DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems
DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems
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杨树茎初生到次生生长过程中DNA甲基化及其对基因表达的影响
DOI：
10.1186/s12864-020-06902-6
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发表时间：
2020-07
期刊：
影响因子：
4.4
通讯作者：
Zhigang Wei
中科院分区：
文献类型：
--
作者：
Yang Zhang;Cong Liu;He Cheng;Shuanghui Tian;Yingying Liu;Shuang Wang;Huaxin Zhang;Muhammad Saqib;Hairong Wei;Zhigang Wei
研究背景5-甲基胞嘧啶(5mC)甲基化作为重要的表观遗传标记，参与许多DNA依赖性生物过程，在多细胞生物的发育和分化过程中发挥作用。然而，对于全局 5mC 甲基化在树干木材形成中的动态方面和作用仍然缺乏了解。在本研究中，我们不仅利用高通量亚硫酸氢盐测序技术对毛果杨初生茎（PS）、过渡茎（TS）和次生茎（SS）的单碱基分辨率甲基化组进行了研究，还分析了5mC甲基化对木材形成相关基因表达的影响。结果杨树茎中CG、CHG和CHH甲基化的总体平均百分比分别为 ~ 53.6%、~ 37.7%和 ~ 8.5%，PS、TS和SS之间全基因组CG/CHG/CHH上下文中5mC的差异具有统计学意义(p< 0.05)。在 PS、TS 和 SS 中观察到 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。进一步的分析揭示了基因体的 5mC 甲基化水平与转录本水平之间存在明显的整体相关性，但未能揭示近端启动子区域的 5mC 甲基化水平与转录本水平之间的相关性。我们在 PS 与 TS 和 TS 与 SS 的比较中分别确定了 653 和 858 个 DMG、4978 和 4780 个 DEG。仅653个DMG和4978个DEG的113个基因以及858个DMG和4780个DEG的114个基因是共有的。已知其他物种（包括拟南芥）中的一些常见基因的对应基因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。结论DNA甲基化仅轻微影响木材形成相关的途径基因或调节因子，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了解甲基化在树种木材形成中的作用。
BackgroundAs 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) ofPopulus trichocarpausing a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.ResultsThe 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, includingArabidopsis 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.ConclusionsDNA 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.
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影响因子：
5.3
作者：
通讯作者：
--
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
4.5
作者：
Seymour DK;Koenig D;Hagmann J;Becker C;Weigel D
通讯作者：
Weigel D
影响因子：
5.3
作者：
Vining K;Pomraning KR;Wilhelm LJ;Ma C;Pellegrini M;Di Y;Mockler TC;Freitag M;Strauss SH
通讯作者：
Strauss SH
影响因子：
12.3
作者：
Niederhuth CE;Bewick AJ;Ji L;Alabady MS;Kim KD;Li Q;Rohr NA;Rambani A;Burke JM;Udall JA;Egesi C;Schmutz J;Grimwood J;Jackson SA;Springer NM;Schmitz RJ
通讯作者：
Schmitz RJ