In angiosperms, epigenetic profiles for genomic imprinting are established before fertilization. However, the causal relationships between epigenetic modifications and imprinted expression are not fully understood. In this study, we classified ‘persistent’ and ‘stage-specific’ imprinted genes on the basis of time-course transcriptome analysis in rice (Oryza sativa) endosperm and compared them to epigenetic modifications at a single time point. While the levels of epigenetic modifications are relatively low in stage-specific imprinted genes, they are considerably higher in persistent imprinted genes. Overall trends revealed that the maternal alleles of maternally expressed imprinted genes are activated by DNA demethylation, while the maternal alleles of paternally expressed imprinted genes with gene body methylation (gbM) are silenced by DNA demethylation and H3K27me3 deposition, and these regions are associated with an enriched motif related to Tc/Mar-Stowaway. Our findings provide insight into the stability of genomic imprinting and the potential variations associated with endosperm development, different cell types and parental genotypes.

在被子植物中，基因组印记的表观遗传谱是在受精前建立的。然而，表观遗传修饰和印记表达之间的因果关系尚未完全了解。在这项研究中，我们根据水稻（ Oryza sativa ）胚乳的时间过程转录组分析对“持久”和“阶段特异性”印记基因进行了分类，并将它们与单个时间点的表观遗传修饰进行比较。虽然阶段特异性印记基因中的表观遗传修饰水平相对较低，但持久性印记基因中的表观遗传修饰水平要高得多。总体趋势显示，母本表达的印记基因的母本等位基因被DNA去甲基化激活，而具有基因体甲基化（gbM）的父本表达的印记基因的母本等位基因被DNA去甲基化和H3K27me3沉积沉默，并且这些区域与与 Tc/Mar-Stowaway 相关的丰富基序。我们的研究结果提供了对基因组印记的稳定性以及与胚乳发育、不同细胞类型和亲本基因型相关的潜在变异的深入了解。