Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602.
Donald Danforth Plant Science Center, St. Louis, Missouri 63132.
Plant Cell. 2019 Oct;31(10):2315-2331. doi: 10.1105/tpc.19.00255. Epub 2019 Aug 22.
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 () 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.
体细胞胚胎发生是一种重要的组织培养技术，它有时会通过遗传和/或表观遗传变化导致表型变异。为了了解体细胞胚胎发生的基因组和表观基因组影响，我们对来自 10 个不同阶段的大豆（）胚胎进行了表型分析，这些阶段的胚胎在连续培养 6 周到 13 年之间。我们发现，从培养样本中鉴定出全基因组 DNA 甲基化增加，尤其是在 CHH 位点。超甲基化几乎只发生在先前具有非 CG 甲基化的区域，并伴随着编码 RNA 指导的 DNA 甲基化（RdDM）机制的基因表达增加。体细胞胚胎发生和合子胚胎发生之间的表观基因组变化是相似的。在最初的全基因组高甲基化波之后，观察到维持甲基化的罕见衰减事件，并且在培养过程中，衰减的程度随着时间的推移而增加。这些 DNA 甲基化的丢失伴随着编码 RdDM 机制的基因的下调和类似于晚期种子发育过程中转录组的转录组重编程。这些结果揭示了一个在短期内通过体细胞胚胎发生来加强已经沉默区域以维持基因组完整性的过程，而在更长的时间尺度上，某些基因座的完整性最终会衰减。
