Genome-wide intergenic repression by polycomb group proteins

Polycomb group (PcG) proteins have been studied as epigenetic regulators of diverse developmental regulatory genes in various organisms. PcG proteins form two major complexes: the Polycomb repressive complex 2 (PRC2) which includes Enhancer of zeste (E(Z)) that methylates the lysine 27 residue of histone H3 (H3K27) and the Polycomb repressive complex 1 (PRC1) which preferentially binds to tri-methylated H3K27 (H3K27me3). Recent genome-wide analysis revealed that the PcG proteins stably bind to hundreds of genomic loci with strong H3K27me3 enrichment. Unlike the focused enrichment of H3K27me3, di-methylation of H3K27 (H3 K27me2) is found on more than half of all nucleosomal H3, raising the interesting possibility that H3K27me2 might have a potential repressive role across the genome. To address the possibility, we generated an E(z) temperature sensitive mutant cell line and examined the effects of E(Z) inactivation. Upon E(Z) inactivation, we observed a strong transcriptional increase from the H3K27me2-enriched intergenic regions along with significant increases of H3K27ac and H3K4me1. The intergenic de-repression was dependent on two dUTX-containing H3K27 de-methylase complexes that are associated with the increased active marks. Genome-wide analysis revealed that these effects are prevailing all over the genome, suggesting an antagonistic relationship between PRC2 and the dUTX complexes for regulating chromatin states genome-wide. In addition, PRC1 involvement in the intergenic repression was indicated by increased intergenic transcription by knock-downs or a mutation of PRC1 components. Moreover, a significant level of H2Aub1, a repressive mark produced by PRC1, was found in silent intergenic regions. These results extend the roles of PcG proteins by showing that PcG complexes not only function as master regulators of several hundred developmental regulators but also set a high inhibitory threshold to suppress the pervasive intergenic transcription all over the genome.