DNA methylation and lipid metabolism in maize PCD DNA methylation and lipid metabolism are involved in maize aleurone PCD as revealed by transcriptome analysis

Abstract Background The aleurone layer is an integral part of many plant seeds, and during seed germination, aleurone cells undergo PCD, which is promoted by GA from the embryo. However, the numerous components of the GA signaling pathway that mediate PCD of the aleurone proteins remain to be identified. Few genes and transcriptomes have been studied thus far in aleurone layers to improve our understanding of how PCD occurs and how the regulatory mechanism functions during PCD. Our previous studies have shown that histone deacetylase (HDAC) is required in GA-induced PCD of aleurone layer. To further explore the molecular mechanisms by which epigenetic modifications regulate aleurone PCD, we performed a global comparative transcriptome analysis of embryoless aleurones treated with GA or histone acetylase (HAT) inhibitors. Results In this study, 7,919 differentially expressed genes (DEGs) had been analyzed, 2,554 DEGs of which were found to be common under two treatments. These DEGs were involved in various biological processes, including DNA methylation, lipid metabolism and ROS signaling. Further investigations revealed that inhibition of DNA methyltransferases prevented aleurone PCD, suggesting that active DNA methylation plays a role in regulating aleurone PCD. GA or HAT inhibitor induced lipoxygenase gene expression, leading to lipid degradation, but this process was not affected by DNA methylation. However, DNA methylation inhibitor could regulate ROS-related gene expression and inhibit GA-induced production of hydrogen peroxide (H 2 O 2 ). Conclusion The linking of lipoxygenase, DNA methylation, and H 2 O 2 may indicate that GA-induced higher HDAC activity in aleurones caused breakdown of lipids via regulating lipoxygenase gene expression, and increased DNA methylation positively mediated H 2 O 2 production; thus, DNA methylation and lipid metabolism pathways may represent an important and complex signaling network in maize aleurone PCD.