Uracil in DNA and its processing by different DNA glycosylases

Visnes, Torkild; Doseth, Berit; Pettersen, Henrik Sahlin; Hagen, Lars; Sousa, Mirta Mittelstedt Leal de; Akbari, Mansour; Otterlei, Marit; Kavli, Bodil; Slupphaug, Geir; Krokan, Hans E.

doi:10.1098/rstb.2008.0186

Cited by 108 publications

(98 citation statements)

References 34 publications

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“…As AID deaminates cytidines on ssDNA, uracil at U:G positions will be mostly formed in a single-stranded context on which UNG2 has more activity (25), while dUTP is incorporated in double-strand DNA on which SMUG1 has more activity when associated to AP-endonuclase 1 (26). It would be interesting to know whether SMUG1 could back up phase II mutations more efficiently than phase Ib mutations in UNG 2/2 mice.…”

Section: Discussionmentioning

confidence: 99%

Deoxyuridine Triphosphate Incorporation during Somatic Hypermutation of Mouse VkOx Genes after Immunization with Phenyloxazolone

Roche

Claës

Rougeon

2010

The Journal of Immunology

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Somatic hypermutation (SHM) of Ig genes is the result of a two-phase process initiated by activation-induced cytidine deaminase, relying on two different strategies for the introduction of mutations at CG pairs (phase I) and at AT pairs (phase II). To explain the selectivity of phase II, two mechanisms were proposed: AT-selective error-prone DNA-polymerases, deoxyuridine triphosphate (dUTP) incorporation, or both. However, there has been no experimental evidence so far of the possible involvement of the latter. We have developed a ligation-anchored PCR method based on the formation of single-strand breaks at uracils. In this study, we show the presence of uracil in hypermutating VkOx genes in wild type (AID+/+) mice, demonstrating that dUTP incorporation via DNA polymerases could be a major mechanism in SHM. Thus, error-prone DNA polymerases would participate in SHM via low-fidelity replication and incorporation of dUTP.

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Section: Discussionmentioning

confidence: 99%

Deoxyuridine Triphosphate Incorporation during Somatic Hypermutation of Mouse VkOx Genes after Immunization with Phenyloxazolone

Roche

Claës

Rougeon

2010

The Journal of Immunology

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“…It had long been thought that the uracil in DNA was an adverse condition arising from inappropriate incorporation of dUTP during replication or spontaneous deamination of cytosine. 36 It is becoming increasingly apparent, however, that nature incorporates uracil into DNA as a central mediator of adaptive immunity and as a strategy against certain viruses during innate responses. 37,38 Thus, uracil incorporation, once thought to be solely a mutagenic burden, has been revealed as a mechanism to modify immunoglobulin DNA in B cells for diversity or even non-self DNA for degradation.…”

Section: Discussionmentioning

confidence: 99%

Targets of somatic hypermutation within immunoglobulin light chain genes in zebrafish

Marianes

Zimmerman

2010

Immunology

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Summary In mammals, somatic hypermutation (SHM) of immunoglobulin (Ig) genes is critical for the generation of high‐affinity antibodies and effective immune responses. Knowledge of sequence‐specific biases in the targeting of somatic mutations can be useful for studies aimed at understanding antibody repertoires produced in response to infections, B‐cell neoplasms, or autoimmune disease. To evaluate potential nucleotide targets of somatic mutation in zebrafish (Danio rerio), an enriched IgL cDNA library was constructed and > 250 randomly selected clones were sequenced and analysed. In total, 55 unique VJ‐C sequences were identified encoding a total of 125 mutations. Mutations were most prevalent in VL with a bias towards single base transitions and increased mutation in the complementarity‐determining regions (CDRs). Overall, mutations were overrepresented at WRCH/DGYW motifs suggestive of activation‐induced cytidine deaminase (AID) targeting which is common in mice and humans. In contrast to mammalian models, N and P addition was not observed and mutations at AID hotspots were largely restricted to palindromic WRCH/DGYW motifs. Mutability indexes for di‐ and trinucleotide combinations confirmed C/G targets within WRCH/DGYW motifs to be statistically significant mutational hotspots and showed trinucleotides ATC and ATG to be mutation coldspots. Additive mutations in VJ‐C sequences revealed patterns of clonal expansion consistent with affinity maturation responses seen in higher vertebrates. Taken together, the data reveal specific nucleotide targets of SHM in zebrafish and suggest that AID and affinity maturation contribute to antibody diversification in this emerging immunological model.

