Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

Tissue culture is a major method for plant regeneration and for production of transgenic plants. Thus far, our knowledge of the dynamic epigenomic during tissue culture is limited. In this study, we generated epigenomes from nine different stages throughout the tissue culture process and found significant genome-wide increases of DNA methylation throughout the soybean genome. This change mostly happens in CHH (H = A, T, C) context and targets transposable elements (TEs). Subsequent analyses of corresponding transcriptomes and small RNA distributions indicate that it is associated with high activity of the RNA-directed DNA methylation (RdDM) pathway. These results provide important insights into the function of a dynamic epigenome throughout tissue culture and extends our understanding of epigenome-wide reprogramming of the DNA methylome in plants.

植物组织培养（Tissue culture）是植物再生与转基因植物生产的核心技术手段。截至目前，学界对组织培养过程中的动态表观基因组（dynamic epigenome）的认知仍较为有限。本研究从组织培养全流程的9个不同阶段生成表观基因组数据集，发现大豆基因组全基因组范围内的DNA甲基化水平出现显著升高。该变化主要发生于CHH（H=A、T、C）序列背景，并靶向转座元件（transposable elements, TEs）。后续对对应转录组与小RNA分布的分析表明，这一变化与RNA指导的DNA甲基化（RNA-directed DNA methylation, RdDM）通路的高活性密切相关。本研究结果为阐明组织培养过程中动态表观基因组的功能提供了重要见解，同时拓展了我们对植物全基因组范围DNA甲基化组重编程的认知。