Regulation and flexibility of genomic imprinting during seed development

Abstract

Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner. It is achieved by the differential epigenetic marking of parental alleles. Over the past decade, studies in the model systems Arabidopsis thaliana and maize (Zea mays) have shown a strong correlation between silent or active states with epigenetic marks, such as DNA methylation and histone modifications, but the nature of the primary imprint has not been clearly established for all imprinted genes. Phenotypes and expression patterns of imprinted genes have fueled the perception that genomic imprinting is specific to the endosperm, a seed tissue that does not contribute to the next generation. However, several lines of evidence suggest a potential role for imprinting in the embryo, raising questions as to how imprints are erased and reset from one generation to the next. Imprinting regulation in flowering plants shows striking similarities, but also some important differences, compared with the mechanisms of imprinting described in mammals. For example, some imprinted genes are involved in seed growth and viability in plants, which is similar in mammals, where imprinted gene regulation is essential for embryonic development. However, it seems to be more flexible in plants, as imprinting requirements can be bypassed to allow the development of clonal offspring in apomicts.

Figure 1.

Expression of MEA in the Arabidopsis Embryo. (A) Expression of a MEA:GUS reporter gene expressing β-glucuronidase (GUS) under the control of a 3.8-kb promoter (Spillane et al., 2004) in an isolated 16-cell stage embryo. GUS stainings were performed as described by Baroux et al. (2006), except for using only 0.1 mM potassium hexacyanoferrate (II) and 0.1 mM potassium hexacyanoferrate (III) and incubating for 4 d at 37°C. As the half-life of GUS in early embryos is <10 h (R. Baskar and U. Grossniklaus, unpublished data), GUS expression of this stage indicates de novo expression. (B) RT-PCR on isolated embryos amplifying MEA (34 cycles), as well as ACTIN1 and ACTIN11 (28 cycles each) as controls. Embryos were isolated in a buffer containing 1.6 units/μL RNase Out (Invitrogen) and 1 mM DTT. An inverted microscope was used to find the right stage and a glass capillary to collect the embryos. Conditions for RT-PCR and the primers detecting MEA, ACTIN1, and ACTIN11 are described by Baroux et al. (2006). Images of isolated embryos and corresponding RNA profiles are shown in Supplemental Figure 1 online. (C) Allele-specific quantitative PCR for MEA on siliques at different time points: before fertilization (BF) and 1 to 4 DAP. No paternal transcript can be detected, suggesting imprinted expression in both embryo and endosperm (Baroux et al., 2006).

Figure 2.

Imprinting Regulation of Maternally Expressed Genes in Arabidopsis and Maize. (A) Imprinting control at the FWA and FIS2 locus. In the central cell (CC), MET1 is thought to be repressed by RBR and MSI1, which should result in a passive reduction of DNA methylation. DME removes DNA methylation marks in the CC. In the egg cell (EC), DME is not expressed and the locus remains silent. In the sperm cells, MET1 methylates and silences the imprinted gene. After fertilization, the maternal alleles are expressed in the endosperm but not in the embryo. (B) Imprinting control at the MEA locus. In the CC, DME specifically removes the DNA methylation marks. In the EC and potentially in the CC as well (see text), an unknown imprinting factor renders the maternal MEA allele active. For simplicity, the autorepression of the maternal MEA allele is not shown. In the sperm cells, the paternal MEA locus remains methylated and silent through the action of MET1. After fertilization, the silencing of the paternal MEA allele is reinforced by the action of the FIS-PRC2 complex via H3K27 methylation in the endosperm. It remains unclear how MEA expression is controlled in the embryo. The maternal MEA allele is expressed, while the paternal MEA allele is not detected in some accessions, while it is in others. (C) Imprinting control of Mez1 and Fie1 in maize. The genetic factors controlling imprinted gene expression in maize are not known, but the associated epigenetic marks for active and silent chromatin are well described. In the CC, the DNA methylation marks are removed, but the maternal alleles remain silent. For Mez1, epigenetic marks and expression patterns are not known in gametes but might follow the same model. In the egg cell and the sperm cells, the loci remain methylated and silent. In the endosperm, the active maternal allele is marked by H3 and H4 acetylation and H3K4 methylation. The silent allele is repressed by DNA methylation and H3K27 methylation. Both, Mez1 and Fie1 are not expressed in the embryo. (D) Imprinting control at the Mee1 locus. The maternal Mee1 allele is active in the endosperm and the embryo. DNA methylation is probably removed after fertilization only, although Mee1 is weakly expressed in the CC. How exactly the maternal alleles are activated is not known. CC, central cell; EC, egg cell.