Genome binding/occupancy profiling by high throughput sequencing
Expression of histone H3.3K27M mutant proteins in diffuse intrinsic pontine glioma (DIPG) results in a global reduction of tri-methylation of H3K27 (H3K27me3), and paradoxically, H3K27me3 peaks remain at hundreds of genomic loci, a dichotomous change that lacks mechanistic insights. Here we show that the PRC2 complex is sequestered at poised enhancers, but not at active promoters with high levels of H3.3K27M proteins, thereby contributing to the global reduction of H3K27me3. Moreover, the levels of H3.3K27M proteins are low at the retained H3K27me3 peaks and consequently having minimal effects on the PRC2 activity at these loci. H3K27me3-mediated silencing at specific tumor suppressor genes, including Wilms Tumor 1, promotes proliferation of DIPG cells. These results support a model in which the PRC2 complex is redistributed to poised enhancers in H3.3K27M mutant cells and supports the proliferation of DIPG cells in part through silencing of tumor suppressor gene WT1.
To analyze how H3K27me3 are altered throughout the epigenome in H3.3K27M mutant cells, we performed H3K27me3, H3.3K27M, and EZH2 ChIP-seq in SF7761 and SF8628 cell lines and tissue samples. To gain further insight into the impact of H3.3K27M mutant proteins on H3K27me3, we also introduce the same heterozygous mutation at the H3F3A gene in mouse embryonic stem cells (ES) using the CRISPR/Cas9 genome editing technology. And performed H3K27me3, H3.3K27M, and EZH2 ChIP-seq in WT and H3.3K27M mouse embryonic stem cells.