Eukaryotic chromatin is modified by a plethora of epigenetic machineries that add or erase specific histone posttranslational modifications. It has been difficult to determine the impact of individual epigenetic factors on chromatin organization due to insufficient resolution and molecular heterogeneity. Using dual-trap optical tweezers, we develop a single-molecule platform to obtain the mechanical fingerprints of chromatin-modifying enzymes on nucleosome arrays. Specifically, we study the Polycomb repressive complex 2 (PRC2), which installs and propagates the repressive histone mark H3K27me3. In collaboration with the Muir Lab, we show experimentally that PRC2 exhibits a diverse repertoire of binding modes on chromatin and can simultaneously engage non-adjacent nucleosome pairs. This energetically favorable binding mode is corroborated by molecular dynamics simulations of PRC2-chromatin assemblies performed by the Zhang Lab. Together, these results suggest that PRC2 does not modify nucleosome arrays in a strictly linear fashion and have implications for the mechanism of heterochromatin formation.

We later conduct another collaborative study with the Zhang Lab, in which we show that PRC2 binding can induce the formation of DNA loops in a cooperative manner and this activity is regulated by accessory subunits such as AEBP2.