Zea mays Epigenomics. Zea mays

Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues. Overall design: Examination of DNA methylated modifications in 2 maize tissues.

表观遗传修饰（Epigenetic modification）在动植物发育过程中发挥关键作用。DNA甲基化可影响转座因子（transposable element, TE）沉默、基因印记，并调控基因表达。本研究通过全基因组分析，分别鉴定并定位了玉米胚与胚乳基因组中的DNA甲基化峰。研究观察到玉米胚与胚乳的甲基化水平存在显著差异：玉米胚基因组的DNA甲基化峰数量多于胚乳基因组，但相较于胚叶绿体基因组，胚乳叶绿体基因组的DNA甲基化峰数量更多。研究人员对基因组中的DNA甲基化区域进行了鉴定与定位，相较于CpG岛（CG island, CGI），玉米中更多的CGI岸发生了甲基化，这表明DNA甲基化水平与CpG密度并非正相关。基因的启动子序列与转录终止区（transcriptional termination region, TTR）内的DNA甲基化发生频率高于基因其他区域。结果显示，本研究鉴定的99%转座因子在玉米胚中均发生了甲基化，但在胚乳中却有34.8%的转座因子未被甲基化。玉米胚与胚乳展现出截然不同的甲基化模式与甲基化水平，二者间差异最显著的甲基化区域为高CpG含量启动子（High CpG content promoters, HCPs）与高CpG含量转录终止区（high CpG content TTRs, HCTTRs）。线粒体与叶绿体DNA的甲基化峰差异程度低于核DNA。本研究结果表明，玉米胚与胚乳中的DNA甲基化与基因沉默或基因激活密切相关。研究发现众多参与胚胎发生与种子发育的基因在胚与胚乳中存在差异甲基化。本研究鉴定出17个胚乳特异性表达的印记基因，它们在胚乳中呈低甲基化状态，而在胚中呈高甲基化状态。相较于玉米胚，胚乳中调控全基因组DNA去甲基化的类DEMETER基因（DEMETER-like, DME-like）与MBD101基因（MBD4同源基因）的表达水平更高，这两类基因可能与玉米胚与胚乳间的甲基化水平差异相关。本研究通过甲基化DNA免疫沉淀测序（MeDIP-seq）方法获取了玉米胚与胚乳的甲基化组。本研究对玉米胚与胚乳甲基化图谱的全局定位，拓展了我们对玉米基因组DNA甲基化模式的认知，为后续玉米种子发育以及不同种子组织代谢途径调控的相关研究提供了有价值的参考信息。整体实验设计：对2种玉米组织中的DNA甲基化修饰进行检测。