Impact of DNA Demethylases on the DNA Methylation and Transcription of Arabidopsis NLR Genes
Impact of DNA Demethylases on the DNA Methylation and Transcription of Arabidopsis NLR Genes
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DNA 去甲基化酶对拟南芥 NLR 基因 DNA 甲基化和转录的影响
DOI：
10.3389/fgene.2020.00460
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发表时间：
2020-05
影响因子：
3.7
通讯作者：
La Honggui
中科院分区：
文献类型：
--
作者：
Kong Weiwen;Xia Xue;Wang Qianqian;Liu Li-Wei;Zhang Shengwei;Ding Li;Liu Aixin;La Honggui
活性DNA去甲基化是一个重要的表观遗传过程，在维持正常基因表达中起着关键作用。在植物中，活跃的DNA去甲基化是由DNA去甲基化酶介导的，包括ROS1、DME、DML2和DML3。本研究分析了来自ros1和rdd突变体的亚硫酸氢盐测序和mRNA测序数据，揭示了活性DNA去甲基化过程如何塑造拟南芥核苷酸结合富亮氨酸重复序列（NLR）基因的DNA甲基化模式，这是一类重要的植物抗病基因。研究表明，与野生型相比，ros1突变体中三个NLR基因（AT5G49140、AT5G35450和AT5G36930）的CG甲基化水平升高，而AT2G17050的CG甲基化水平降低。我们还观察到rdd突变体中AT4G11170和AT5G47260的CG甲基化水平升高，AT5G38350的CG甲基化水平降低。我们进一步发现，三个NLR基因（AT1G12280、AT1G61180和AT4G19520）在ros1和rdd突变体中表达被激活，而另外三个NLR基因（AT1G58602、AT1G59620和AT1G62630）在这两个突变体中表达被抑制。定量逆转录聚合酶链反应检测显示，在ros1突变体中，AT1G58602.1、AT4G19520.3、AT4G19520.4、AT4G19520.5的表达水平降低；与col0相比，rdd突变体中的AT3G50950.1和AT3G50950.2的表达量也有所降低，而rdd突变体中的AT1G57630.1、AT1G58602.2和AT5G45510.1的表达量相对于col0有所上调。这些结果表明一些NLR基因受DNA去甲基化酶的调控。我们的研究表明，每种DNA去甲基化酶（ROS1、DML2和DML3）对NLR基因的DNA甲基化都有特定的影响，活跃的DNA去甲基化是调控部分拟南芥NLR基因DNA甲基化和转录活性的一部分。
Active DNA demethylation is an important epigenetic process that plays a key role in maintaining normal gene expression. In plants, active DNA demethylation is mediated by DNA demethylases, including ROS1, DME, DML2, and DML3. In this study, the available bisulfite sequencing and mRNA sequencing data from ros1 and rdd mutants were analyzed to reveal how the active DNA demethylation process shapes the DNA methylation patterns of Arabidopsis nucleotide-binding leucine-rich repeat (NLR) genes, a class of important plant disease resistance genes. We demonstrate that the CG methylation levels of three NLR genes (AT5G49140, AT5G35450, and AT5G36930) are increased in the ros1 mutants relative to the wild-type plants, whereas the CG methylation level of AT2G17050 is decreased. We also observed increased CG methylation levels of AT4G11170 and AT5G47260 and decreased CG methylation levels of AT5G38350 in rdd mutants. We further found that the expression of three NLR genes (AT1G12280, AT1G61180, and AT4G19520) was activated in both ros1 and rdd mutants, whereas the expression of another three NLR genes (AT1G58602, AT1G59620, and AT1G62630) was repressed in these two mutants. Quantitative reverse transcriptase–polymerase chain reaction detection showed that the expression levels of AT1G58602.1, AT4G19520.3, AT4G19520.4, and AT4G19520.5 were decreased in the ros1 mutant; AT3G50950.1 and AT3G50950.2 in the rdd mutant were also decreased in expression compared to Col-0, whereas AT1G57630.1, AT1G58602.2, and AT5G45510.1 were upregulated in the rdd mutant relative to Col-0. These results indicate that some NLR genes are regulated by DNA demethylases. Our study demonstrates that each DNA demethylase (ROS1, DML2, and DML3) exerts a specific effect on the DNA methylation of the NLR genes, and active DNA demethylation is part of the regulation of DNA methylation and transcriptional activity of some Arabidopsis NLR genes.
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影响因子：
0.6
作者：
B. Vanyushin
通讯作者：
B. Vanyushin
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
9.5
作者：
Zhang H;Zhu JK
通讯作者：
Zhu JK
影响因子：
9.5
作者：
Bauer MJ;Fischer RL
通讯作者：
Fischer RL