DNA methylation marks and histone modifications are important factors involved in regulating gene expression and genome structure. By destabilizing these vital factors we can create novel epi-alleles that are transgenerational. To investigate the potential of destabilizing an epigenetic function, we over-expressed DNA METHYLTRANSFERASE1 (MET1) in both Arabidopsis and tomato. In Arabidopsis thaliana, MET1 controls maintenance of cytosine methylation at symmetrical CG positions. At certain densely methylated loci, loss of MET1 causes the loss of all cytosine methylation marks. Over-expression of either the catalytically active or inactive versions of MET1 in Arabidopsis stochastically generates new epi-alleles at loci encoding transposable elements, non-coding RNAs, and proteins, which mainly results in increased expression. These altered expression states can be transmitted to the next generation, without the need for increased MET1 concentration, but long-term stability differs for individual loci. Destabilizing epigenetic factors in tomato appears to be more sensitive, causing lethality when levels of MET1 are increased at certain stages of development. The over-expression of MET1, or other epigenetic factors, offers an alternative strategy to create novel epi-alleles, identify phenotypes under epigenetic control and determine which genes are epigenetically regulated.