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Molecular Genetics and Genomics

, Volume 287, Issue 10, pp 785–792 | Cite as

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
Original Paper

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 deficiency 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 characterized 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 transcribed during development and their amino acid sequences are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orientation 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 potentially active transposons for rice functional genomics.

Keywords

Rice Arabidopsis DNA methylation Repeated sequences Transposons 

Notes

Acknowledgments

We thank Y. Iguchi, K. Munakata, A. Terui, K. Hioki, and M. Arai for technical assistance. Special thanks to S. Iida for comments on the manuscript, H. Hirochika, H. Ohtsubo, F. Takaiwa, and S. Tsuchimoto for rice DNA clones and sequences used for probes. This work was supported by Grant-in-Aid for Creative Scientific Research 14GS0321 to TK and for Scientific Research (C) 24580016 to YH.

Supplementary material

438_2012_717_MOESM1_ESM.pptx (614 kb)
Supplementary material 1 (PPTX 613 kb)
438_2012_717_MOESM2_ESM.doc (157 kb)
Supplementary material 2 (DOC 157 kb)

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Hiromi Higo
    • 1
  • Muhammad Tahir
    • 2
    • 3
  • Kazuya Takashima
    • 4
  • Asuka Miura
    • 4
    • 5
  • Koichi Watanabe
    • 1
    • 6
  • Akemi Tagiri
    • 2
  • Masashi Ugaki
    • 2
    • 6
  • Ryuji Ishikawa
    • 7
  • Mitsugu Eiguchi
    • 4
    • 8
  • Nori Kurata
    • 9
  • Takuji Sasaki
    • 2
    • 10
  • Eric Richards
    • 11
    • 12
  • Makoto Takano
    • 2
    • 13
  • Naoki Kishimoto
    • 14
  • Tetsuji Kakutani
    • 1
    • 2
    • 4
  • Yoshiki Habu
    • 14
  1. 1.CREST, Japan Science and Technology AgencyKawaguchiJapan
  2. 2.Department of Molecular GeneticsNational Institute of Agrobiological SciencesTsukubaJapan
  3. 3.Department of Plant ScienceUniversity of ManitobaWinnipegCanada
  4. 4.Department of Integrated GeneticsNational Institute of GeneticsMishimaJapan
  5. 5.Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
  6. 6.Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
  7. 7.Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
  8. 8.Experimental Farm, National Institute of GeneticsMishimaJapan
  9. 9.Genetic Strains Research CenterNational Institute of GeneticsMishimaJapan
  10. 10.NODAI Research InstituteTokyo University of AgricultureTokyoJapan
  11. 11.Department of BiologyWashington UniversitySt. LouisUSA
  12. 12.Boyce Thompson Institute for Plant ResearchNew YorkUSA
  13. 13.Genetically Modified Organism Research CenterNational Institute of Agrobiological SciencesTsukubaJapan
  14. 14.Agrogenomics Research CenterNational Institute of Agrobiological SciencesTsukubaJapan

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