Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
J Exp Bot. 2024 Feb 2;75(3):868-882. doi: 10.1093/jxb/erad427.
The gene regulatory networks that govern seed development are complex, yet very little is known about the genes and processes that are controlled by DNA methylation. Here, we performed single-base resolution DNA methylome analysis and found that CHH methylation increased significantly throughout seed development in litchi. Based on the association analysis of differentially methylated regions and weighted gene co-expression network analysis (WGCNA), 46 genes were identified as essential DNA methylation-regulated candidate genes involved in litchi seed development, including LcSR45, a homolog of the serine/arginine-rich (SR) splicing regulator SR45. LcSR45 is predominately expressed in the funicle, embryo, and seed integument, and displayed increased CHH methylation in the promoter during seed development. Notably, silencing of LcSR45 in a seed-aborted litchi cultivar significantly improved normal seed development, whereas the ectopic expression of LcSR45 in Arabidopsis caused seed abortion. Furthermore, LcSR45-dependent alternative splicing events were found to regulate genes involved in seed development. Together, our findings demonstrate that LcSR45 is hypermethylated, and plays a detrimental role in litchi seed development, indicating a global increase in DNA methylation at this stage.
调控种子发育的基因调控网络十分复杂，但人们对受 DNA 甲基化调控的基因和过程知之甚少。在这里，我们进行了单碱基分辨率的 DNA 甲基化组分析，发现荔枝种子发育过程中 CHH 甲基化显著增加。基于差异甲基化区域的关联分析和加权基因共表达网络分析（WGCNA），鉴定出 46 个与 DNA 甲基化调控相关的重要候选基因，包括 LcSR45，它是丝氨酸/精氨酸丰富（SR）剪接调节因子 SR45 的同源物。LcSR45 在种柄、胚和种皮中表达丰富，在种子发育过程中启动子区的 CHH 甲基化增加。值得注意的是，在一个种子败育的荔枝品种中沉默 LcSR45 显著改善了正常种子的发育，而在拟南芥中异位表达 LcSR45 导致种子败育。此外，发现 LcSR45 依赖的可变剪接事件调节参与种子发育的基因。总之，我们的研究结果表明 LcSR45 发生超甲基化，在荔枝种子发育中发挥有害作用，表明该阶段 DNA 甲基化程度普遍增加。
