Experimental DNA demethylation associates with changes in growth and gene expression of oak tree seedlings

Datasets on DNA methylation levels, phenotypic measurements, and soil microbiome (and associated metadata) for Quercus lobata seedlings treated with 5-Azacytidine and controls<br>Abstract: Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, <i>Quercus lobata</i>, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3-6% absolute reductions and 6.7-43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (<i>i.e.</i>, deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development.

针对经5-氮杂胞苷（5-Azacytidine）处理组与对照组的加州白栎（Quercus lobata）幼苗的DNA甲基化水平、表型测定数据、土壤微生物组（及相关元数据）数据集
摘要：表观遗传修饰（如DNA甲基化，即甲基基团结合至胞嘧啶碱基对）可影响表型变异与基因表达，并可能调控植物对环境变化的响应。验证这一作用的常用手段之一是施用化学去甲基化试剂（如5-氮杂胞苷），这类试剂可抑制DNA甲基化，使全基因组范围内的甲基化水平出现一定程度的降低。本研究通过叶面喷施5-氮杂胞苷，对5月龄的加州白栎（Quercus lobata）幼苗进行处理，以探究全基因组甲基化水平降低是否会引发基因差异表达并改变表型发育进程。
首先，本研究证实，去甲基化处理可使CG、CHG及CHH序列背景下的全基因组甲基化水平出现3%~6%的绝对降幅与6.7%~43.2%的相对降幅，其中CHH序列背景的相对降幅最为显著。经5-氮杂胞苷处理的幼苗新生生长量显著降低，仅为对照组幼苗的一半以下。为验证该结果是否源于处理对土壤微生物组的影响，本研究对两组样本的土壤微生物组进行了比较，尽管样本量有限，但发现两组间仅存在极细微的差异。本研究未发现叶片波动不对称性（即两侧对称偏差）存在显著差异，这一结果与部分已有研究的发现一致。尽管如此，经处理的幼苗中共检测到23个基因出现差异表达。
综上，本研究为DNA甲基化参与幼苗的基因表达与表型变异提供了初步证据，并表明去除DNA甲基化会对植物发育产生影响。