To understand function and control of DNA methylation, we are taking genetic approaches using mutants of Arabidopsis. An Arabidopsis DNA hypomethylation mutation ddm1 (decrease in DNA methylation) induces several types of developmental abnormalities through heritable changes in other loci. Genetic analysis of two of the abnormalities reveled that the loss of DNA methylation causes mobilization of endogenous transposons and de-repression of an imprinted gene with a transposon-derived promoter. A different mechanism was found by characterization of another ddm1-induced developmental abnormality, named bonsai . The bonsai phenotype was due to local DNA hyper-methylation in the background of global DNA hypomethylation. By genetic screen of mutants affecting DNA methylation in the BONSAI locus, we identified a novel jmjC domain gene IBM1 (increase in BONSAI methylation). The ibm1 mutations induce several types of developmental abnormalities through ectopic deposition of heterochromatin marks (see Figure).

Kakutani T, Kato M, Kinoshita T, and Miura, A (2004) Control of development and transposon movement by DNA methylation in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol. 69, 139-143.

Kinoshita, T., Miura, A., Choi, Y., Kinoshita, Y., Cao, X., Jacobsen, S., Fischer, R., and Kakutani, T. (2004). One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303, 521-523.

Saze H and Kakutani T (2007) Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J 26 , 3641-3652.

Saze H, Shiraishi A, Miura A, and Kakutani T (2008) Control of genic DNA methylation by a jmjC-domain containing protein in Arabidopsis thaliana. Science 319, 462-465.