Epigenetic reprogramming occurs during reproduction to reset the genome for early development. In flowering plants, mechanistic details of parental methylation remodeling in zygote remain elusive. Here we analyze allele-specific DNA methylation in rice hybrid zygotes and during early embryo development and show that paternal DNA methylation is predominantly remodeled to match maternal allelic levels upon fertilization, which persists after the first zygotic division. The DNA methylation remodeling pattern supports the predominantly maternal-biased gene expression during zygotic genome activation (ZGA) in rice. However, parental allelic-specific methylations are reestablished at the globular embryo stage and associate with allelic-specific histone modification patterns in hybrids. These results reveal that paternal DNA methylation is remodeled to match the maternal pattern during zygotic genome reprogramming and suggest existence of a chromatin memory allowing parental allelic-specific methylation to be maintained in the hybrid.

表观遗传重编程发生在繁殖过程中，以重置基因组以进行早期发育。在开花植物中，受精卵中亲本甲基化重塑的机制细节仍然难以捉摸。在这里，我们分析了水稻杂交受精卵和早期胚胎发育过程中的等位基因特异性 DNA 甲基化，并表明父系 DNA 甲基化主要在受精时重塑以匹配母体等位基因水平，这在第一次合子分裂后仍然存在。DNA 甲基化重塑模式支持水稻合子基因组激活 （ZGA） 期间主要偏向母体的基因表达。然而，亲本等位基因特异性甲基化在球状胚胎阶段重新建立，并与杂交种中的等位基因特异性组蛋白修饰模式相关。这些结果表明，在合子基因组重编程过程中，父系 DNA 甲基化被重塑以匹配母体模式，并表明存在染色质记忆，允许在杂交体中维持亲本等位基因特异性甲基化。