Key Laboratory of Molecular Epigenetics, Ministry of Education, and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
Plant Physiol. 2011 Aug;156(4):1955-66. doi: 10.1104/pp.111.176842. Epub 2011 Jun 1.
It has been well established that DNA cytosine methylation plays essential regulatory roles in imprinting gene expression in endosperm, and hence normal embryonic development, in the model plant Arabidopsis (Arabidopsis thaliana). Nonetheless, the developmental role of this epigenetic marker in cereal crops remains largely unexplored. Here, we report for sorghum (Sorghum bicolor) differences in relative cytosine methylation levels and patterns at 5'-CCGG sites in seven tissues (endosperm, embryo, leaf, root, young inflorescence, anther, and ovary), and characterize a set of tissue-specific differentially methylated regions (TDMRs). We found that the most enriched TDMRs in sorghum are specific for the endosperm and are generated concomitantly but imbalanced by decrease versus increase in cytosine methylation at multiple 5'-CCGG sites across the genome. This leads to more extensive demethylation in the endosperm than in other tissues, where TDMRs are mainly tissue nonspecific rather than specific to a particular tissue. Accordingly, relative to endosperm, the other six tissues showed grossly similar levels though distinct patterns of cytosine methylation, presumably as a result of a similar extent of concomitant decrease versus increase in cytosine methylation that occurred at variable genomic loci. All four tested TDMRs were validated by bisulfite genomic sequencing. Diverse sequences were found to underlie the TDMRs, including those encoding various known-function or predicted proteins, transposable elements, and those bearing homology to putative imprinted genes in maize (Zea mays). We further found that the expression pattern of at least some genic TDMRs was correlated with its tissue-specific methylation state, implicating a developmental role of DNA methylation in regulating tissue-specific or -preferential gene expression in sorghum.
已经证实，DNA 胞嘧啶甲基化在调节模式植物拟南芥（Arabidopsis thaliana）胚乳中印迹基因的表达以及正常胚胎发育方面发挥着重要的调控作用。尽管如此，这种表观遗传标记在谷类作物中的发育作用在很大程度上仍未得到探索。在这里，我们报告了高粱（Sorghum bicolor）在七个组织（胚乳、胚胎、叶、根、幼花序、花药和子房）中 5'-CCGG 位点的相对胞嘧啶甲基化水平和模式的差异，并描述了一组组织特异性差异甲基化区域（TDMRs）。我们发现，高粱中最丰富的 TDMRs 是胚乳特异性的，并且是由多个 5'-CCGG 位点的胞嘧啶甲基化同时减少或增加不平衡产生的，这种不平衡导致胚乳中的去甲基化比其他组织更广泛，而在其他组织中，TDMR 主要是非组织特异性的，而不是特定于特定组织。因此，与胚乳相比，其他六个组织的胞嘧啶甲基化水平虽然相似，但模式明显不同，这可能是由于在不同的基因组位置同时发生的胞嘧啶甲基化减少或增加程度相似所致。所有四个测试的 TDMR 都通过亚硫酸氢盐基因组测序进行了验证。在 TDMR 下发现了各种不同的序列，包括那些编码各种已知功能或预测蛋白、转座元件以及与玉米（Zea mays）中推定的印迹基因具有同源性的序列。我们进一步发现，至少一些基因 TDMR 的表达模式与其组织特异性甲基化状态相关，这表明 DNA 甲基化在调节高粱中组织特异性或优先基因表达方面具有发育作用。
