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Methylated DNA (methylated + dna)

Distribution by Scientific Domains

Medical Sciences	66%

Selected Abstracts

Solution structure of the matrix attachment region-binding domain of chicken MeCP2

FEBS JOURNAL, Issue 15 2003
Björn Heitmann
Methyl-CpG-binding protein 2 (MeCP2) is a multifunctional protein involved in chromatin organization and silencing of methylated DNA. MAR-BD, a 125-amino-acid residue domain of chicken MeCP2 (cMeCP2, originally named ARBP), is the minimal protein fragment required to recognize MAR elements and mouse satellite DNA. Here we report the solution structure of MAR-BD as determined by multidimensional heteronuclear NMR spectroscopy. The global fold of this domain is very similar to that of rat MeCP2 MBD and MBD1 MBD (the methyl-CpG-binding domains of rat MeCP2 and methyl-CpG-binding domain protein 1, respectively), exhibiting a three-stranded antiparallel ,-sheet and an ,-helix ,1. We show that the C-terminal portion of MAR-BD also contains an amphipathic helical coil, ,2/,3. The hydrophilic residues of this coil form a surface opposite the DNA interface, available for interactions with other domains of MeCP2 or other proteins. Spectroscopic studies of the complex formed by MAR-BD and a 15-bp fragment of a high-affinity binding site from mouse satellite DNA indicates that the coil is also involved in protein·DNA interactions. These studies provide a basis for discussion of the consequences of six missense mutations within the helical coil found in Rett syndrome cases. [source]

Association of circulating tumor cells with tumor-related methylated DNA in patients with hormone-refractory prostate cancer

INTERNATIONAL JOURNAL OF UROLOGY, Issue 5 2010
Takatsugu Okegawa
Objectives: To assess whether circulating tumor cells with tumor-related methylated DNA can be used to predict survival in patients with hormone-refractory prostate cancer. Methods: Blood samples from 76 patients with hormone-refractory prostate cancer were analyzed. Circulating tumor cells were enumerated with the CellSearch System in whole blood. This system was developed using an epithelial cell adhesion molecule antibody-based immunomagnetic capture and automated staining methodology. Hypermethylation at adenomatosis polyposis coli, glutathione-S-transferase-,, prostaglandin-endoperoxide synthase 2, multidrug resistance 1 and Ras association domain family 1 isoform A was analyzed using a sensitive SYBR green methylation-specific polymerase chain reaction. Patient charts were retrospectively examined. Results: Median overall survival time was 19.3 months (range 11,48). Of the 76 patients, 47 (62%) had five or more circulating tumor cells, with a median overall survival of 12.0 months compared with 26.0 months for patients with fewer than five circulating tumor cells (P < 0.001). Circulating tumor cells were detected in 36 of 39 (92%) patients with tumor-related methylated DNA but only 11 of 37 (30%) patients without methylated DNA (P < 0.001). Thirty-nine (51%) patients had one or more methylated marker. Their median overall survival time was 12.0 months compared with 48.0 months or more for patients without methylated DNA (P < 0.001). Prostate-specific antigen-doubling time, circulating tumor cells and methylated DNA were independent predictors of overall survival time. Conclusions: Hormone refractory prostate cancer patients with circulating tumor cells and/or tumor-related methylated DNA show a significantly poorer outcome than those without these blood markers. [source]

Genetic and epigenetic alterations of the KLF6 gene in hepatocellular carcinoma

JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 8 2006
Jaehwi Song
Abstract Background and Aim:, Kruppel-like factor 6 (KLF6) is a zinc finger tumor suppressor gene that is frequently mutated in several human cancers and is broadly involved in differentiation and development, growth-related signal transduction, cell proliferation, apoptosis, and angiogenesis. The aim of this study was to elucidate the potential etiological role of KLF6 in the development of hepatocellular carcinoma (HCC) in Korea. Methods:, The gene mutation, allelic loss, and methylation status of the KLF6 gene was analyzed in a series of 85 Korean patients: 21 with dysplastic nodules and 85 with HCC. Results:, No somatic mutations were observed in the patients with dysplastic nodules or with HCC. Allelic loss was found in five (6.8%) of 73 informative HCC tissues. Three of the five patients with allelic loss had HCC with hepatitis B virus infection and cirrhosis, and the remaining two had no viral infection and a non-specific background. In methylation analysis, unmethylated and methylated DNAs of the KLF6 gene were amplified in all corresponding non-neoplastic liver tissues. Only one HCC tissue showed methylated DNA without unmethylated DNA. Conclusions:, The results suggest that genetic and epigenetic alteration of KLF6 may play a minor role in the development of HCC. [source]

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice

THE PLANT JOURNAL, Issue 3 2010
Huihuang Yan
Summary We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The chromosomal distribution pattern of methylated DNA is similar to the heterochromatin distribution pattern on rice chromosomes. The DNA methylation patterns of rice genes are similar to those in Arabidopsis thaliana, including distinct methylation patterns asssociated with gene bodies and promoters. The DNA sequences in the core domains of rice Cen4, Cen5 and Cen8 showed elevated methylation levels compared with sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains, compared with the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared with the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin. [source]