An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.
An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.
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DOI：
10.1038/emboj.2009.59
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发表时间：
2009-04-22
期刊：
影响因子：
11.4
通讯作者：
Kakutani, Tetsuji
中科院分区：
文献类型：
--
作者：
Miura, Asuka;Nakamura, Miyuki;Inagaki, Soichi;Kobayashi, Akie;Saze, Hidetoshi;Kakutani, Tetsuji
基因和转座子的差异胞嘧啶甲基化对于维持植物基因组的完整性是重要的。在拟南芥中，转座子在CG和非CG位点都高度甲基化，而非CG甲基化在活性基因中很少发现。我们以前的遗传分析表明，含有jmjC结构域的蛋白IBM1(盆景甲基化增加1)阻止了非CG甲基化的异位沉积，这一过程是拟南芥正常发育所必需的。在这里，我们通过DNA甲基化的高分辨率全基因组分析直接确定了IBM1的基因组靶点。Ibm1突变导致了数千个基因的广泛超甲基化。转座子未受影响。值得注意的是，长时间转录的基因受到的影响最严重。在野生型中，基因的甲基化仅限于CG位点，但在ibm1突变体中，CHG位点也发生了甲基化。Ibm1诱导的超甲基化不依赖于先前基于RNAi的DNA甲基化机制的特征成分。我们的结果提示了新的转录偶联机制，不仅在CG处，而且在CHG位点上引导基因甲基化。IBM1可以防止基因中的CHG甲基化，但不能防止转座子中的甲基化。
Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites, whereas the non-CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain-containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non-CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high-resolution genome-wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper-methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1-induced hyper-methylation did not depend on previously characterized components of the RNAi-based DNA methylation machinery. Our results suggest novel transcription-coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons.
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