Now as I noted earlier, some genes silenced by the introduction of transgenes are re-expressed when segregated from the transgene and in other cases they are not.
1. Transgenes that are readily reactivated upon segregation are generally not methylated and are inactivated post-transcriptionally. This is called post-transcriptional gene silencing or PTGS.
2. Transcription from such genes, as detected by run-on transcription assays, is not inhibited. That is, the phenotypically silenced genes are transcribed, often at high levels, but there is little steady-state RNA accumulation. This means that the silencing occurs by a post-transcriptional mechanism that either destabilizes the RNA or results in its premature truncation.
3. Promoter methylation is generally detected when transgenes are transcriptionally silenced, while post-transcriptionally silenced genes are often methylated in the coding region.
4. There is evidence from Herve Vaucheret�s lab that promoter methylation is required for the mainenance of transcriptional gene silencing, but not its initiation.
Having made all these generalizations, I have to remind you that all generalizations, including the present ones, are suspect. Going back a moment to maize and paramutation, what I described for the R locus clearly falls into the category of TGS. But paramutation is likely to involve more than one epigenetic mechanism. Paramutation has also been studied at the maize B locus and found to have quite different properties. In this case, the paramutagenic allele exerts its influence in the F1 heterozygote and methylation has never been detected. What�s common to both is that the interaction between alleles results in a heritable change in gene expression of the paramutable allele.