Figure 3

Distinct expression patterns of genes that were potentially regulated by DNA methylation during seed maturation. (a) Expression patterns of gene clusters based on gene transcription patterns in cotyledon at three stages and DNA methylation in DMRs in ^mCHH, ^mCHG and ^mCG contexts. The green to red color gradient represents low to high gene expression, respectively. Genes with 1) more than 30% DNA methylation changes among three different seed stages S2, S6, and S8; 2) statistically significant changes in gene expression; and 3) negative correlation (PCC < −0.85) between gene expression and methylation levels, were used for a cluster analysis. (b) Relationship between gene transcription and DNA methylation in clusters. For each specific cluster, the Z-score of log₂ expression (Red) and the Z-score of DNA methylation levels (Green) were shown at each stage. The mean PCC between Z-score of log₂ expression and Z-score of DNA methylation levels was also calculated and shown. The complete data set is shown in Figure S3.