3D GENOME ORGANIZATION UNDERLIES SYNERGISM BETWEEN SILENCERS

Abstract

The 3-dimensional organization of human genomes is important for gene regulation. The mechanisms underlying gene repression and silencers are poorly understood. Here we investigate the hypothesis that clusters of H3K27me3 peaks are a rich source of silencers that can repress gene expression. We find that MRR component removal at interaction anchors of IGF2 and FGF18 by CRISPR leads to upregulation of interacting genes, altered H3K27me3 and H3K27ac levels, and altered chromatin interactions. We find that two silencers can repress FGF18 gene synergistically through compensated chromatin interactions. Double knock-out of two silencers causes synergistic upregulation of FGF18 and synergistic cell identity changes. Double knock-out leads to dramatic alteration of chromatin interactions and gain of enhancers resulting more active chromatin interactions to FGF18. Taken together, silencer constituents of a larger MRR can work synergistically, suggesting silencer constituents can cooperate to form a "super-silencer", and chromatin interactions appear to underlie this synergism.