Abstract
BackgroundRecent 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.ResultsWe 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.ConclusionOur 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.
Highlights
Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation
Recent genome-wide analyses using high-throughput methods revealed that plant genomes show differential methylation states between genes and repetitive sequences: gene-rich regions are present in the hypomethylated fraction, while repetitive sequences are often found in the hypermethylated fraction of the genome [5,6,7]
transposon display (TD) analysis facilitated a comparison of the methylation degrees among different TEs
Summary
Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. Recent genome-wide analyses using high-throughput methods revealed that plant genomes show differential methylation states between genes and repetitive sequences: gene-rich regions are present in the hypomethylated fraction, while repetitive sequences are often found in the hypermethylated fraction of the genome [5,6,7]. Tran et al [10] reported that the major epigenetic systems (DNA methylation and histone H3 lysine-9) in the Arabidopsis genome target TEs in a genome-wide manner, irrespective of element type and position. Plant genomes contain an enormous number of repetitive sequences that are widely distributed over chromosomal segments that include hypomethylated euchromatic regions [11,12]. We are interested in the methylation state surrounding the various types of plant repetitive sequences
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