ORIGINAL PAPER DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa) Hiromi Higo • Muhammad Tahir • Kazuya Takashima • Asuka Miura • Koichi Watanabe • Akemi Tagiri • Masashi Ugaki • Ryuji Ishikawa • Mitsugu Eiguchi • Nori Kurata • Takuji Sasaki • Eric Richards • Makoto Takano • Naoki Kishimoto • Tetsuji Kakutani • Yoshiki Habu Received: 9 April 2012 / Accepted: 3 August 2012 / Published online: 24 August 2012 Ó Springer-Verlag 2012 Abstract Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to defi- ciency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best char- acterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic DNA. Although cytosine methylation could affect various aspects of plant growth and development including those related to agricultural importance, orthologs of DDM1 in plants other than Arabidopsis has not been studied in detail. In this study, we identified two rice genes with similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are tran- scribed during development and their amino acid sequen- ces are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orienta- tion exhibited genomic DNA hypomethylation. In those lines, repeated sequences were more severely affected than a single copy sequence as is the case in Arabidopsis ddm1 mutants. Transcripts derived from endogenous transposon- related loci were up-regulated in the antisense OsDDM1 lines, opening a possibility to identify and utilize poten- tially active transposons for rice functional genomics. Keywords Rice Á Arabidopsis Á DNA methylation Á Repeated sequences Á Transposons Communicated by S. Hohmann. H. Higo and M. Tahir contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s00438-012-0717-5) contains supplementary material, which is available to authorized users. H. Higo Á K. Watanabe Á T. Kakutani (&) CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan e-mail: tkakutan@lab.nig.ac.jp M. Tahir Á A. Tagiri Á M. Ugaki Á T. Sasaki Á M. Takano (&) Á T. Kakutani Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan e-mail: mtakano@nias.affrc.go.jp Present Address: M. Tahir Department of Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada K. Takashima Á A. Miura Á M. Eiguchi Á T. Kakutani Department of Integrated Genetics, National Institute of Genetics, Mishima 411-0801, Japan Present Address: A. Miura Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan Present Address: K. Watanabe Á M. Ugaki Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan R. Ishikawa Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8560, Japan Present Address: M. Eiguchi Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan 123 Mol Genet Genomics (2012) 287:785–792 DOI 10.1007/s00438-012-0717-5