Figure 2.

Developmental enhancers are bound by PcG proteins and associated with gene repression. (A) Pc and Ph (PRC1) occupancy is significantly higher at Pho-RC-bound developmental enhancers compared with PhoRC-bound promoter regions. Log₂ odds ratios were 1.39 (Pc) and 0.79 (Ph). P-value = 3.24 × 10⁻⁰⁶; 4P-value = .43 × 10⁻⁰³, Fisher's exact test. The general TFs Dsp1 and Gaf are more enriched at PhoRC-bound promoters, although not significantly. (*) P-value < 0.05, Fisher's exact test. (B, left) Heat map showing H3K27me3 signal (H3 subtracted) centered on PhoRC peaks showing a bimodal broad distribution at enhancers (green) and repressed promoters (dark blue) and a unimodal peak at nonrepressed promoters (light blue). (Right) Average signal for each class; shadings indicate 95% confidence intervals from bootstrap estimation. (C) Enhancer signals for H3K27me3 and H3K27ac on PhoRC-bound (green) and PhoRC-nonbound (gray) enhancers, the latter being bound by developmental TFs. The shaded area indicates 95% confidence intervals. PhoRC-bound enhancers are enriched for H3K27me3 and depleted for H3K27ac, in contrast to TF-bound enhancers. (D) Mesoderm-specific gene expression at genes associated with PhoRC binding. The Y-axis shows the median RPKM (reads per kilobase per million reads) of mesoderm RNA sequencing (RNA-seq) data (Gaertner et al. 2012) on ubiquitous (ubiq), mesoderm-expressed (meso), and non-meso genes (Bonn et al. 2012a); genes associated with PhoRC-bound promoters (PhoRC-repressed promoter; dark blue) or enhancers (PhoRC dev enhancer; green); genes associated with TF-bound CRMs (TF-bound enhancer); and genes without occupancy of mesoderm-specific TFs at 6–8 h (nonbound enhancer). Genes with PcG-bound enhancers have low transcription, with RPKM levels similar to inactive genes.