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“…Identification of DNA Glycosylases Acting at Bulged Nucleotides-There are four human glycosylases that are known to excise U from DNA (30). The most active of these is uracil DNA glycosylase (UDG) (31).…”

Section: Glycosylase-catalyzed Excision Of Bulged Nucleotides In Helamentioning

confidence: 99%

Human Base Excision Repair Creates a Bias Toward −1 Frameshift Mutations

Lyons

O’Brien

2010

Journal of Biological Chemistry

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Frameshift mutations are particularly deleterious to protein function and play a prominent role in carcinogenesis. Most commonly these mutations involve the insertion or omission of a single nucleotide by a DNA polymerase that slips on a damaged or undamaged template. The mismatch DNA repair pathway can repair these nascent polymerase errors. However, overexpression of enzymes of the base excision repair (BER) pathway is known to increase the frequency of frameshift mutations suggesting competition between these pathways. We have examined the fate of DNA containing single nucleotide bulges in human cell extracts and discovered that several deaminated or alkylated nucleotides are efficiently removed by BER. Because single nucleotide bulges are more highly exposed we anticipate that they would be highly susceptible to spontaneous DNA damage. As a model for this, we have shown that chloroacetaldehyde reacts more than 18-fold faster with an A-bulge than with a stable A⅐T base pair to create alkylated DNA adducts that can be removed by alkyladenine DNA glycosylase. Reconstitution of the BER pathway using purified components establishes that bulged DNA is efficiently processed. Single nucleotide deletion is predicted to repair ؉1 frameshift events, but to make ؊1 frameshift events permanent. Therefore, these findings suggest an additional factor contributing to the bias toward deletion mutations.The loss or gain of one or more base pairs is one of the most common types of genetic instability (1). Single nucleotide deletions or insertions occur more frequently than larger deletions or insertions and they cause frameshift mutations if they occur within the open reading frame of a gene. Genomic instability is proposed to be a hallmark of carcinogenesis and the loss or alteration of DNA replication or repair pathways is an early step in the progression of cancer (2, 3). Normally the mismatch DNA repair (MMR) 3 pathway suppresses frameshift mutations by performing replication-coupled DNA repair, but many cancer cells inactivate this pathway through mutations or changes in promoter methylation that reduce expression of one or more proteins in this pathway (4 -6). However, not all cases of increased frameshift frequency can be attributed to defects in MMR (7, 8). Here we consider the possibility that other DNA repair pathways might also play a role in frameshift mutagenesis. Many of the factors that influence the frequency of frameshift mutations are known (9, 10). Streisinger and co-workers (11) proposed that slipping of a primer/template pair within a polymerase active site could lead to a misaligned intermediate that would subsequently be extended to generate a bulged intermediate. Subsequent models for frameshift mutations (1, 6), including the effects of damaged templates and DNA intercalators (12, 13), have incorporated this essential feature (Fig. 1). It is generally assumed that another round of DNA replication is required to make this frameshift event permanent, with one copy that retains the original sequence and ...

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Uracil in DNA and its processing by different DNA glycosylases

Cited by 108 publications

References 34 publications

Deoxyuridine Triphosphate Incorporation during Somatic Hypermutation of Mouse VkOx Genes after Immunization with Phenyloxazolone

Deoxyuridine Triphosphate Incorporation during Somatic Hypermutation of Mouse VkOx Genes after Immunization with Phenyloxazolone

Targets of somatic hypermutation within immunoglobulin light chain genes in zebrafish

Human Base Excision Repair Creates a Bias Toward −1 Frameshift Mutations

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