Rice transposable elements are characterized by various methylation environments in the genome.
Rice transposable elements are characterized by various methylation environments in the genome.
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DOI：
10.1186/1471-2164-8-469
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发表时间：
2007-12-20
期刊：
影响因子：
4.4
通讯作者：
Sano Y
中科院分区：
文献类型：
--
作者：
Takata M;Kiyohara A;Takasu A;Kishima Y;Ohtsubo H;Sano Y
最近使用高通量方法的研究表明，转座因子（te）是DNA甲基化的综合靶点。然而，te与其甲基化基因组环境之间的关系尚不清楚。水稻基因组包含所有已知TE家族的代表，这些家族在染色体分布、结构、转位、大小和拷贝数方面具有不同的特征。本文研究了栽培稻及其近缘野生稻9个基因组DNA中12个TEs附近的DNA甲基化状态。我们采用转座子显示（TD）方法分析基因组中的甲基化环境。12个TE家族由4个I类元件、7个II类元件和1个不同类别元件组成，它们在水稻染色体上的分布存在差异：一些元件集中在着丝粒区或着丝粒区，而另一些元件则集中在常染区。TD分析显示TE家族嵌入在不同甲基化程度的侧翼序列中。在9个水稻品系中，每个TE的侧翼序列的甲基化程度相似。I类元素倾向于出现在高度甲基化的区域，而II类元素的甲基化程度差异很大。在一些TE家族中，甲基化程度明显低于基因组的平均甲基化状态。在两个家族中，甲基化状态的剧烈变化取决于与TE的距离。我们的研究结果表明，水稻基因组中的TE家族可以通过其周围环境的甲基化状态来表征。TE家族的拷贝数和保守程度不太可能与甲基化程度相关。我们讨论了te的甲基化状态与其周围环境之间的可能关系。这是第一个证明基因组中TE与特定甲基化环境相关的报告，甲基化环境是给定TE的一个特征。
Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains. We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE. Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating that TEs in the genome are associated with a particular methylation environment that is a feature of a given TE.
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影响因子：
1.1
作者：
Nagano, H;Kunii, M;Sano, Y
通讯作者：
Sano, Y
影响因子：
2.4
作者：
Takagi, K;Nagano, H;Sano, Y
通讯作者：
Sano, Y
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
DOI：
10.1073/pnas.93.15.7783
发表时间：
1996-07-23
影响因子：
11.1
作者：
Hirochika, H;Sugimoto, K;Kanda, M
通讯作者：
Kanda, M
影响因子：
56.9
作者：
Irvine, Danielle V.;Zaratiegui, Mikel;Martienssen, Robert A.
通讯作者：
Martienssen, Robert A.