Thymine-DNA glycosylase and G to A transition mutations at CpG sites

Waters, T.P.; Swann, Peter F.

doi:10.1016/s1383-5742(00)00031-4

Cited by 61 publications

(80 citation statements)

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“…Our findings offer an explanation for the relatively weak G·T glycosylase activity of TDG, a trait that may contribute to the high mutational frequency at CpG sites in cancer and genetic disease (13,20). Although enhanced G·T repair activity by TDG could potentially be beneficial to the cell, we find that active-site mutations that confer enhanced G·T activity cause even larger increases in aberrant A·T activity.…”

Section: Discussionmentioning

confidence: 60%

“…Previous studies show that TDG activity is weak for G·T mispairs compared with most in vitro substrates (e.g., G·U), even though G·T mispairs are an important biological substrate for TDG (8,9,(16)(17)(18)(19). This might reflect a mechanism used by TDG to strike a balance between the requirement for efficient repair of mutagenic G·T lesions and the need for avoiding aberrant removal of T from A·T pairs, which can be mutagenic and cytotoxic (13,20,21). Notably, such a compromise in G·T repair activity could account in part for the high frequency of C→T transitions at CpG sites in cancer and genetic disease (20,(22)(23)(24).…”

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confidence: 99%

“…This might reflect a mechanism used by TDG to strike a balance between the requirement for efficient repair of mutagenic G·T lesions and the need for avoiding aberrant removal of T from A·T pairs, which can be mutagenic and cytotoxic (13,20,21). Notably, such a compromise in G·T repair activity could account in part for the high frequency of C→T transitions at CpG sites in cancer and genetic disease (20,(22)(23)(24). A mechanism for limiting thymine excision could be needed if the capacity of TDG to discriminate between G·T and A·T pairs, which is approximately 10 4.3 -fold (17), is not sufficient to allow for highly efficient G·T repair in the absence of aberrant A·T activity.…”

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confidence: 99%

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Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

Maiti

Noon

MacKerell

et al. 2012

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

168

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DNA base excision repair is essential for maintaining genomic integrity and for active DNA demethylation, a central element of epigenetic regulation. A key player is thymine DNA glycosylase (TDG), which excises thymine from mutagenic G·T mispairs that arise by deamination of 5-methylcytosine (mC). TDG also removes 5-formylcytosine and 5-carboxylcytosine, oxidized forms of mC produced by Tet enzymes. Recent studies show that the glycosylase activity of TDG is essential for active DNA demethylation and for embryonic development. Our understanding of how repair enzymes excise modified bases without acting on undamaged DNA remains incomplete, particularly for mismatch glycosylases such as TDG. We solved a crystal structure of TDG (catalytic domain) bound to a substrate analog and characterized active-site residues by mutagenesis, kinetics, and molecular dynamics simulations. The studies reveal how TDG binds and positions the nucleophile (water) and uncover a previously unrecognized catalytic residue (Thr197). Remarkably, mutation of two active-site residues (Ala145 and His151) causes a dramatic enhancement in G·T glycosylase activity but confers even greater increases in the aberrant removal of thymine from normal A·T base pairs. The strict conservation of these residues may reflect a mechanism used to strike a tolerable balance between the requirement for efficient repair of G·T lesions and the need to minimize aberrant action on undamaged DNA, which can be mutagenic and cytotoxic. Such a compromise in G·T activity can account in part for the relatively weak G·T activity of TDG, a trait that could potentially contribute to the hypermutability of CpG sites in cancer and genetic disease. D NA base excision repair (BER) plays an established role in maintaining genomic integrity, and recent studies indicate that BER is also essential for active DNA demethylation, a key element of epigenetic gene regulation (1-3). A central player in both processes is thymine DNA glycosylase (TDG), which initiates BER by excising damaged or modified forms of 5-methylcytosine (mC) that arise at 5′-CpG-3′ sites. TDG was discovered for its ability to selectively remove T from G·T mispairs, mutagenic lesions that can arise from deamination of mC to T (4, 5). TDG also excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), oxidized forms of mC that are generated by Tet enzymes (6, 7). In addition, TDG was shown to be essential for active DNA demethylation and for embryonic development (8, 9), a role that likely involves excision of deaminated or oxidized forms of mC generated by a deaminase or Tet enzyme (7,(10)(11)(12). Thus, the ability of TDG to remove deaminated and oxidized forms of mC is important for genetic and epigenetic integrity.The question of how DNA glycosylases remove modified bases without acting upon the huge excess of undamaged DNA remains largely unresolved, particularly for mismatch glycosylases such as TDG and MBD4 (methyl binding domain IV) (13-15). These enzymes face the formidable task of removing a normal base, t...

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Section: Discussionmentioning

confidence: 60%

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confidence: 99%

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confidence: 99%

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Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

Maiti

Noon

MacKerell

et al. 2012

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

168

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“…1,2 In human cancer, CpG transitions account for about 24% of tumor-suppressor gene TP53 mutations, including all mutation hotspots. 3 The predominance of these mutations is due, to a large extent, to the highly mutable characteristics of G:C to A:T base pairs within CpG sites. They originate from non-repaired G:T mismatches resulting from the Thymine DNA glycosylase (TDG) belongs to the superfamily of uracil DNA glycosylases (UDG) and is the first enzyme in the base-excision repair pathway (BeR) that removes thymine from G:T mismatches at CpG sites.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional regulation of thymine DNA glycosylase (TDG) by the tumor suppressor protein p53

et al. 2012

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“…A major fraction of these transitions occurs in a CpG context and they have therefore been suggested to result from deamination of 5-methylcytosine (5-meC) to thymine, or cytosine to uracil. DNA replication would then insert A in the place of G (reviewed by Waters and Swann, 2000). However, C?T transitions are common in other sequences as well.…”

Section: Introductionmentioning

confidence: 99%