Multi-layered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm

Abstract In the offspring, imprinted genes show differential expression from the maternal and paternal alleles. Our time-course analysis in rice (Oryza sativa) revealed persistent and stage-specific classes of imprinted genes, including over a hundred novel genes, especially in the early stage of endosperm development. In the persistent maternally expressed genes (MEGs), CG and CHG sequences are heavily methylated, while these sites are less methylated in the stage-specific MEGs. Similarly, differences in H3K27me3 defined the two classes of paternally expressed genes (PEGs). The imprinting for MEGs involves activating silent genes. By contrast, many PEGs are active in various tissues and carry gene body DNA methylation (gbM); the maternally inherited alleles of these PEGs undergo silencing via gbM demethylation and deposition of H3K27me3. Stage-specific imprinting indicates that parental marks can be differentially interpreted during development. Its developmental variability contrasts the robustness of persistent imprinting, revealing the dynamic layering of parental effects and suggesting new mechanisms for evolution and manipulation of rice endosperm development.