MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network

(A) Normalized density of EZH2 ChIP enrichment scores (−log₁₀ Q-value calculated using MACS2, left) and EZH2 ChIP-seq reads (right) in the 10-kb region spanning the TSS of the feed-forward regulated genes in cells treated with Dox (+ Dox) and untreated (− Dox). (B) Genome Browser view of FRMD4B showing tracks for EZH2 ChIP-seq in WT +Dox and WT −Dox cells containing VP55. (C) Heat map showing differential expression of miRNAs in response to EZH2 knockout. Rows are ordered from low to high log₂ fold change between WT and EZH2^−/− miRNA counts. (D) Predicted interactions between 1000 random sets of 14 miRNAs and feed-forward regulated genes. The average across 1000 intersections is marked “Average.” The number of observed interactions between EZH2-activated miRNAs and feed-forward regulated genes is marked “Observed.” P-value = 0.024 was calculated using the bootstrap method (Methods). (E) Luciferase assay comparing miRNA inhibition of WT 3′ UTR transfected into WT and EZH2^−/− cells.