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The Effects of DNA Methylation on the Expression of Non-imprinted Genes in Rice

Hongyu Zhang, Yutong Liu, Mipeng Han, Limei Wu, Zhijian Liu, Xiaotong Chen, Peizhou Xu and Xianjun Wu

The expression of imprinted genes is regulated by well-known genetic mechanisms such as DNA and histone methylation. However the mechanism regulating the expression of non-imprinted genes that are specifically expressed in endosperm is currently unknown. To determine whether DNA methylation is involved in the regulation of non-imprinted gene expression in endosperm, we used rice seeds from a reciprocal cross between cultivars Nipponbare and 9311 treated with a methylation inhibitor 5-aza-2’-deoxycytidine to investigate the expression patterns of four non-imprinted genes in seedlings. We found these endosperm specific genes were activated in F1 with two types of expression patterns: 1) either both parental alleles were expressed in F1 leaves; 2) or only one parental allele was expressed in the leaves of the progeny. We speculate that the altered expression patterns of parental alleles may be associated with F1 heterosis. We also observed that the expression of non-imprinted genes underwent dynamic changes at different development stages with two showing imprinted expression patterns, suggesting that DNA methylation is involved in regulating the expression of some imprinted as well as non-imprinted genes. The results of this study provide a reference for further exploring epigenetic mechanisms underlying seed development and, potentially, the association of dynamic changes of DNA methylation with heterosis.