Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
School of Resources and Chemical Engineering, Sanming University, Sanming 365000, China.
Tree Physiol. 2020 Dec 5;40(12):1807-1826. doi: 10.1093/treephys/tpaa097.
DNA methylation plays essential roles in gene regulation, chromatin structure stability, gene imprinting, X chromosome inactivation and embryonic development. However, the dynamics and functions of DNA methylation during the early stage of longan (Dimocarpus longan) somatic embryogenesis (SE) are still unclear. In this study, we carried out whole genome bisulphite sequencing and transcriptome sequencing analyses for embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC) and globular embryos (GE) in an early SE system. At a global level, the DNA 5-methylcytosine content in EC, ICpEC and GE was 24.59, 19.65 and 19.74%, respectively, suggesting a global decrease in DNA methylation from EC to ICpEC and then a slight increase from ICpEC to GE. Differentially methylated region (DMR) analysis showed that hypomethylation mainly occurred in CHH contexts. Gene ontology and Kyoto encyclopedia of genes and genomes analysis of hypomethylated-CHH-DMR-associated genes revealed that zein biosynthesis, fatty acid biosynthesis, circadian rhythm and mitophagy pathways were involved in longan early SE. Expression patterns of DNA methyltransferase and demethylase genes during longan early SE suggested that the decrease in DNA methylation was probably regulated by DNA methyltransferase genes and the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1). The correlation between DNA hypomethylation and gene expression revealed that decreased DNA methylation did not cause extensive changes in gene expression during early longan SE and that gene expression may be affected by methylation changes in gene and downstream regions. Inhibiting DNA methylation with 5-azacytidine treatment in EC promoted the formation of GE and enhanced the capability of longan SE. Our results suggest that DNA demethylation has important roles in longan SE development.
DNA 甲基化在基因调控、染色质结构稳定性、基因印记、X 染色体失活和胚胎发育中发挥着重要作用。然而，龙眼体细胞胚胎发生（SE）早期阶段 DNA 甲基化的动态和功能仍不清楚。在这项研究中，我们对胚性愈伤组织（EC）、不完全致密原胚性培养物（ICpEC）和球形胚（GE）进行了全基因组亚硫酸氢盐测序和转录组测序分析，以研究早期 SE 系统。在全局水平上，EC、ICpEC 和 GE 的 DNA 5-甲基胞嘧啶含量分别为 24.59%、19.65%和 19.74%，这表明从 EC 到 ICpEC 的 DNA 甲基化程度普遍降低，然后从 ICpEC 到 GE 略有增加。差异甲基化区域（DMR）分析表明，去甲基化主要发生在 CHH 环境中。低甲基化-CHH-DMR 相关基因的基因本体和京都基因与基因组百科全书分析表明，玉米醇溶蛋白生物合成、脂肪酸生物合成、昼夜节律和线粒体自噬途径参与了龙眼早期 SE。龙眼早期 SE 过程中 DNA 甲基转移酶和去甲基化酶基因的表达模式表明，DNA 甲基化的降低可能受到 DNA 甲基转移酶基因和 DNA 去甲基化酶基因 REPRESSOR OF SILENCING 1（ROS1）的调控。DNA 低甲基化与基因表达之间的相关性表明，在龙眼早期 SE 过程中，DNA 低甲基化并没有导致基因表达的广泛变化，基因表达可能受到基因和下游区域甲基化变化的影响。用 5-氮杂胞苷处理 EC 抑制 DNA 甲基化可促进 GE 的形成并增强龙眼 SE 的能力。我们的研究结果表明，DNA 去甲基化在龙眼 SE 发育中具有重要作用。
