surfaces within PRC2 that are utilized for most of these interactions would lead to discover how the function of PRC2 is regulated by these interactions and how these interactions are dysregulated in disease. To this end, we developed workflows to automatically detect, filter and aggregate binding sites from two methods of cross-linking with mass spectrometry: chemical cross-linking mass spectrometry (XL-MS) for mapping protein-protein interactions and UV cross-linking with mass spectrometry for RNA-binding domain mapping (RBDmap). XL-MS and RBDmap were used to map protein–protein and protein–RNA interactions between PRC2 to its co-factors and ligands. The most common protein–protein interactions within subunits of the core PRC2 complex varied slightly between the presence and absence of various protein cofactors. We identified domains and surfaces in PRC2 that bind different proteins and RNA; this provide a mechanistic framework to explain why certain factors are mutually exclusive for PRC2 binding while others can co-occupy the same complex. Given that >3000 amino acids within PRC2 subunits identified with disease-associated mutations — mostly in cancer — this workflow can help determine how protein–protein and protein–RNA interactions are altered during disease and what are the probable functional consequences of these mutations.