全球分析揭示DNA甲基化在水稻种子发育过程中的关键作用。
Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.
作者信息
Xing Mei-Qing, Zhang Yi-Jing, Zhou Shi-Rong, Hu Wen-Yan, Wu Xue-Ting, Ye Ya-Jin, Wu Xiao-Xia, Xiao Yun-Ping, Li Xuan, Xue Hong-Wei
机构信息
National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.).
National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, China (M.-Q.X., Y.-J.Z., S.-R.Z., W.-Y.H., X.-T.W., Y.-J.Y., X.L., H.-W.X.);College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China (X.-X.W.); andShanghai OEbiotech, 201210 Shanghai, China (Y.-P.X.)
出版信息
Plant Physiol. 2015 Aug;168(4):1417-32. doi: 10.1104/pp.15.00414. Epub 2015 Jul 5.
Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development.
种子发育是生殖发育的一个重要过程，包括胚胎发育和胚乳发育；这两个过程都包含几个关键步骤。为了确定和研究种子发育过程中动态DNA甲基化组的功能，我们通过甲基胞嘧啶免疫沉淀结合Illumina测序，对水稻（Oryza sativa）胚胎和胚乳一系列发育阶段的全基因组DNA甲基化进行了分析。结果表明，与胚乳相比，胚胎在非转座元件（TE）基因、短DNA-TEs和短散在TEs周围主要呈现高甲基化状态，并且非TE基因在整个种子发育过程中具有最多样化的甲基化状态。此外，低表达基因在高甲基化基因中显著富集，但反之则不然，这证实了DNA甲基化在抑制基因转录中的关键作用。进一步分析发现，在发育早期阶段（授粉后2至3天）甲基化显著降低，表明去甲基化在胚乳早期发育中起主要作用，并且DNA甲基化变化与表达变化之间具有一致负相关的基因可能受到DNA甲基化的直接调控。有趣的是，DNA甲基化图谱的比较分析表明，籼稻和粳稻亚种在整个种子发育过程中，胚胎和胚乳的DNA甲基化水平均呈现强烈的波动图谱，在授粉后6天（粳稻胚乳授粉后2天）甲基化水平最高，这表明复杂且精细调控的甲基化模式与种子发育调控密切相关。对发育中的水稻种子动态DNA甲基化组的系统表征将有助于我们理解表观遗传调控在种子发育中的作用和机制。
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