School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
Plant Mol Biol. 2018 Apr;96(6):563-575. doi: 10.1007/s11103-018-0715-z. Epub 2018 Mar 10.
The relationships between transcription and methylation were revealed in Arabidopsis thaliana NB-LRR-encoding genes in wild type (Col-0) and different mutants. Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins constitute a large family that plays predominant roles in disease resistance. However, the regulation of NB-LRR-encoding genes at the transcriptional level is still poorly understood. Recently, DNA cytosine methylation in eukaryotes has been described as serving an important function in regulating gene expression. Here, we analysed the DNA methylation patterns of NB-LRR-encoding genes in Arabidopsis thaliana in samples from a wild type (Col-0) and ago4, met1, cmt3, drm1/2, and ddm1 mutants. Our results revealed that the vast majority of the NB-LRR-encoding genes in Col-0 were methylated, and the DNA methylation occurred predominantly in the CG sequence context. Moreover, DNA methylation was widely distributed in both the promoters and the bodies of most NB-LRR-encoding genes. Our results also showed that the loss of AGO4, MET1, CMT3, DRM1/2 or DDM1 functions generally led to decreased cytosine methylation in the NB-LRR-encoding genes. Analysis of the available transcriptome data from the wild type and the met1, cmt3, drm1/2 and ddm1 mutants revealed that differences in the transcription levels between the wild type and mutants were statistically significant for 63 of the NB-LRR-encoding genes. Of these genes, 38 were significantly upregulated, and the other 25 were significantly downregulated. Some NB-LRR-encoding genes with differential expression levels, which were revealed by the mRNA-Seq data, were confirmed to be significantly upregulated or downregulated in the mutants compared to the wild type by using quantitative RT-PCR. These data suggest that some Arabidopsis NB-LRR-encoding genes are likely to be regulated by altered DNA methylation patterns.
真核生物中的 DNA 胞嘧啶甲基化被描述为在调控基因表达方面起着重要作用。在这里，我们分析了野生型（Col-0）和 ago4、met1、cmt3、drm1/2 和 ddm1 突变体的拟南芥中 NB-LRR 编码基因的 DNA 甲基化模式。我们的结果表明，Col-0 中的绝大多数 NB-LRR 编码基因都被甲基化，DNA 甲基化主要发生在 CG 序列背景中。此外，DNA 甲基化广泛分布于大多数 NB-LRR 编码基因的启动子和主体中。我们的结果还表明，AGO4、MET1、CMT3、DRM1/2 或 DDM1 功能的丧失通常会导致 NB-LRR 编码基因中的胞嘧啶甲基化减少。对野生型和 met1、cmt3、drm1/2 和 ddm1 突变体的可用转录组数据进行分析，结果表明，在 63 个 NB-LRR 编码基因中，野生型和突变体之间的转录水平差异具有统计学意义。在这些基因中，有 38 个基因显著上调，另外 25 个基因显著下调。一些通过 mRNA-Seq 数据显示表达水平不同的 NB-LRR 编码基因，通过定量 RT-PCR 证实与野生型相比，在突变体中显著上调或下调。这些数据表明，一些拟南芥 NB-LRR 编码基因可能受到改变的 DNA 甲基化模式的调控。
