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  • genome
  • Whole-genome approaches have recently been used with different levels of success to delineate breast-cancer-specific DNA methylation signatures, and to test whether they can classify breast cancer and whether they could be associated with specific clinical outcomes. (biomedcentral.com)
  • I discuss the role of DNA methylation in normal gene regulation, the aberrations in DNA methylation in cancer, and candidate-gene and whole-genome approaches to classify breast cancer subtypes using DNA methylation markers. (biomedcentral.com)
  • proteins
  • DNA methylation is a robust biomarker, vastly more stable than RNA or proteins, and is therefore a promising target for the development of new approaches for diagnosis and prognosis of breast cancer and other diseases. (biomedcentral.com)
  • amino acid residues
  • All high-resolution structures of C-protein/DNA-protein complexes solved to date relate to C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or the phosphate backbone could be observed. (jove.com)
  • amplification
  • The resulting DNA can be used in many downstream applications, such as endpoint or real-time PCR analysis of the methylation status of particular loci in normal and diseased samples, bisulfite conversion followed by cloning and sequencing, or amplification and labeling for microarray analysis. (activemotif.com.cn)
  • demethylation
  • Demethylation may take place as a passive process because of lack of maintenance methylation during several cycles of DNA replication or as an active mechanism in the absence of replication ( 8 ). (pnas.org)
  • 1986). Thus, demethylation of DNA seemed to be achieved by an enzymatic mechanism whereby 5mC was replaced by cytosine. (ebrary.net)
  • The first step of demethylation was the formation of specific 5' nick at the 5mC residue. (ebrary.net)
  • global DNA methylation
  • Finally, global DNA methylation varied according to the interaction of receptivity group and day of estrous, and a divergent trend, which correlated with abundance of DNMT1 transcript, was observed in LR and HR along the estrous cycle days. (jove.com)
  • Assay
  • Researchers interested in studying the DNA methyltransferase enzymes, DNMT1, DNMT3a and DNMT3b, that are responsible for transferring the methyl group to the fifth carbon of cytosine to produce 5-methylcytosine should use the DNMT Activity / Inhibition Assay . (activemotif.com)
  • This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray), provides several advantages over existing methods used for methylation analysis. (biomedcentral.com)
  • bases
  • Our results indicate that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding affinity than mutations to those residues that bind directly to the bases (T36, R46), and the contributions of each side chain to the binding energies are compared. (jove.com)
  • involves
  • Direct removal of the methyl group from 5-meC residues has been claimed ( 11 ), but this mechanism, which involves a thermodynamically unfavorable breakage of the carbon-carbon bond, has been questioned ( 12 ) and could not be independently reproduced ( 13 , 14 ). (pnas.org)
  • Traditional DNA methylation involves the transfer of a methyl group to the carbon 5 position of cytosine to produce 5-methylcytosine (5-mC). (activemotif.com)
  • reversible
  • DNA methylation has long been thought to be a static epigenetic mark, but emerging evidence suggests that it undergoes dynamic and reversible remodeling in somatic cells during developmental and pathogenic processes ( 12 , 13 ), making its machinery and effects attractive drug targets. (diabetesjournals.org)
  • Recent data that will be discussed here that supports the hypothesis that DNA methylation is a reversible biological signal. (caister.com)
  • repeats
  • Asymmetrically located cytosines in plant telomeric DNA repeats may be substrates for a DNA methyltransferase enzyme and indeed, it was shown that these repeats are methylated. (jove.com)
  • Our results show that cytosine methylation in telomeric repeats depends on the activity of MET1 and DDM1 enzymes. (jove.com)
  • Aberrant
  • In GBMs, aberrant methylation in the promoter of the O 6 -methylguanine-DNA methyltransferase gene has been associated with significantly longer survival in patients treated with radiation and the alkylating agent temozolomide ( 8 ). (aacrjournals.org)
  • specificity
  • Different methods of post PCR analysis may be utilized, depending on the degree of specificity and resolution of methylation required. (jove.com)
  • enzymes
  • 5-mC is amenable to enzymatic oxidation to 5-hmC by the Tet family of enzymes, which are believed to be involved in development and disease. (jove.com)
  • However, research has shown that the Tet family of cytosine oxygenase enzymes are involved in oxidizing 5-methylcytosine into 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). (activemotif.com)
  • We identified unique signatures of both DNA methylation and expression of epigenetic modifying enzymes in airway epithelial cells and showed that epithelial cells were epigenetically distinct from other cell types. (ubc.ca)
  • Although these enzymatic steps can be accomplished by purified enzymes on naked DNA in vitro, there are accessory factors in cells, including XRCC1, that ensure efficiency and coordination of the repair process ( 6 , 7 ). (pnas.org)