To understand control and function of DNA methylation, we are taking genetic approaches using mutants of Arabidopsis. An Arabidopsis protein DDM1 (decrease in DNA methylation) is necessary for methylating transposons and repeats. On the other hand, IBM1 (increase in BONSAI methylation) is necessary for not methylating genes. In mutants of genes encoding these proteins, several types of developmental abnormalities were induced. Characterization of these abnormalities is revealing impact of DNA methylation on genome evolution and appropriate gene expression.
The ibm1 (increase in BONSAI methylation) mutation induces developmental defects, which are suppressed by mutation in the H3K9 methylase gene KYP or non-CG methylase gene CMT3. The results suggest that these phenotypes are due to ectopic deposition of heterochromatin marks, such as H3K9 methylation and non-CG methylation.
Inagaki, S., Takahashi, M., Hosaka, A., Ito, T., Toyoda, A., Fujiyama, A., Tarutani, Y., and Kakutani, T. (2017). Gene-body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis. EMBO J 36, 970-980.
Fu, Y., Kawabe, A., Etcheverry, M., Ito, T., Toyoda, A., Fujiyama, A., Colot, V., Tarutani, Y., and Kakutani, T. (2013). Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor. EMBO J 32, 2407-2417.
Tsukahara, S., Kawabe, A., Kobayashi, A., Ito, T., Aizu, T., Shin-I, T., Toyoda, A., Fujiyama, A., Tarutani, Y., and Kakutani, T. (2012). Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata. Genes Dev 26, 705-713.