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Analysis of target sequences of DDM1s in Brassica rapa by MSAP

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Abstract

DNA methylation is an important epigenetic modification regulating gene expression and transposon silencing. Although epigenetic regulation is involved in some agricultural traits, there has been relatively little research on epigenetic modifications of genes in Brassica rapa, which includes many important vegetables. In B. rapa, orthologs of DDM1, a chromatin remodeling factor required for maintenance of DNA methylation, have been characterized and DNA hypomethylated knock-down plants by RNAi (ddm1-RNAi plants) have been generated. In this study, we investigated differences of DNA methylation status at the genome-wide level between a wild-type (WT) plant and a ddm1-RNAi plant by methylation-sensitive amplification polymorphism (MSAP) analysis. MSAP analysis detected changes of DNA methylation of many repetitive sequences in the ddm1-RNAi plant. Search for body methylated regions in the WT plant revealed no difference in gene body methylation levels between the WT plant and the ddm1-RNAi plant. These results indicate that repetitive sequences are preferentially methylated by DDM1 genes in B. rapa.

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Acknowledgments

We are grateful to Dr. T. Kakutani for his advice on our experiments and to Dr. K. Shirasawa for his technical advice. This work was supported in part by NIG Cooperative Research Program (2006-A-76).

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Author notes

  1. Taku Sasaki

    Present address: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030, Vienna, Austria

  2. Ryo Fujimoto

    Present address: CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia

Authors and Affiliations

  1. Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan

    Taku Sasaki, Ryo Fujimoto, Sachie Kishitani & Takeshi Nishio

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  1. Taku Sasaki
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  2. Ryo Fujimoto
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  3. Sachie Kishitani
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Correspondence to Takeshi Nishio.

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Communicated by K. Toriyama.

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Sasaki, T., Fujimoto, R., Kishitani, S. et al. Analysis of target sequences of DDM1s in Brassica rapa by MSAP. Plant Cell Rep 30, 81–88 (2011). https://doi.org/10.1007/s00299-010-0946-1

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  • DOI: https://doi.org/10.1007/s00299-010-0946-1

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