There is increasing evidence in both plants and animals that epigenetic marks are not always cleared between generations. Incomplete erasure at genes associated with a measurable phenotype results in unusual patterns of inheritance from one generation to the next, termed transgenerational epigenetic inheritance. The Agouti viable yellow (Avy) allele is the best-studied example of this phenomenon in mice. The Avy allele is the result of a retrotransposon insertion upstream of the Agouti gene. Expression at this locus is controlled by the long terminal repeat (LTR) of the retrotransposon, and expression results in a yellow coat and correlates with hypomethylation of the LTR. Isogenic mice display variable expressivity, resulting in mice with a range of coat colours, from yellow through to agouti. Agouti mice have a methylated LTR. The locus displays epigenetic inheritance following maternal but not paternal transmission; yellow mothers produce more yellow offspring than agouti mothers. We have analysed the DNA methylation in mature gametes, zygotes, and blastocysts and found that the paternally and maternally inherited alleles are treated differently. The paternally inherited allele is demethylated rapidly, and the maternal allele is demethylated more slowly, in a manner similar to that of nonimprinted single-copy genes. Interestingly, following maternal transmission of the allele, there is no DNA methylation in the blastocyst, suggesting that DNA methylation is not the inherited mark. We have independent support for this conclusion from studies that do not involve direct analysis of DNA methylation. Haplo-insufficiency for Mel18, a polycomb group protein, introduces epigenetic inheritance at a paternally derived Avy allele, and the pedigrees reveal that this occurs after zygotic genome activation and, therefore, despite the rapid demethylation of the locus.
There is now a reasonable amount of evidence from both epidemiological studies in humans and from genetic studies in animals and plants that information in addition to the primary DNA sequence is inherited across generations and can influence the phenotype of the offspring. Researchers refer to this information as epigenetic, and there is much interest in discovering the molecular basis for this epigenetic information. They now know a great deal about the various types of epigenetic marks that regulate the expression of the genome within the life of an organism, and these include both modifications to the DNA molecule itself, specifically DNA methylation and modifications to the proteins that package the DNA into chromosomes, termed chromatin. DNA methylation appears to be one of the most stable epigenetic modifications and has been the primary candidate for the molecule responsible for transgenerational epigenetic inheritance. The results presented here suggest that DNA methylation is not the inherited epigenetic mark, at least in the mouse model used in this study.