Selker 1997

Selker EU. 1997. Epigenetic phenomena in filamentous fung: useful paradigms or repeat-induced confusion? Trends in Genetics 13: 296-301.

This author reviews point mutations, methylation, and other mechanisms of gene silencing in two common model fungi, Neurospora and Ascobolus. Repeat induced point mutation (RIP) acts in Neurospora, and causes GC to AT transitions in both copies of duplicate genes, and a low level of CpG methylation in both copies. Methylation induced meiotically (MIP) acts in Ascobolus, and causes methylation without point mutation, again in both copies of duplicate genes. Both processes detect larger sequences and tandem duplications more reliably.

Methylation reduces gene expression by interfering with transcription elongation, not transcription initiation as previously suggested.

There are two components to methylation: de novo methylation of previously unmethylated sites, and maintenance of methylation through DNA replication. Maintenance may be carried out primarily by a system that preferentially methylates hemimethylated CpG sites, as are generated during DNA replication, but other mechanisms must also occur to account for a set of observations other maintenance patterns. The mechanism of de novo methylation was apparently not understood in 1997; I do not know if that situation has changed.
The author describes the phenomenon termed “quelling”, in which transformed DNA in some fungi causes gene silencing of homologous genes; I suspect this is one of the observations that led to the discovery of RNA interference (RNAi), as the author describes further evidence that quelling is caused by some factor that diffuses from the nucleus to the cytoplasm.

The author also describes transvection, in which loci that do not occur in allelic positions on chromosomes have reduced expression. I do not know how widespread this phenomenon is, or if a mechanism has been proposed since 1997.All of these epigenetic processes are considered to function in cells as defenses against transposable elements, as they all would reduce expression (and, in the case of RIP, inheritance) of actively-transposing sequences. RIP and MIP act on very large duplications, up to the scale of chromosome rearrangements; thus they preserve chromosome structure at a range of scales.