Local DNA hypomethylation activates genes in rice endosperm

Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, ZILBERMAN D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.


Journal Article | Published | English

Scopus indexed
Author
Zemach, Assaf; Kim, M. Yvonne; Silva, Pedro; Rodrigues, Jessica A.; Dotson, Bradley; Brooks, Matthew D.; ZILBERMAN, DanielIST Austria
Abstract
Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.
Publishing Year
Date Published
2010-10-26
Journal Title
Proceedings of the National Academy of Sciences
Volume
107
Issue
43
Page
18729-18734
ISSN
eISSN
IST-REx-ID

Cite this

Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734. doi:10.1073/pnas.1009695107
Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., & ZILBERMAN, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1009695107
Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel ZILBERMAN. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
A. Zemach et al., “Local DNA hypomethylation activates genes in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, ZILBERMAN D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.
Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
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