Enzymic removal of 5-methylcytosine from DNA by a human DNA-glycosylase

Vairapandi, Mariappan; Duker, Nahum J.

doi:10.1093/nar/21.23.5323

Cited by 66 publications

(50 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5-MeC is apparently removed and replaced by cytosine by an enzymic mechanism resembling the BER process [171]. While one report suggested that 5-meC is removed by an endonucleolytic process [172], others have demonstrated release of the free base (5-meC, which is subsequently deaminated to thymine) by HeLa nuclear extracts [173]. Recently, release of 5-meC by a partially purified enzyme from HeLa cells [174] and by a highly purified enzyme from chick embryos [175] was reported, indicating that a DNA glycosylase activity is responsible for 5-meC removal.…”

Section: -Mec-dna Glycosylasementioning

confidence: 99%

DNA glycosylases in the base excision repair of DNA

Krokan

Standal

Slupphaug

1997

Biochemical Journal

771

566

View full text Add to dashboard Cite

A wide range of cytotoxic and mutagenic DNA bases are removed by different DNA glycosylases, which initiate the base excision repair pathway. DNA glycosylases cleave the Nglycosylic bond between the target base and deoxyribose, thus releasing a free base and leaving an apurinic\apyrimidinic (AP) site. In addition, several DNA glycosylases are bifunctional, since they also display a lyase activity that cleaves the phosphodiester backbone 3h to the AP site generated by the glycosylase activity. Structural data and sequence comparisons have identified common features among many of the DNA glycosylases. Their active sites have a structure that can only bind extrahelical target bases, as observed in the crystal structure of human uracil-DNA glycosylase in a complex with double-stranded DNA. Nucleotide flipping is apparently actively facilitated by the enzyme. With bacteriophage T4 endonuclease V, a pyrimidine-

show abstract

Section: -Mec-dna Glycosylasementioning

confidence: 99%

DNA glycosylases in the base excision repair of DNA

Krokan

Standal

Slupphaug

1997

Biochemical Journal

771

566

View full text Add to dashboard Cite

show abstract

“…Recently, Vairapandi and Duker proposed an alternative pathway for removal of5-MeC involving a 5-MeC-specific DNA glycosylase (6). They found that incubation of a [methyl-3H]poly(dG-5-methyl-dC) polymer with a HeLa cell nuclear extract caused the release of radioactivity in an ethanolsoluble form.…”

Section: Introductionmentioning

confidence: 99%

Enzymic removal of 5-methylcytosine from poly(dG-5-methyl-dC) by HeLa cell nuclear extracts is not by a DNA glycosylase

Steinberg

1995

Nucl Acids Res

View full text Add to dashboard Cite

A recent report in this joumal [Vairapandi,M. and Duker,N.J. (1993) Nucleic Acids Res. 21, [5323][5324][5325][5326][5327] presented evidence of an activity in HeLa cell nuclear extracts that released radiolabeled material from a poly(dG.dC) polymer that had been methylated and simultaneously labeled on cytosine residues by incubation with a CpG-specific DNA methylase and [methyl-3H]S-adenosylmethionine. Based on chromatographic evidence that the released products were thymine and 5-methylcytosine and on radiolabeling data suggesting a concomitant increase in abasic sites, the authors concluded that the releasing activity was a 5-methylcytosine-specific glycosylase and that the solubilized 5-imethylcytosine was converted to thymine by a nuclear deaminase. We have confirmed that HeLa nuclear extracts promote release of ethanol-soluble radioactivity from a methyl-labeled poly(dG-5-methyldC)polymer, but the products released were neither 5-methylcytosine nor thymine. Furthermore, free 5-methylcytosine was not deaminated by incubation with the nuclear extract. The labeled compound released initially from the polymer appeared to be 5-methyldeoxycytidine monophosphate, which was converted to 5-methyl-deoxycytidine, thymidine monophosphate, and/or thymidine by further incubation with the nuclear extract. The activity responsible for the release, therefore, was a nuclease. Release of 32P-labeled nucleotides from a 32P-labeled poly(dG-dC) polymer suggested, furthermore, that the activity was not specific for methylated DNA.

