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.
H3K9 directs loss of H3K4me1 (from Inagaki et al 2017). Wild type plants have H3K9me2 in transposons (gray) and H3K4me1 in gene bodies (light green). In the mutant of H3K9 methylase genes (suvh456), transposons loose H3K9me2 and accumulate H3K4me1.
Hosaka, A., Saito, R., Takashima, K., Sasaki, T., Fu, Y., Kawabe, A., Ito, T., Toyoda, A., Fujiyama, A., Tarutani, Y., and Kakutani, T. (2017). Evolution of sequence-specific anti-silencing systems in Arabidopsis. Nat Commun 8, 2161.
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.