Zhang Yang, Liu Cong, Cheng He, Tian Shuanghui, Liu Yingying, Wang Shuang, Zhang Huaxin, Saqib Muhammad, Wei Hairong, Wei Zhigang
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, 150040, People's Republic of China.
Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China.
BMC Genomics. 2020 Jul 20;21(1):498. doi: 10.1186/s12864-020-06902-6.
As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.
The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.
DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
作为一种重要的表观遗传标记，5-甲基胞嘧啶（5mC）甲基化参与许多依赖DNA的生物学过程，并在多细胞生物体的发育和分化过程中发挥作用。然而，关于树干木材形成过程中全局5mC甲基化的动态变化及其作用，我们仍知之甚少。在本研究中，我们不仅使用高通量亚硫酸氢盐测序技术仔细研究了毛果杨初级茎（PS）、过渡茎（TS）和次生茎（SS）的单碱基分辨率甲基化组，还分析了5mC甲基化对参与木材形成的基因表达的影响。
杨树茎中CG、CHG和CHH甲基化的总体平均百分比分别约为53.6%、37.7%和8.5%，PS、TS和SS之间全基因组CG/CHG/CHH背景下5mC的差异具有统计学意义（p < 0.05）。在PS、TS和SS之间观察到2 kb近端启动子、基因体和2 kb下游区域的CG、CHG和CHH甲基化背景存在明显差异。进一步分析发现基因体的5mC甲基化水平与转录水平之间存在明显的全局相关性，但未发现近端启动子区域的5mC甲基化水平与转录水平之间存在相关性。在PS与TS以及TS与SS的比较中，我们分别鉴定出653个和858个差异甲基化基因（DMG）以及4978个和4780个差异表达基因（DEG）。653个DMG和4978个DEG中只有113个基因，858个DMG和4780个DEG中只有114个基因是共同的。这些共同基因在包括拟南芥在内的其他物种中的对应基因已知参与次生细胞壁生物合成和激素信号传导。这表明甲基化可能直接调节木材形成基因，并间接调节激素信号基因，进而影响木材形成。
DNA甲基化仅对参与木材形成的途径基因或调节因子产生轻微影响，这表明对木材形成的进一步研究应倾向于甲基化的间接影响。我们在此提供的信息和数据将有助于理解甲基化在树种木材形成中的作用。
