Use of mutation spectra analysis software

Rogozin, Igor B.; Kondrashov, Fyodor A.; Glazko, Galina V.

doi:10.1002/1098-1004(200102)17:2<83::aid-humu1>3.0.co;2-e

Cited by 35 publications

(29 citation statements)

References 71 publications

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“…A Monte Carlo modification of the Pearson 2 test of spectra homogeneity (37) and the Kendall's correlation coefficient (38,39) were used to compare distribution of mutations along the intron sequence. Calculations were done using the programs CORR12 (38) and COLLAPSE (40).…”

Section: Statistical Analysesmentioning

confidence: 99%

DNA Polymerase η Contributes to Strand Bias of Mutations of A versus T in Immunoglobulin Genes

Mayorov

Rogozin

Adkison

et al. 2005

The Journal of Immunology

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DNA polymerase (pol) η participates in hypermutation of A:T bases in Ig genes because humans deficient for the polymerase have fewer substitutions of these bases. To determine whether polymerase η is also responsible for the well-known preference for mutations of A vs T on the nontranscribed strand, we sequenced variable regions from three patients with xeroderma pigmentosum variant (XP-V) disease, who lack polymerase η. The frequency of mutations in the intronic region downstream of rearranged JH4 gene segments was similar between XP-V and control clones; however, there were fewer mutations of A:T bases and correspondingly more substitutions of C:G bases in the XP-V clones (p < 10−7). There was significantly less of a bias for mutations of A compared with T nucleotides in the XP-V clones compared with control clones, whereas the frequencies for mutations of C and G were identical in both groups. An analysis of mutations in the WA sequence motif suggests that polymerase η generates more mutations of A than T on the nontranscribed strand. This in vivo data from polymerase η-deficient B cells correlates well with the in vitro specificity of the enzyme. Because polymerase η inserts more mutations opposite template T than template A, it would generate more substitutions of A on the newly synthesized strand.

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Section: Statistical Analysesmentioning

confidence: 99%

DNA Polymerase η Contributes to Strand Bias of Mutations of A versus T in Immunoglobulin Genes

Mayorov

Rogozin

Adkison

et al. 2005

The Journal of Immunology

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“…Monte Carlo modification of the Pearson 2 test of spectra homogeneity (39,40) and the Kendall's correlation coefficient (41)(42)(43) were used to compare spectra. Pcc is the probability that an observed correlation between two spectra is due to random fluctuations.…”

Section: Yeast Strains For Measuring Forward Mutation Rates In Vivo-mentioning

confidence: 99%

“…Calculations were done using the programs HG-PUBL (44), CORR12, and COMP12 (41). The CLUSTERM program (43,45) was used for hot spot prediction. The known list of detectable positions in lacZ (46) was used for analysis of spectra.…”

Section: Yeast Strains For Measuring Forward Mutation Rates In Vivo-mentioning

confidence: 99%

Unique Error Signature of the Four-subunit Yeast DNA Polymerase ϵ

Shcherbakova

Pavlov

Chilkova

et al. 2003

Journal of Biological Chemistry

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112

137

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We have purified wild type and exonuclease-deficient four-subunit DNA polymerase ⑀ (Pol ⑀) complex from Saccharomyces cerevisiae and analyzed the fidelity of DNA synthesis by the two enzymes. Wild type Pol ⑀ synthesizes DNA accurately, generating single-base substitutions and deletions at average error rates of <2 ؋ 10 ؊5 and <5 ؋ 10 ؊7 , respectively. Pol ⑀ lacking 3 3 5 exonuclease activity is less accurate to a degree suggesting that wild type Pol ⑀ proofreads at least 92% of base substitution errors and at least 99% of frameshift errors made by the polymerase. Surprisingly the base substitution fidelity of exonuclease-deficient Pol ⑀ is severalfold lower than that of proofreading-deficient forms of other replicative polymerases. Moreover the spectrum of errors shows a feature not seen with other A, B, C, or X family polymerases: a high proportion of transversions resulting from T⅐dTTP, T⅐dCTP, and C⅐dTTP mispairs. This unique error specificity and amino acid sequence alignments suggest that the structure of the polymerase active site of Pol ⑀ differs from those of other B family members. We observed both similarities and differences between the spectrum of substitutions generated by proofreading-deficient Pol ⑀ in vitro and substitutions occurring in vivo in a yeast strain defective in Pol ⑀ proofreading and DNA mismatch repair. We discuss the implications of these findings for the role of Pol ⑀ polymerase activity in DNA replication.Replication of chromosomes in eukaryotes is believed to require three DNA polymerases, Pol ␣, 1 Pol ␦, and Pol ⑀ (for reviews, see Refs. 1-3). Pol ␣ has an associated DNA primase activity and synthesizes short RNA-DNA primers to initiate replication at origins and start Okazaki fragments on the lagging DNA strand. The roles of Pol ␦ and Pol ⑀ in chromosomal replication are not clearly defined. Evidence for essential roles of Pol ␦ and Pol ⑀ in replication comes from genetic studies in Saccharomyces cerevisiae. Mutational inactivation of catalytic subunits and some of the additional subunits of both polymerases is lethal. Strains carrying temperature-sensitive mutations in POL3 gene (encoding the catalytic subunit of Pol ␦), POL2, or DPB2 genes (encoding subunits of Pol ⑀) arrest in S phase of the cell cycle with a terminal morphology characteristic of a DNA replication defect upon shift to non-permissive temperature (4 -6). Incorporation of labeled precursors into DNA stops in these mutants at non-permissive temperature (4, 5, 7). The POL3, POL2, and DPB2 genes, as well as the DPB3 gene encoding the third subunit of Pol ⑀, are expressed periodically in the cell cycle with a peak in G 1 to S phase transition (4, 5, 8), which is characteristic of genes encoding DNA replication proteins. Both Pol ␦ and Pol ⑀ have intrinsic 3Ј 3 5Ј exonuclease activities that correct polymerase errors during replication (9, 10). Mutations in POL3 or POL2 inactivating the exonucleases result in a mutator phenotype (11,12).To accommodate roles for Pol ␦ and Pol ⑀ at a replication fork, it was proposed...

