Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18729-34. doi: 10.1073/pnas.1009695107. Epub 2010 Oct 11.
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.
胞嘧啶甲基化使植物、脊椎动物和真菌中的转座元件沉默，但也调节基因表达。植物甲基化由三个家族的酶催化，每个家族都有一个优先的序列背景：CG、CHG（H=A、C 或 T）和 CHH，其中 CHH 甲基化由 RNAi 途径靶向。拟南芥胚乳是一种胎盘样组织，为胚胎提供营养，其 CG 背景下的整体甲基化程度较低，而非 CG 甲基化程度较高。为人类提供大部分营养的谷类作物种子中的全球甲基化动态仍然未知。在这里，我们表明水稻胚乳 DNA 在所有序列背景下都呈低甲基化状态。非 CG 甲基化在整个基因组中均匀减少，而 CG 低甲基化则局限于特定区域。小转座元件的 CHH 甲基化在胚胎中增加，表明胚乳去甲基化增强了转座子沉默。在胚乳中优先表达的基因，包括编码主要储存蛋白和淀粉合成酶的基因，在胚乳中经常呈低甲基化状态，表明 DNA 甲基化是水稻胚乳发生的关键调节因子。我们的数据表明，被子植物中种子 DNA 甲基化的全基因组重塑是保守的，并且对谷类作物中的基因表达有深远影响。
