1. Figure SOM1. Functional roles of the genes affected in zmet2-m1 mutants. Although the genes localized on the intracellular membranes were slightly over-represented and the genes located in plastids were slightly under-represented among the genes affected in the zmet2-m1 mutant plants, these variations are likely insignificant. Cellular Localization Molecular Function Biological Process

2. B73 zmet2-m1 0.25 0.5 1.0 2.0 4.0 Coloring Figure SOM2. The expression profile of maize genes in zmet2-m1 mutants based on the spotted long oligonucleotide arrays. The expression of 179 genes defined as differentially expressed is shown for three biological replicates for B73 and B73 zmet2-m1 plants.

3. Normalized long oligonucleotide array log 2 expression values Normalized Affymetrix log 2 expression values B A Affymetrix log 2 (B73/B73 zmet2-m1) Long oligonucleotide array log 2 (B73/B73 zmet2-m1) Figure SOM3. Correlation between Affymetrix and the long oligonucleotide array platforms. (A) Correlation between log 2 ratios between average signals from B73 and B73 zmet2-m1 samples produced by two array platforms. (B) Scatter plots representing the correlation between normalized values for both platforms. The values for genes determined as differentially expressed in the Affymetrix data comparisons between B73 and B73 zmet2-m1genotype and present on the long oligonucleotide array. The normalized average expressions for these genes from both platforms were compared for B73 (circles) and the B73 zmet2-m1 plants (squares).

4. Figure SOM4. Classification of genes affected in zmet2-m1 mutant plants. (A) Clustering (Pearson correlation) results for each of the five groups of genes. The profile shown is the average between three biological replicates performed for each of four genotypes. Gene coloring is based on the normalized expression values (normalized to value of 1) for two genetic backgrounds compared on each part of the figure. (B) Examples of expression patterns observed for genes in the 10 different classes. For this graph, the expression of one gene per group is shown as average normalized expression values from three biological replicates. The specific expression values for all of the genes in each of the groups are shown in Table SOM2. Gene expression Group - 1 down 2 down 3 down 4 down 5 down 1 up 2 up 3 up 4 up 5 up B73 B73 zmet2 Mo17 Mo17 zmet2 B A

5. B73Mo17 4.0 0.25 1.0 2.0 0.5 Coloring Figure SOM5. Genes affected in zmet2-m1 mutant plants exhibit large variation in expression between wild type inbred lines B73 and Mo17. The expression of 126 genes defined as differentially expressed in either of the comparisons is shown for three biological replicates for B73 and Mo17. Gene coloring is based on the expression ratios between B73 and Mo17 genotypes. This comparison indicates that the genes most influenced by ZMET2 have large baseline expression differences in wild-type lines, possibly due to methylation differences in these lines.