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“…Monte Carlo modification of the Pearson 2 test of spectra homogeneity (26) and the Kendall's tau correlation coefficient (27,28) were used to compare spectra. Calculations were done by using the programs CORR12 (27,28) and HG-PUBL (29). To simultaneously examine the correlation between three spectra by multiple regression analysis, the ''linear regression module'' of the program STATISTICA was used.…”

Section: Construction Of New M13mp2mentioning

confidence: 99%

“…Small values (Ͻ 0.05) of the probability P(W Յ W random ) indicate a significant correlation between a mutable motif and mutations (5,8). Hotspots were predicted as described (28).…”

Section: Construction Of New M13mp2mentioning

confidence: 99%

Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase η during copying of a mouse immunoglobulin κ light chain transgene

Pavlov

Rogozin

Galkin

et al. 2002

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

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117

110

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To test the hypothesis that inaccurate DNA synthesis by mammalian DNA polymerase (pol ) contributes to somatic hypermutation (SHM) of Ig genes, we measured the error specificity of mouse pol during synthesis of each strand of a mouse Ig light chain transgene. We then compared the results to the base substitution specificity of SHM of this same gene in the mouse. The in vitro and in vivo base substitution spectra shared a number of common features. A highly significant correlation was observed for overall substitutions at A-T pairs but not for substitutions at G-C pairs. Sixteen mutational hotspots at A-T pairs observed in vivo were also found in spectra generated by mouse pol in vitro. The correlation was strongest for errors made by pol during synthesis of the non-transcribed strand, but it was also observed for synthesis of the transcribed strand. These facts, and the distribution of substitutions generated in vivo, support the hypothesis that pol contributes to SHM of Ig genes at A-T pairs via short patches of low fidelity DNA synthesis of both strands, but with a preference for the non-transcribed strand.H igh affinity antibodies result from somatic hypermutation (SHM) of Ig genes followed by selection. The SHM process introduces base substitutions at a very high rate into DNA encoding the variable regions of immunoglobulins (1-4). Although the mechanism for introducing these sequence changes is currently unknown, several features of SHM specificity offer clues to the DNA transactions that might be involved. For example, SHM primarily occurs in two highly mutable DNA sequence motifs (5-9). One is the RGYW sequence (the underlined G is mutated, R ϭ A or G, Y ϭ T or C, and W ϭ A or T), which is found in SHM substitution spectra in equal proportions in both DNA strands. The other is the WA motif, where substitutions are more likely in one strand than the other (5, 7-10). A clue to the origins of the substitutions in the WA motif is the observation that their type and location correlates with the base substitution error specificity of human DNA polymerase when copying a bacterial gene sequence in a model system in vitro (8). Based on that correlation and additional considerations of the two mutable motifs (11), we suggested that errors at A-T base pairs by pol may contribute to as much as one third of somatic mutations in Ig genes, preferentially during synthesis of the non-transcribed strand. This hypothesis is supported by the observation that XP-V patients lacking active polymerase have a lower proportion of somatic substitutions at A-T base pairs in Ig genes (12). Because pol error specificity does not correlate with substitutions in the RGYW sequence motif, and because those substitutions are distributed equally on both strands, we further suggested that SHM may involve more than one DNA transaction and more than one DNA polymerase (8). This finding is consistent with the two-phase model of SHM proposed earlier (9, 13). Other DNA polymerases suggested to participate in SHM include pol (14-16), pol (17, 18) ...

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Use of mutation spectra analysis software

Cited by 35 publications

References 71 publications

DNA Polymerase η Contributes to Strand Bias of Mutations of A versus T in Immunoglobulin Genes

DNA Polymerase η Contributes to Strand Bias of Mutations of A versus T in Immunoglobulin Genes

Unique Error Signature of the Four-subunit Yeast DNA Polymerase ϵ

Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase η during copying of a mouse immunoglobulin κ light chain transgene

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