RESEARCH ARTICLE Locus- and Site-Specific DNA Methylation of 19 kDa Zein Genes in Maize

An interesting question in maize development is why only a single zein gene is highly expressed in each of the 19-kDa zein gene clusters (A and B types), z1A2-1 and z1B4, in the immature endosperm. For instance, epigenetic marks could provide a structural differ-ence. Therefore, we investigated the DNA methylation of the arrays of gene copies in both promoter and gene body regions of leaf (non-expressing tissue as a control), normal endo-sperm, and cultured endosperm. Although we could show that expressed genes have much lower methylation levels in promoter regions than silent ones in both leaf and normal endo-sperm, there was surprisingly also a difference in the pattern of the z1A and z1B gene clus-ters. The expression of z1B gene is suppressed by increased DNA methylation and activated with reduced DNAmethylation, whereas z1A gene expression is not. DNA methyl-ation in gene coding regions is higher in leaf than in endosperm, whereas no significant dif-ference is observed in gene bodies between expressed and non-expressed gene copies. A median CHGmethylation (25–30%) appears to be optimal for gene expression. Moreover, tissue-cultured endosperm can reset the DNA methylation pattern and tissue-specific gene expression. These results reveal that DNAmethylation changes of the 19-kDa zein genes is subject to plant development and tissue culture treatment, but varies in different chromo-somal locations, indicating that DNA methylation changes do not apply to gene expression in a uniform fashion. Because tissue culture is used to produce transgenic plants, these studies provide new insights into variation of gene expression of integrated sequences