Rice transposable elements are characterized by various methylation environments in the genome

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

Figure 1

Average numbers of bands obtained by TD analyses for the 12 rice TEs. Each column shows the average number of bands that were estimated from the TD analyses of the nine cultivated and wild rice strains. The TD bands smaller than 500 bp in the MspI-digested samples were counted in this study. Standard deviations were calculated from the data from the nine rice strains.

Figure 2

Methylation degrees in the 5' flanking sequences of the 12 rice TEs. The TD bands smaller than 500 bp in the MspI-digested samples were compared with those in the corresponding HpaII-digested samples. Methylation degrees are expressed as the proportion of the methylated bands in the total bands of the MspI-digested samples. The average methylation degree (24.3%) for the whole genomes from the nine strains was estimated by AFLP analyses as described in the Methods, and is indicated by a dotted line. Standard deviations were calculated with the data from the nine rice strains.

Figure 3

Transposon displays for p-SINE1 and Mashu in the nine cultivated and wild rice strains. The rice strains consist of A58 (no. 1), T65 (no. 2), Nipponbare (no. 3), IR36 (no. 4), Kasalath (no. 5), #108 (no. 6), W107 (no. 7), W593 (no. 8), and W630 (no. 9). In each strain, the two TD samples digested with MspI (M) and HpaII (H) were loaded and electrophoresed in a 50% polyacrylamide gel. Methylated fragments are denoted by the fact that a fragment of the MspI-digested sample has no corresponding fragment in the HpaII-digested sample. The sizes from 60 bp to 600 bp are indicated by the arrows.

Figure 4

Differential methylation degrees dependent on the distance from the copies of p-SINE1 and TabitoII. Based on the band sizes in the TD profiles of the MspI-digested samples, the fragments were divided into two groups: one ranging from 60 to 200 bp and the other ranging from 200 to 500 bp. Methylation degrees were estimated for the fragments in these two ranges and the fragments in the full range from 60 to 500 bp. Within a 500-bp range from the elements, the proximal regions of both p-SINEI and TabitoII are markedly methylated compared with the distal regions. This tendency was also found in the individual rice strains, as illustrated for Japonica (including A58, T65, and Nipponbare), Indica (IR36, Kasalath, and #108), and O. rufipogon (W107, W593, and W630) along with the overall degrees.