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

Immunoglobulin G4-Related Hepatic Inflammatory Pseudotumor Diagnosed with Endoscopic Ultrasound-Guided Fine-Needle Biopsy

A 71-year-old man with obstructive jaundice was referred to our department. He underwent cholangiojejunostomy 15 years ago for palliative drainage. At that time, he had obstructive jaundice caused by an unresectable pancreatic head tumor. Contrast-enhanced computed tomography (CE-CT) now revealed a mass with low enhancement in the hepatic hilum that occluded the hilar bile duct and infiltrated extensively along the portal vein and hepatic artery. CE-CT also showed marked atrophy of the left hepatic lobe. No swelling or tumors were observed in the pancreas. Serum immunoglobulin G4 (IgG4) levels were as high as 465 mg/dL. Endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) was performed targeting the hepatic hilar lesion. Immunohistological results of the biopsy specimens suggested that the lesion was an IgG4-related hepatic inflammatory pseudotumor (IPT) with no atypical cells. Steroid treatment resulted in rapid clinical improvement. This case suggested the usefulness of EUS-FNB for diagnosing IgG4-related hepatic hilar IPT

c-Fos protein as a target of anti-osteoclastogenic action of vitamin D, and synthesis of new analogs

Although active vitamin D drugs have been used for the treatment of osteoporosis, how the vitamin D receptor (VDR) regulates bone cell function remains largely unknown. Using osteoprotegerin-deficient mice, which exhibit severe osteoporosis due to excessive receptor activator of NF-κB ligand/receptor activator of NF-κB (RANKL/RANK) stimulation, we show herein that oral treatment of these mice with 1α,25-dihydroxyvitamin D(3) [1α,25(OH)(2)D(3)] inhibited bone resorption and prevented bone loss, suggesting that VDR counters RANKL/RANK signaling. In M-CSF–dependent osteoclast precursor cells isolated from mouse bone marrow, 1α,25(OH)(2)D(3) potently and dose-dependently inhibited their differentiation into multinucleate osteoclasts induced by RANKL. Among signaling molecules downstream of RANK, 1α,25(OH)(2)D(3) inhibited the induction of c-Fos protein after RANKL stimulation, and retroviral expression of c-Fos protein abrogated the suppressive effect of 1α,25(OH)(2)D(3) on osteoclast development. By screening vitamin D analogs based on their c-Fos–suppressing activity, we identified a new analog, named DD281, that inhibited bone resorption and prevented bone loss in ovariectomized mice, more potently than 1α,25(OH)(2)D(3), with similar levels of calcium absorption. Thus, c-Fos protein is an important target of the skeletal action of VDR-based drugs, and DD281 is a bone-selective analog that may be useful for the treatment of bone diseases with excessive osteoclastic activity

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-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-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-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