show abstract

“…One potential mechanism to achieve this is through the action of 5-methylcytosine DNA glycosylase, which removes the methylcytosine from DNA leaving the deoxyribose intact (10). Local DNA repair then removes the abasic nucleotide and adds back an unmethylated cytosine nucleotide (11). Using chicken embryo nuclear extracts that can promote demethylation (12), a putative demethylase was purified; this was found to be a G͞T mismatch repair DNA glycosylase (13).…”

mentioning

confidence: 99%

Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation

Agius

Kapoor

Zhu

2006

Proc. Natl. Acad. Sci. U.S.A.

278

239

View full text Add to dashboard Cite

DNA methylation is a stable epigenetic mark for transcriptional gene silencing in diverse organisms including plants and many animals. In contrast to the well characterized mechanism of DNA methylation by methyltransferases, the mechanisms and function of active DNA demethylation have been controversial. Genetic evidence suggested that the DNA glycosylase domain-containing protein ROS1 of Arabidopsis is a putative DNA demethylase, because loss-of-function ros1 mutations cause DNA hypermethylation and enhance transcriptional gene silencing. We report here the biochemical characterization of ROS1 and the effect of its overexpression on the DNA methylation of target genes. Our data suggest that the DNA glycosylase activity of ROS1 removes 5-methylcytosine from the DNA backbone and then its lyase activity cleaves the DNA backbone at the site of 5-methylcytosine removal by successive ␤-and ␦-elimination reactions. Overexpression of ROS1 in transgenic plants led to a reduced level of cytosine methylation and increased expression of a target gene. These results demonstrate that ROS1 is a 5-methylcytosine DNA glycosylase͞lyase important for active DNA demethylation in Arabidopsis.DNA methylation ͉ epigenetics ͉ transcriptional gene silencing D NA cytosine methylation is important for many epigenetic processes including X chromosome inactivation, genomic imprinting, epigenetic changes during carcinogenesis, and silencing of transposons, of specific genes during development and of certain transgenes (1-5). The enzymes responsible for de novo as well as maintenance methylation at the 5Ј position of cytosines have been well characterized, and mutations in these enzymes can release transcriptional gene silencing and cause various developmental phenotypes (2,3,6,7). In contrast, the mechanism of DNA demethylation is less understood. DNA demethylation can be passive or active. Passive demethylation occurs automatically for newly synthesized DNA during replication if the new DNA is not acted upon by DNA methyltransferases. The biochemical mechanism of active DNA demethylation has been controversial (8).The chemistry of demethylating 5-methylcytosine DNA is challenging because it requires the disruption of carbon-carbon bonds. Earlier work has shown that 5-methylcytosine was replaced by labeled cytosine during the demethylation reaction in erythroleukemia cells, indicating a replacement of the entire nucleotide or base alone (9). One potential mechanism to achieve this is through the action of 5-methylcytosine DNA glycosylase, which removes the methylcytosine from DNA leaving the deoxyribose intact (10). Local DNA repair then removes the abasic nucleotide and adds back an unmethylated cytosine nucleotide (11). Using chicken embryo nuclear extracts that can promote demethylation (12), a putative demethylase was purified; this was found to be a G͞T mismatch repair DNA glycosylase (13). MBD4, a human homolog of the chicken enzyme, also has 5-methylcytosine DNA glycosylase activity (14). At least in vitro, these G͞T mismatch repair ...

show abstract

Enzymic removal of 5-methylcytosine from DNA by a human DNA-glycosylase

Cited by 66 publications

References 41 publications

DNA glycosylases in the base excision repair of DNA

DNA glycosylases in the base excision repair of DNA

Enzymic removal of 5-methylcytosine from poly(dG-5-methyl-dC) by HeLa cell nuclear extracts is not by a DNA glycosylase

Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation

Contact Info

Product

Resources

About