Strategies to alter DNA methylation patterns in plants

Epigenetic regulation is achieved through cytosine DNA methylation and histone modification. Epigenetic regulation is not only responsible for regulating gene-coding regions, it is also involved in silencing harmful transposable elements and repetitive elements. Naturally, DNA methylation patterns may vary between individual plants of the same species, influenced by difference exposures to environmental stresses. These changes are heritable, as the plants adapt to challenges in their growth environment. The dynamics and heritability of DNA methylation changes makes producing an epi-mutant variety of crop plants interesting. New epi-varieties may potentially carry interesting phenotypes, with high commercial values. Establishment and maintenance of DNA methylation is controlled by DNA methyltransferases, which creates an opportunity for inducing DNA methylation changes by interfering with the expression of DNA methyltransferases in plants. In this study, we used different strategies in various plant species to induce DNA methylation changes. The first strategy used inverted repeats to silence the MET1 gene, and indicates the importance of having the appropriate level of MET1 expression in maize for plant growth and development. The second strategy employed the TALEN and CRISPR genome editing tools for inducing point mutagenesis in the tomato MET1 gene. However, high dependency of tomato to MET1 gene have inhibited callus regeneration. The third strategy used over-expression of the CMT2 gene to induce phenotype and methylation pattern changes. In addition to using the available strategies, we developed a novel tool for the proof-of-concept targeted demethylation of stable methylated regions in Arabidopsis, which could be extended as epigenome editing tools.