Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean
Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean
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DOI：
10.1105/tpc.19.00255
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发表时间：
2019-10-01
期刊：
影响因子：
11.6
通讯作者：
Schmitz, Robert J.
中科院分区：
文献类型：
--
作者：
Ji, Lexiang;Mathioni, Sandra M.;Schmitz, Robert J.
体细胞胚胎发生是一种重要的组织培养技术，有时会通过遗传和/或表观遗传改变导致表型变异。为了了解体细胞胚胎发生对基因组和表观基因组的影响，我们对从胚胎连续培养6周到13年的10个不同阶段取样的大豆（Glycine max）表观基因组进行了表征。我们从培养样本中发现了全基因组DNA甲基化的增加，特别是在CHH位点。高甲基化几乎完全发生在先前具有非cg甲基化的区域，并伴随着编码rna定向DNA甲基化（RdDM）机制的基因表达的增加。体细胞胚胎和合子胚胎的表观基因组变化相似。在最初的全球高甲基化浪潮之后，观察到罕见的维持性甲基化衰减事件，并且随着培养时间的推移，衰减的程度增加。这些DNA甲基化的缺失伴随着编码RdDM机制的基因下调和转录组重编程，使人联想到种子发育后期的转录组。这些结果揭示了一个过程，在体细胞胚胎发生过程中，在短期内加强已经沉默的区域以维持基因组的完整性，最终在较长时间尺度上在某些位点上衰减。
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.