and other epigenetic mechanisms reflect a much more fundamental ability to recognize and regulate gene dosage (Kooter et al., 1999). McClintock understood that transposable elements exist in a genetically intact, but cryptic form in the genome and she carried out genetic analyses of Spm transposons undergoing epigenetic changes in their ability to transpose (McClintock, 1962). We later found that the genetically inactive Spm transposons are methylated in critical regulatory sequences (Banks and Fedoroff, 1989). It also has been reported that the large intergenic retrotransposon blocks in maize are extensively methylated (Bennetzen et al., 1994).

The discovery that the introduction of a transgene can lead to the transcriptional silencing and methylation of both the introduced gene and its endogenous homolog brought gene silencing mechanisms under intense study (Park et al., 1996; Kooter et al., 1999). Genes can be silenced both transcriptionally and posttranscriptionally consequent on the introduction of additional copies. Posttranscriptional silencing appears to be caused by RNA destabilization, whereas transcriptional gene silencing involves DNA methylation (Vaucheret et al., 1998; Kooter et al., 1999). There is also some evidence that posttranscriptional silencing triggers DNA methylation (Wassenegger et al., 1994). The results of recent studies on the classical epigenetic phenomenon of R locus paramutation in maize have revealed that local endoreduplication of a chromosomal segment both triggers silencing and can render the endoreduplicated locus capable of silencing an active allele of the gene on a homolog (Kermicle et al., 1995). Similar observations have been made with transgenes, as well as endogenous gene duplications at different chromosomal locations in tobacco and Arabidopsis (Matzke et al., 1994; Luff et al., 1999).

A connection between gene silencing and chromatin structure has come from the analysis of mutants altered in methylation and in transcriptional gene silencing (Jeddeloh et al., 1998; Kooter et al., 1999). Both approaches have identified alleles of the ddm1 locus, which encodes a protein with homology to known chromatin remodeling proteins. This suggests that the repressive mechanisms of DNA methylation and chromatin structure are linked in plants, as they are in animal cells (Ng et al., 1999; Wade et al., 1999). Evidence also is accumulating that double-stranded RNA mediates gene silencing, both in plants and in a variety of other organisms (Waterhouse et al., 1998; Fire, 1999). Analyses of mutants altered in posttranscriptional gene silencing in Neurospora have identified an RNA-dependent RNA polymerase, as well as a RecQ helicase-like protein, homologs of which are known to be involved in DNA repair and recombination (Cogoni and Macino, 1999a, b).