Ding Chang-Jun, Liang Li-Xiong, Diao Shu, Su Xiao-Hua, Zhang Bing-Yu
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
PLoS One. 2018 Jan 2;13(1):e0190299. doi: 10.1371/journal.pone.0190299. eCollection 2018.
DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.
DNA甲基化是一种重要的表观遗传修饰机制。应激反应和发育过程中的甲基化变化已得到充分研究；然而，它们在植物适应昼夜循环中的作用却知之甚少。在本研究中，我们通过甲基化DNA免疫沉淀测序（MeDIP-seq）检测了黑杨Populus nigra 'N46'叶片在8:00和24:00时的全基因组甲基化模式。我们发现，在8:00和24:00的样本中分别有10,027个和10,242个基因发生了甲基化。甲基化基因似乎参与了多个生物学过程、分子功能和细胞成分，表明DNA甲基化在杨树细胞中具有重要作用。比较8:00和24:00的样本，只有440个差异甲基化区域（DMR）与基因区域重叠，其中包括193个高甲基化和247个低甲基化的DMR，可能影响137个下游基因的表达。大多数高甲基化基因与转移酶活性、激酶活性和磷酸转移酶活性相关，而大多数低甲基化基因与蛋白质结合、ATP结合和腺苷核糖核苷酸结合相关，这表明白天和夜晚激活了不同的生物学过程。我们的结果表明，甲基化基因在杨树基因组中普遍存在，但其中只有少数参与昼夜基因表达调控。
