Summary DNA methylation is an essential epigenetic modification for gene regulation in plant growth and development. However, the precise mechanisms of DNA methylation remain poorly understood, especially in woody plants. We employed whole‐genome bisulfite sequencing (WGBS), assays for transposase‐accessible chromatin using sequencing (ATAC‐seq), and RNA‐Seq to investigate epigenetic regulatory relationships in Populus tomentosa treated with DNA methylation inhibitor 5‐azacitidine. Expression‐quantitative trait methylation analysis (eQTM), epigenome‐wide association study (EWAS), and joint linkage‐linkage disequilibrium mapping were used to explore the epigenetic regulatory genes, and using CRISPR/Cas9 to identify the role of candidate genes. Plant developmental abnormalities occurred when DNA methylation levels were substantially reduced. DNA methylation regulated 112 expressed genes via chromatin accessibility, of which 61 genes were significantly influenced by DNA methylation variation at the population level. One DNA methylation‐regulated gene, PtoGntK, was located in a major quantitative trait locus (QTL) for poplar growth. Overexpression and CRISPR/Cas9 of PtoGntK revealed it affected poplar height and stem diameter. The PtoRAP2.12 was found to bind to the demethylated accessible region in the PtoGntK promoter, thereby promoting growth in poplar. This study identified key genes with epigenetic regulation for plant growth and provides insights into epigenetic regulation mechanisms in woody plants.

中文翻译：

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PtoRAP2.12 与 PtoGntK 启动子中去甲基化和可接近的染色质区域的结合刺激杨树的生长


摘要 DNA 甲基化是植物生长发育中基因调控的重要表观遗传修饰。然而，DNA 甲基化的确切机制仍然知之甚少，尤其是在木本植物中。我们采用全基因组亚硫酸氢盐测序 （WGBS）、使用测序法测定转座酶可及染色质 （ATAC-seq） 和 RNA-Seq 来研究用 DNA 甲基化抑制剂 5-阿扎胞苷处理的毛白杨的表观遗传调控关系。采用表达-数量性状甲基化分析 （eQTM） 、表观全基因组关联研究 （EWAS） 和关节连锁-连锁不平衡作图研究探讨表观遗传调控基因，并使用 CRISPR/Cas9 鉴定候选基因的作用。当 DNA 甲基化水平显著降低时，就会发生植物发育异常。DNA 甲基化通过染色质可及性调节 112 个表达基因，其中 61 个基因在种群水平上受到 DNA 甲基化变异的显著影响。一个 DNA 甲基化调控基因 PtoGntK 位于杨树生长的主要数量性状基因座 （QTL） 中。PtoGntK 的过表达和 CRISPR/Cas9 表明它影响杨树高度和茎粗。发现 PtoRAP2.12 与 PtoGntK 启动子中的去甲基化可及区域结合，从而促进杨树的生长。本研究确定了植物生长表观遗传调控的关键基因，并为木本植物的表观遗传调控机制提供了见解。