Linked spontaneous CG----TA mutations at CpG sites in the gene for protein kinase regulatory subunit

Frequent p53 and H-ras Mutations in Benzene- and Ethylene Oxide-Induced Mammary Gland Carcinomas from B6C3F1 Mice

Benzene and ethylene oxide are multisite carcinogens in rodents and classified as human carcinogens by the National Toxicology Program. In 2-year mouse studies, both chemicals induced mammary carcinomas. We examined spontaneous, benzene-, and ethylene oxide-induced mouse mammary carcinomas for p53 protein expression, using immunohistochemistry, and p53 (exons 5–8) and H -ras (codon 61) mutations using cycle sequencing techniques. p53 protein expression was detected in 42% (8/19) of spontaneous, 43% (6/14) of benzene-, and 67% (8/12) of ethylene oxide-induced carcinomas. However, semiquantitative evaluation of p53 protein expression revealed that benzene- and ethylene oxide-induced carcinomas exhibited expression levels five- to six-fold higher than spontaneous carcinomas. p53 mutations were found in 58% (7/12) of spontaneous, 57% (8/14) of benzene-, and 67% (8/12) of ethylene oxide-induced carcinomas. H -ras mutations were identified in 26% (5/19) of spontaneous, 50% (7/14) of benzene-, and 33% (4/12) of ethylene oxide-induced carcinomas. When H- ras mutations were present, concurrent p53 mutations were identified in 40% (2/5) of spontaneous, 71% (5/7) of benzene-, and 75% (3/4) of ethylene oxide-induced carcinomas. Our results demonstrate that p53 and H -ras mutations are relatively common in control and chemically induced mouse mammary carcinomas although both chemicals can alter the mutational spectra and more commonly induce concurrent mutations.

Through a glass, darkly: reflections of mutation from lacI transgenic mice

The study of mutational frequency (Mf) and specificity in aging Big Blue lacI transgenic mice provides a unique opportunity to determine mutation rates (MR) in vivo in different tissues. We found that MR are not static, but rather, vary with the age or developmental stage of the tissue. Although Mf increase more rapidly early in life, MR are actually lower in younger animals than in older animals. For example, we estimate that the changes in Mf are 4.9x10(-8) and 1.1 x 10(-8) mutations/base pair/month in the livers of younger mice (<1. 5 months old) and older mice (> or =1.5 months old), respectively (a 4-fold decrease), and that the MR are 3.9 x 10(-9) and 1.3 x 10(-7) mutations/base pair/cell division, respectively ( approximately 30-fold increase). These data also permit an estimate of the MR of GC --> AT transitions occurring at 5'-CpG-3' (CpG) dinucleotide sequences. Subsequently, the contribution of these transitions to age-related demethylation of genomic DNA can be evaluated. Finally, to better understand the origin of observed Mf, we consider the contribution of various factors, including DNA damage and repair, by constructing a descriptive mutational model. We then apply this model to estimate the efficiency of repair of deaminated 5-methylcytosine nucleosides occurring at CpG dinucleotide sequences, as well as the influence of the Msh2(-/-) DNA repair defect on overall DNA repair efficiency in Big Blue mice. We conclude that even slight changes in DNA repair efficiency could lead to significant increases in mutation frequencies, potentially contributing significantly to human pathogenesis, including cancer.

Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes

A highly abundant repetitive DNA sequence family of Arabidopsis, AtCon, is composed of 178-bp tandemly repeated units and is located at the centromeres of all five chromosome pairs. Analysis of multiple copies of AtCon showed 95% conservation of nucleotides, with some alternative bases, and revealed two boxes, 30 and 24 bp long, that are 99% conserved. Sequences at the 3' end of these boxes showed similarity to yeast CDEI and human CENP-B DNA-protein binding motifs. When oligonucleotides from less conserved regions of AtCon were hybridized in situ and visualized by using primer extension, they were detected on specific chromosomes. When used for polymerase chain reaction with genomic DNA, single primers or primer pairs oriented in the same direction showed negligible amplification, indicating a head-to-tail repeat unit organization. Most primer pairs facing in opposite directions gave several strong bands corresponding to their positions within AtCon. However, consistent with the primer extension results, some primer pairs showed no amplification, indicating that there are chromosome-specific variants of AtCon. The results are significant because they elucidate the organization, mode of amplification, dispersion, and evolution of one of the major repeated sequence families of Arabidopsis. The evidence presented here suggests that AtCon, like human alpha satellites, plays a role in Arabidopsis centromere organization and function.

The role of DNA methylation in cancer genetic and epigenetics

The past few years have seen a wider acceptance of a role for DNA methylation in cancer. This can be attributed to three developments. First, the documentation of the over-representation of mutations at CpG dinucleotides has convincingly implicated DNA methylation in the generation of oncogenic point mutations. The second important advance has been the demonstration of epigenetic silencing of tumor suppressor genes by DNA methylation. The third development has been the utilization of experimental methods to manipulate DNA methylation levels. These studies demonstrate that DNA methylation changes in cancer cells are not mere by-products of malignant transformation, but can play an instrumental role in the cancer process. It seems clear that DNA methylation plays a variety of roles in different cancer types and probably at different stages of oncogenesis. DNA methylation is intricately involved in a wide diversity of cellular processes. Likewise, it appears to exert its influence on the cancer process through a diverse array of mechanisms. It is our task not only to identify these mechanisms, but to determine their relative importance for each stage and type of cancer. Our hope then will be to translate that knowledge into clinical applications.

Arginine 210 is not a critical residue for the allosteric interactions mediated by binding of cyclic AMP to site A of regulatory (RIalpha) subunit of cyclic AMP-dependent protein kinase

The guanidinium groups of conserved arginines in the two intrachain cAMP-binding sites of regulatory (R) subunit of cAMP-dependent protein kinase have been implicated in the allosteric interactions by which cAMP binding leads to kinase activation. We have investigated the functional role of Arg-210, the conserved arginine in site A of murine type Ialpha R subunit, by analyzing the effects of nine different substitutions at this residue on cAMP binding and allosteric properties of bacterially expressed RIalpha subunits. All substitutions reduced the cAMP binding affinity of site A, but the magnitude of reduction varied from several hundredfold to 10(6)-fold. The differential effects of the different substitutions could not easily be rationalized by interactions with cAMP and might, in part, reflect interactions with other residues in the unoccupied cAMP-binding pocket. None of the Arg-210 substitutions appeared to disrupt the allosteric interaction by which occupation of site A slows dissociation of cAMP from site B, although the effect was difficult to elicit in full with mutations that had strong effects on cAMP binding. The two weakest substitutions, Arg-210 --> Ile and Arg-210 --> Thr, could be shown to have essentially no effect on the allosteric interaction by which occupation of site A reduces the affinity of R subunit for the catalytic subunit. The weaker mutations had a smaller effect on kinase activation by the suboptimal activator Rp-adenosine cyclic 3',5'-phosphorothioate than by cAMP, suggesting that the analog largely bypasses interactions with the guanidinium group of Arg-210.

Second-site mutations in cyclic AMP-sensitive revertants of a Ka mutant of S49 mouse lymphoma cells reduce the affinity of regulatory subunit of cyclic AMP-dependent protein kinase for catalytic subunit

Ka mutants of S49 mouse lymphoma cells are generally heterozygous for expression of wild-type and mutant regulatory (R) subunits of type I alpha cyclic AMP-(cAMP)-dependent protein kinase, where the mutant R subunit has a defect in cAMP-binding to one of two intrachain cAMP-binding sites. Several cAMP-sensitive revertants of such a Ka mutant were found previously to harbor second-site mutations in the mutant allele, and we have now identified three such mutations by sequence analysis of PCR-amplified cDNAs. The resulting amino acid changes were Ala98 to Thr, Gly179 to Arg, or Gly224 to Asp. The Ka mutation in these strains (Glu201 to Lys) eliminated cAMP-binding to the more aminoterminal cAMP-binding site (site A). None of the second-site mutations restored this activity in bacterially expressed recombinant R subunit. On the other hand, all three second-site mutations reduced the apparent affinity of the mutant R subunit for catalytic (C) subunit with the effects of the substitutions at Ala98 and Gly179 substantially greater than the effect of the substitution at Gly224. Patterns of phosphorylation and turnover of wild-type and mutant R subunits in intact revertant cells were consistent with reduced association of the doubly mutant subunits with C subunit, but the free mutant subunits apparently were more stable than free wild-type subunits. Differences in metabolic turnover of mutant and wild-type subunits did not correlate with the sensitivities of the isolated proteins to proteolytic cleavage.

Achondroplasia is defined by recurrent G380R mutations of FGFR3

Genomic DNA from 154 unrelated individuals with achondroplasia was evaluated for mutations in the fibroblast growth factor receptor 3 (FGFR3) transmembrane domain. All but one, an atypical case, were found to have a glycine-to-arginine substitution at codon 380. Of these, 150 had a G-to-A transition at nt 1138, and 3 had a G-to-C transversion at this same position. On the basis of estimates of the prevalence of achondroplasia, the mutation rate at the FGFR3 1138 guanosine nucleotide is two to three orders of magnitude higher than that previously reported for tranversions and transitions in CpG dinucleotides. To date, this represents the most mutable single nucleotide reported in the human genome. The homogeneity of mutations in achondroplasia is unprecedented for an autosomal dominant disorder and may explain the relative lack of heterogeneity in the achondroplasia phenotype.

Gene inactivation in Arabidopsis thaliana is not accompanied by an accumulation of repeat-induced point mutations

Chromosomal integration of multicopy transgene inserts in higher plants is often followed by loss of expression. We have analysed whether this inactivation can trigger repeat-induced point mutations (RIP) as has been observed in Neurospora crassa. We have previously characterized transgenic lines of Arabidopsis thaliana containing the hygromycin phosphotransferase (hpt) gene either as a unique sequence in plants expressing the gene, or as multimeric, closely linked repeats in clones that were resistant to hygromycin directly after transformation but exhibited gene inactivation in the subsequent generation. At the sequence level, we have determined the mutation frequencies in the promoter and coding regions of active and inactive copies of transgene inserts after passage through three sexual generations. No RIP-like mutations were found in inactivated genes. Comparison of our data with those from Neurospora suggest that sequence divergence within plant repetitive DNA is either much slower than in Neurospora or is generated by a different mechanism.

Spectrum of spontaneous missense mutations causing cyclic AMP-resistance phenotypes in cultured S49 mouse lymphoma cells differs markedly from those of mutations induced by alkylating mutagens

Mutants of S49 mouse lymphoma cells resistant to cytolysis by analogs of cyclic AMP (cAMP) generally have missense mutations in the gene encoding the regulatory subunit of cAMP-dependent protein kinase. We have compared the mutations in 95 spontaneous isolates with those in 60 mutagen-induced isolates by sequence analysis of amplified cDNAs. Twenty-nine single basepair substitutions in 19 codons produced selectable phenotypes. The spontaneous mutant spectrum was dominated by a CpG transition hotspot in the codon for Arg334. This and other nearby CpG sites were found to be methylated in genomic S49 cell DNA by restriction enzyme analyses. Most of the remaining spontaneous mutants had either G-C-->C-G or T-A-->G-C transversions, which have been associated with damage caused by oxygen radicals. In contrast, the majority of mutants induced with the alkylating mutagens ethyl methanesulfonate (EMS) and N-methyl-N'-nitro-N-nitrosoguanidine had G-C-->A-T mutations at non-CpG sites; in addition, EMS induced several A-T-->G-C, A-T-->T-A, and G-C-->T-A substitutions. A single ICR191-induced mutant analyzed had a unique A-T-->G-C lesion. A number of spontaneous and mutagen-induced isolates had closely linked double or triple substitutions, and two isolates had tandem triple substitutions.

Strand bias in mutation involving 5-methylcytosine deamination in the human hprt gene

Despite being generally under-represented in the genome, CpG sequences represent a disproportionately high fraction of sites involved in mutational events leading to human genetic disease. Cytosine within CpG dinucleotides is often modified to 5-methylcytosine. Deamination of 5-methylcytosine in situ yields a thymine, which being mispaired with guanine, is potentially mutagenic. Previous reports have indicated that most mutations recovered at these sites appear to originate on the non-transcribed strand as C-->T transitions. This trend may however, reflect the lack of detectable mutant phenotypes resulting from this transition at the complementary positions on the transcribed strand. To date, there has not been a good model system in which mutations can be recovered on both strands at the same CpG site. The human hprt gene has MeCpG sites contained within arginine codons for which mutations have been recovered on both strands. From an analysis of a database of hprt mutations, a statistically significant strand bias is observed in mutations recovered at CpG sites. We describe some models for the bias of mutation distribution observed at MeCpG sites in light of this and previous work are described.

Deoxycytidine methylation and the origin of spontaneous transition mutations in mammalian cells

Previously we described a recurrent, site-specific G4784 --> A transition mutation affecting exon V of the Chinese hamster ovary cell RPS14 gene. Because the mutation is located within a CpG dinucleotide, we considered the possibility that deoxycytidine methylation might be responsible for the transition's unusually high frequency and site specificity. Therefore, we used a procedure based on the PCR amplification of bisulfite-modified genomic DNA to analyze the pattern of DNA cytosine methylation in exon V of the CHO cell RPS14 locus. Our data indicate that the CpG dinucleotide targeted by the transition mutation is stably methylated in CHO cell chromosomes. This finding supports the notion that deoxycytidine methylation promotes "spontaneous", site-specific transition mutations in mammalian cells.

High frequency mutagenesis by a DNA methyltransferase

HpaII methylase (M. HpaII), an example of a DNA (cytosine-5)-methyltransferase, was found to induce directly a high frequency of C-->U transition mutations in double-stranded DNA. A mutant pSV2-neo plasmid, constructed with an inactivating T-->C transition mutation creating a CCGG site, was incubated with M. HpaII in the absence of S-adenosylmethionine (SAM). This caused an approximately 10(4)-fold increase in the rate of reversion when the mutant neo plasmid was transformed into bacteria lacking uracil-DNA glycosylase. The mutation frequency was very sensitive to SAM concentration and was reduced to background when the concentration of the methyl donor exceeded 300 nM. The data support current models for the formation of a covalent complex between the methyltransferase and cytosine. They also suggest that the occurrence of mutational hot spots at CpG sites may not always be due to spontaneous deamination of 5-methylcytosine, but might also be initiated by enzymatic deamination of cytosine and proceed through a C-->U-->T pathway.