Defining CBX7-Dependent Chromatin Architecture with Rapid Small-Molecule Inhibition

While the repressive roles of Polycomb complexes have been well-established with in vitro systems, it remains unclear how subtypes of these complexes function in living cells. Conditional alleles have enabled studies of Polycomb Repressive Complex 1 (PRC1), but the available timescales on which inducible deletion occurs is not sufficient to define its direct regulatory targets. We have used short-term treatments with a new PRC1 probe UNC4976, that antagonizes recognition of H3K27me3 by the chromodomain-containing subunit CBX7. This methyl-lysine binding domain targeted strategy has enabled the discovery that hundreds of chromatin loop and contact domains are repressed by the chromodomain function of PRC1. Repressive chromatin architecture that is dependent specifically upon methyl-lysine recognition by the PRC1 chromodomain is rapidly de-repressed by 4 hours of CBX antagonism. Utilizing Hi-C experiments after compound treatment, and defining UNC4976-sensitive chromatin by ChIP-seq before major transcriptional changes occur, we characterize, for the first time, direct canonical PRC1-dependent chromatin architecture in human T lymphocytes.