Figure 2.

Methylation profiles of DE genes. A. The meta-profile of DNA methylation levels in wild-type B73 seedling leaf tissue was assessed for different sets of DE genes. The DNA methylation levels surrounding the TSS and TTS were plotted for all expressed genes and genes DE in CMT (blue) and RdDM (orange) mutants. The three panels show the levels of CG, CHG, and CHH methylation, with the y-axis showing DNA methylation levels. Error bars represent standard error. B-C Histogram of the average methylation level in the first 400 bp downstream of the TSS for genes up-regulated in CMT mutants in the CG (B) and CHG (C) contexts, showing a bimodal distribution of methylation values. D. Wild-type methylation levels in the CG and CHG contexts are correlated. zmet2-m1 mutant methylation data are shown for those genes with high (>50%) CHG methylation in wild-type (orange dots), showing a loss of CHG but not CG methylation in the mutant. E. Histogram of the difference between mutant and WT methylation in the CG (red) and CHG (blue) contexts for those genes up-regulated in CMT mutants that have WT CHG methylation >50%. F. IGV view of two up-regulated genes in CMT mutants: Zm00001d045627 and Zm00001d021982, which have high CG and CHG methylation in WT and reduced CHG methylation near the TSS (yellow box) in zmet2-m1 mutants. G. The proportion of genes within 2 kb of mCHH islands (mCHH) is shown for different sets of genes. The black bar shows the proportion of all genes with a mCHH island while the other bars show the proportion of genes with altered expression in specific mutant backgrounds that have mCHH islands, and * denotes significantly higher proportion than expected relative to all genes (p-value < 0.01, chi squared test).