Liang Lixiong, Chang Yingying, Lu Junqian, Wu Xiaojuan, Liu Qi, Zhang Weixi, Su Xiaohua, Zhang Bingyu
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.
Front Plant Sci. 2019 Feb 28;10:243. doi: 10.3389/fpls.2019.00243. eCollection 2019.
Changes in DNA methylation patterns in different tissues, at various developmental stages, and under environmental stimuli have been investigated in plants. However, the involvement of DNA methylation in daily gene expression regulation and the plant circadian clock have not been reported. Here, we investigated DNA methylomes and mRNA transcriptomes from leaves of over 24 h by high-throughput sequencing. We found that approximately 15.63-19.50% of the genomic cytosine positions were methylated in mature poplar leaves, with approximately half being in the form of asymmetric CHH sites. Repetitive sequences and transposable elements (TEs) were heavily methylated, and the hAT and CMC-EnSpm transposons were more heavily methylated than other TEs. High methylation levels were observed upstream and downstream of the transcribed region, medium in exon and intron, low in untranslated region (5'-UTR and 3'-UTR) of genic regions. In total, about 53,689 differentially methylated regions (DMRs) were identified and CHH context was the most abundant type among daily DNA methylation changes. The DMRs overlapped with over one third of the total poplar genes, including plant defense genes. In addition, a positive correlation between expression levels and DNA methylation levels in the gene body region were observed in DMR overlapping genes. About 1,895 circadian regulated genes overlapped with DMRs, with 871 hypermethylated genes with down-regulated expression levels and 881 hypomethylated genes with up-regulated expression levels, indicating the possible regulation of DNA methylation on the daily rhythmic expression of these genes. But rhythmic DNA methylation changes were not detected in any oscillator component genes controlling the plant circadian clock. Our results suggest that DNA methylation participates widely in daily gene expression regulation, but is not the main mechanism modulating the plant circadian clock.
植物中不同组织、不同发育阶段以及环境刺激下DNA甲基化模式的变化已得到研究。然而，DNA甲基化在日常基因表达调控和植物生物钟中的作用尚未见报道。在此，我们通过高通量测序研究了超过24小时内杨树叶片的DNA甲基化组和mRNA转录组。我们发现，成熟杨树叶片中约15.63 - 19.50%的基因组胞嘧啶位点发生了甲基化，其中约一半为不对称CHH位点形式。重复序列和转座元件（TEs）高度甲基化，hAT和CMC - EnSpm转座子比其他TEs甲基化程度更高。在基因区域的转录区域上游和下游观察到高甲基化水平，外显子和内含子中甲基化水平中等，非翻译区域（5'-UTR和3'-UTR）甲基化水平低。总共鉴定出约53,689个差异甲基化区域（DMRs），且CHH背景是日常DNA甲基化变化中最丰富的类型。DMRs与超过三分之一的杨树基因重叠，包括植物防御基因。此外，在DMR重叠基因的基因体区域观察到表达水平与DNA甲基化水平之间呈正相关。约1,895个生物钟调控基因与DMRs重叠，其中871个高甲基化基因表达水平下调，881个低甲基化基因表达水平上调，表明DNA甲基化可能对这些基因的日常节律性表达具有调控作用。但在控制植物生物钟的任何振荡器组件基因中均未检测到节律性DNA甲基化变化。我们的结果表明，DNA甲基化广泛参与日常基因表达调控，但不是调节植物生物钟的主要机制。
