Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms
Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms
复制标题
基因组 DNA 甲基化分析揭示了具有持久胚乳的蓖麻子种子的独特特征
DOI：
10.1104/pp.16.00056
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发表时间：
2016
期刊：
影响因子：
7.4
通讯作者：
Liu Aizhong
中科院分区：
文献类型：
--
作者：
Xu Wei;Yang Tianquan;Dong Xue;Li De-Zhu;Liu Aizhong
种子中基因组DNA甲基化的研究仅限于少数模式植物。被子植物胚乳基因组DNA低甲基化现象已被证实，但由于大多数双子叶植物的胚乳是短命的，并随着种子的发育而消失，因此很难剖析这种低甲基化是如何建立和维持的。蓖麻（Ricinus communis）与拟南芥（Arabidopsis thaliana）不同，胚乳在整个种子发育过程中是持续存在的，这为研究双子叶植物胚乳基因组低甲基化机制提供了一个很好的模型。我们对编码DNA甲基转移酶和脱甲基酶的DNA甲基化相关基因进行了鉴定，并分析了它们在不同组织中的表达谱。我们研究了基因组甲基化，包括CG，CHG，和CHH上下文在胚乳和胚组织中使用亚硫酸氢盐测序，并揭示了CHH甲基化程度在胚乳和胚，出乎意料的是，大大高于以前研究的植物，无论其基因组中的CHH百分比。特别是，我们发现，胚乳表现出一个整体降低CG和CHG甲基化程度相对于胚胎，显着切换全球基因表达。然而，CHH甲基化发生在胚乳中没有表现出显着的减少。结合转座因子（TE）区域内的24个核苷酸的小干扰RNA（siRNA）的表达和参与RNA指导的DNA甲基化途径的基因，我们证明了24个核苷酸的siRNA在维持CHH甲基化和抑制持续胚乳发育中TE的激活中起着关键作用。本研究发现了一种新的基因组DNA甲基化模式，并提出了可能的机制发生在双子叶植物种子宿存胚乳。
Investigations of genomic DNA methylation in seeds have been restricted to a few model plants. The endosperm genomic DNA hypomethylation has been identified in angiosperm, but it is difficult to dissect the mechanism of how this hypomethylation is established and maintained because endosperm is ephemeral and disappears with seed development in most dicots. Castor bean (Ricinus communis), unlike Arabidopsis (Arabidopsis thaliana), endosperm is persistent throughout seed development, providing an excellent model in which to dissect the mechanism of endosperm genomic hypomethylation in dicots. We characterized the DNA methylation-related genes encoding DNA methyltransferases and demethylases and analyzed their expression profiles in different tissues. We examined genomic methylation including CG, CHG, and CHH contexts in endosperm and embryo tissues using bisulfite sequencing and revealed that the CHH methylation extent in endosperm and embryo was, unexpectedly, substantially higher than in previously studied plants, irrespective of the CHH percentage in their genomes. In particular, we found that the endosperm exhibited a global reduction in CG and CHG methylation extents relative to the embryo, markedly switching global gene expression. However, CHH methylation occurring in endosperm did not exhibit a significant reduction. Combining with the expression of 24-nucleotide small interfering RNAs (siRNAs) mapped within transposable element (TE) regions and genes involved in the RNA-directed DNA methylation pathway, we demonstrate that the 24-nucleotide siRNAs played a critical role in maintaining CHH methylation and repressing the activation of TEs in persistent endosperm development. This study discovered a novel genomic DNA methylation pattern and proposes the potential mechanism occurring in dicot seeds with persistent endosperm.