Fig. 7

Disruption of histone methylation patterns around Pax6 peaks in Pax6 KD cell line sh2. a αTN4 Pax6 promoter peaks (n = 34) showed decreased H3K4me1 and H3K4me3 modification but no change of H3K4me2 in Pax6 KD cell line (vs wt). Pol2 data are also shown to indicate promoters. b Non-promoter αTN4 Pax6 peaks showed decreased H3K4me1 modification in Pax6 KD cell line (n = 468). Heatmaps show read densities from ±5 kb of the Pax6 peak summits, sorted by the Pax6 ChIP-seq signal in WT, with the profiles of mean ChIP-seq read densities plotted in the right (top for WT and bottom for shPax6 data). c Changes (wt vs Pax6 KD) of H3K4me1/2/3 at two groups of enhancers (used WT H3K4me1 peaks as a proxy here) separated by their overlap with Pax6 peaks. Upon Pax6 KD, the enhancers with Pax6 binding showed a greater reduction of H3K4me1 (but no change in H3K4me2/3) than those without Pax6 binding in WT. The boxplots show RPKM (reads per kb peak per million ChIP-seq reads) differences between control and Pax6 KD αTN4 cells; the RPKMs were computed for at ±5 kb of the centers of H3K4me1 peaks