In this article, we present a likelihood-based framework for modeling site dependencies. Our approach builds upon standard evolutionary models but incorporates site dependencies across the entire tree by letting the evolutionary parameters in these models depend upon the ancestral states at the neighboring sites. It thus avoids the need for introducing new and high-dimensional evolutionary mode...

We designed a detection system of 5-methylcytosine ((m)C) in DNA by a combination of photooxidative DNA cleavage reaction of 2-methyl-1,4-naphthoquinone chromophore with invader technology. Enzymatic treatment of a mixture of photochemically fragmented target oligodeoxynucleotides (ODNs) at (m)C and probe oligomer possessing a fluorophore and a quencher resulted in a dramatic enhancement of flu...

5-Methylcytosine was distinguished from cytosine using the large difference of their osmium oxidation rates, and this reaction was applied to detection of the cytosine methylation status at a specific site of a long sequence using the formation of a bulge structure by hybridization with a guide DNA.

Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a co...

Restriction Fragment Length Polymorphism (RFLP) analysis in human genetics can be confounded by sensitivity of restriction enzymes to the cytosine methylation that occurs at many cytosine-guanine (CpG) dinucleotides. Previous reports provided conflicting information on the sensitivity of Hindi to C methylation (1-3). We identified alleles at a chromosome 4pl6 locus that were inherited in a non-...

The epidermal growth factor receptor (EGFR) T790M mutation, a missense mutation from CpG cytosine to thymine, in non-small cell lung cancer is drug-resistant induced by the administration of tyrosine kinase inhibitors (TKIs). It important detect this with high sensitivity, as effective therapies have been developed for patients mutation. We confirmed that at point methylated various tissues, an...

The presence of 5-methylcytosine (5-mC) in DNA is a vital epigenetic mark in vertebrates. While the enzymes responsible for methylating DNA in vertebrates have been identified, the means by which this mark can be removed are still unclear. Recently, it has been shown that activation-induced cytidine deaminase (AID) contributes to the demethylation of DNA in certain systems. This enzyme has been...