(A–E) Average H3K4me3 and H3K27me3 ChIP-seq profiles in X1 NBs across three biological replicates. The y-axis is percentage coverage after normalization to input to allow both ChIP-seq profiles to be directly compared. Plots are shown for the following: (A) top 1000 ranked X1 genes by expression; (B) top 1000 ranked X2 genes; (C) top 1000 ranked Xins genes; and (D) 285 Smed-mex3-1 down-regulated loci with greater than twofold change (P < 0.05). (E) A distribution of Pearson correlation values for the top 500 X1 expressed loci, the top 500 X2 expressed loci, and 285 loci ≥ twofold down-regulated after mex3-1(RNAi). The Pearson correlation coefficient was calculated between the H3K4me3 and H3K27me3 values at each 50-bp window −1000 bp and +1500 bp around the TSS.
