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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

Influence of Cold-Hardening and Soil Matric Potential on Resistance to Speckled Snow Mold in Wheat

The influence of soil matric potential, cold-hardening temperature, and duration on resistance to speckled snow mold caused by Typhula ishikariensis in wheat was investigated. Six winter wheat lines were subjected to cold-hardening temperatures of 2 or 4°C for 1, 2, 3, or 4 weeks with soil matric potential of –0.1 or –0.01 MPa. Plants were inoculated with T. ishikariensis after cold-hardening, incubated at 10°C for 25 days in the dark, and then evaluated for regrowth. Overall recovery from snow mold was least when plants were hardened at 2°C for 1 week at –0.01 MPa and greatest when hardened at 4°C for 4 weeks at –0.1 MPa. Survival of plants following snow mold was greater when plants were cold-hardened at 4 than at 2°C and at –0.1 than –0.01 MPa soil matric potential. The greatest difference in survival among lines and correlation with field observations occurred when plants were hardened at 4°C at –0.1 MPa matric potential for 3 weeks. Understanding the influence of temperature and soil matric potential during cold-hardening on speckled snow mold resistance will be useful to breeding programs developing snow-mold-resistant cultivars under controlled environment conditions

Rice transposable elements are characterized by various methylation environments in the genome-1

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>esponding II-digested samples. Methylation degrees are expressed as the proportion of the methylated bands in the total bands of the I-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

Rice transposable elements are characterized by various methylation environments in the genome-2

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>h (no. 5), #108 (no. 6), W107 (no. 7), W593 (no. 8), and W630 (no. 9). In each strain, the two TD samples digested with I (M) and II (H) were loaded and electrophoresed in a 50% polyacrylamide gel. Methylated fragments are denoted by the fact that a fragment of the I-digested sample has no corresponding fragment in the II-digested sample. The sizes from 60 bp to 600 bp are indicated by the arrows

Rice transposable elements are characterized by various methylation environments in the genome-0

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>ine cultivated and wild rice strains. The TD bands smaller than 500 bp in the I-digested samples were counted in this study. Standard deviations were calculated from the data from the nine rice strains

Rice transposable elements are characterized by various methylation environments in the genome-3

<p><b>Copyright information:</b></p><p>Taken from "Rice transposable elements are characterized by various methylation environments in the genome"</p><p>http://www.biomedcentral.com/1471-2164/8/469</p><p>BMC Genomics 2007;8():469-469.</p><p>Published online 20 Dec 2007</p><p>PMCID:PMC2222647.</p><p></p>d 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 and 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 (W107, W593, and W630) along with the overall degrees