Analysis of the DNA methylation patterns and transcriptional regulation of the NB-LRR-encoding gene family in Arabidopsis thaliana
Analysis of the DNA methylation patterns and transcriptional regulation of the NB-LRR-encoding gene family in Arabidopsis thaliana
复制标题
拟南芥NB-LRR编码基因家族DNA甲基化模式及转录调控分析
DOI：
10.1007/s11103-018-0715-z
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发表时间：
2018-04-01
影响因子：
5.1
通讯作者：
La, Honggui
中科院分区：
文献类型：
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作者：
Kong, Weiwen;Li, Bin;La, Honggui
拟南芥（Arabidopsis thaliana）NB-LRR编码基因在野生型（Col-0）和不同突变体中的转录和甲基化关系已被揭示，植物核苷酸结合富亮氨酸重复序列（NB-LRR）蛋白组成了一个大家族，在植物抗病性中发挥着重要作用。然而，NB-LRR编码基因在转录水平上的调控仍然知之甚少。最近，DNA胞嘧啶甲基化在真核生物中被描述为在调节基因表达中起重要作用。在这里，我们分析了拟南芥NB-LRR编码基因的DNA甲基化模式，从野生型（Col-0）和ago 4，met 1，cmt 3，drm 1/2和ddm 1突变体的样品。我们的研究结果表明，绝大多数的NB-LRR编码基因在Col-0的甲基化，和DNA甲基化主要发生在CG序列的背景下。此外，DNA甲基化广泛分布在大多数NB-LRR编码基因的启动子和体中。我们的研究结果还表明，AGO 4，MET 1，CMT 3，DRM 1/2或DDM 1功能的丧失通常会导致NB-LRR编码基因中胞嘧啶甲基化的降低。从野生型和met 1，cmt 3，drm 1/2和ddm 1突变体的可用转录组数据的分析显示，野生型和突变体之间的转录水平的差异有统计学意义的63 NB-LRR编码基因。在这些基因中，38个显著上调，其他25个显著下调。通过定量RT-PCR证实了一些具有差异表达水平的NB-LRR编码基因在突变体中与野生型相比显著上调或下调。这些数据表明，一些拟南芥NB-LRR编码基因可能是由改变DNA甲基化模式。
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.