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Significance The fidelity of gene expression is regulated by chromosome-associated protein complexes. A traditional approach to characterizing complexes bound to chromosomes requires their release from the DNA to solubilize them. Here we develop an alternative approach, BioTAP-XL, that allows identification of protein–protein interactions while complexes remain linked to the DNA. We focus on protein interactions and genome localization of human EZH2 and two of its relatively uncharacterized interactors, C10orf12 and C17orf96. Our results provide strong evidence for diversity in human Polycomb repressive complexes, which are composed of factors essential for gene silencing during development in higher organisms. We propose that BioTAP-XL is an effective general approach for investigating the composition and subunit diversity of chromosome-associated complexes.

Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification