Abstract
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 difference. 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 endosperm, 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 endosperm, there was surprisingly also a difference in the pattern of the z1A and z1B gene clusters. The expression of z1B gene is suppressed by increased DNA methylation and activated with reduced DNA methylation, whereas z1A gene expression is not. DNA methylation in gene coding regions is higher in leaf than in endosperm, whereas no significant difference is observed in gene bodies between expressed and non-expressed gene copies. A median CHG methylation (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 DNA methylation changes of the 19-kDa zein genes is subject to plant development and tissue culture treatment, but varies in different chromosomal 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.
Highlights
Methylation of chromosomal DNA is a major mark of epigenetic regulation of gene expression, which is present in some fungi and insects, but in all mammals and higher plants [1,2,3,4]
We found that the differential DNA methylation of 19-kDa zein genes in both promoters and gene bodies, and in tissue culture affected locus-specific DNA methylation with different impact in the regulation of zein gene expression
The average DNA methylation in the promoter region of z1A genes was less than 10% in leaf tissue; some of them were even lower than in endosperm (Figs 1A and 2)
Summary
Methylation of chromosomal DNA is a major mark of epigenetic regulation of gene expression, which is present in some fungi and insects, but in all mammals and higher plants [1,2,3,4]. It can be divided into three types of CG, CHG, and CHH (H = A, C, or T). High DNA methylation within the promoter region can strongly correlate with gene inactivity [6,7]. DNA methylation of the promoter is correlated with transgene silencing in plants [11,12]
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