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Results for “Genome mutation”

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At least 739 records · Page 41Linked to original sources
PubMed2007

A mutation in separase causes genome instability and increased susceptibility to epithelial cancer.

Proper chromosome segregation is essential for maintenance of genomic integrity and instability resulting from failure of this process may contribute to cancer. Here, we demonstrate that a mutation in the mitotic regulator separase is responsible for the cell cycle defects seen in the zebrafish mutant, cease&desist (cds). Analysis of cds homozygous mutant embryos reveals high levels of polyploidy and aneuploidy, spindle defects, and a mitotic exit delay. Carcinogenesis studies demonstrated that cds heterozygous adults have a shift in tumor spectrum with an eightfold increase in the percentage of fish bearing epithelial tumors, indicating that separase is a tumor suppressor gene in vertebrates. These data strongly support a conserved cross-species role for mitotic checkpoint genes in genetic stability and epithelial carcinogenesis.

Animals↗
PubMed2004

Mutated E-cadherin: genomic and functional characterization in thyroid cells from the KAT family.

Members of a family of thyroid cell lines (KAT) were analyzed because they expressed a higher molecular weight (135 kd) form of E-cadherin at their surface. We found that this aberrant E-cadherin is the result of a point mutation in the exon 9 donor splice site causing a skipping of exon 9 with consequent deletion of the corresponding aminoacids on E-cadherin protein. As a spin-off, we report that the various members of the KAT family share this mutation as well as the genetic background. Furthermore we found that this mutated protein leads to disturbed cell-cell adhesion although E-cadherin is still able to mediate the formation of the cadherin/ catenin complex. We also demonstrate the presence of another cell-cell adhesion complex, formed by Pcadherin and the catenins. The latter is also not able to mediate cell-cell adhesion. Although these cells lack cell-cell adhesion they are not invasive without exogenous stimulus.

Base Sequence↗
PubMed2006

High-throughput mutational analysis of the human cancer genome.

Cancer is essentially a genetic disease. Recent high-throughput mutational analyses of gene families in human colorectal, breast and lung cancer, myeloproliferative disorders, and other tumor types have identified a number of kinases and phosphatases that are mutated in the human cancer genome. This approach has been proven to be an efficient way to catalog tumor-specific mutations in human cancers. Although there are still some technical hurdles to overcome, it is not a far-reaching goal to perform genome-wide mutational analysis in all different tumor types. Systematic cataloging of tumor-specific mutations in the human cancer genome not only will lead to new insights into the mechanisms of tumorigenesis, but also provide unprecedented opportunities in the design of novel therapeutics for cancer patients. Personalized cancer therapy based on tumor-specific mutations will be a realistic goal in the near future.

Breast Neoplasms↗
PubMed1986

Mutation in the polyomavirus genome that activates the properties of large T associated with neoplastic transformation.

We have constructed a polyomavirus mutant genome which exhibits an increased immortalization potential when transfected into primary rat embryo fibroblasts. The mutation is a 30-base-pair deletion (nucleotides 1367 through 1396) that inactivates the transforming potential of middle T but activates some of the properties of large T associated with neoplastic transformation. Unlike the wild-type large T, the mutant large T can fully complement polyoma middle T in the tumorigenic process in vivo as well as in the transformation of primary cells in vitro. The activity of the mutant can be explained by its inability to replicate in cells and, hence, its inability to exert a cytopathic effect after gene transfer at high multiplicity. A recombinant which encodes the middle and small T antigens, but not the large T antigen, can also elicit a fully transformed phenotype when introduced into primary rat fibroblasts. These results confirm previous observations from this laboratory indicating that two, and not three, viral gene functions are required for polyomavirus-mediated oncogenic transformation.

Animals↗
PubMed1999

[A mutation specific polymerase chain reaction for detecting hepatitis B virus genome with A-to-C mutation at nt585].

OBJECTIVE: To investigate the prevalence of hepatitis B virus (HBV) nt585 A-to-C mutants in China. METHODS: A mutation specific polymerase chain reaction (msPCR) was established for amplifying HBV DNAs with A-to-C mutation at nt585. Two sets of primer pairs with same sequences except for one base at 3' terminus were designed and synthesized according to 48 of the known HBV genome sequences and the popular HBV subtypes, adr and adw, in China. RESULTS: 57 of HBV S gene fragments amplified by a nested PCR from different and child adult hepatitis B patients were characterized by using the msPCR. It was shown that HBV mutants with A-to-C mutation at nt585 could be confirmed. CONCLUSION: The msPCR is a specific and sensitive method for detecting the HBV nt585 A-to-C mutants.

Adult↗
PubMed1984

[Introduction of the hybrid plasmid RP4::D3112 into Pseudomonas putida cells requires the presence of specific mutation in the phage genome].

The wild type of D3112, a transposable phage of Pseudomonas aeruginosa can not be introduced as a portion of the hybrid plasmid RP4::D3112 into Pseudomonas putida cells. It is only possible when phage D3112 carries mutations designated lpc (lethal for P. putida and Escherichia coli). Analysis of heteroduplex molecules between DNAs of phages D3112w+ and D3112lpc demonstrated the absence of nonhomology regions, which suggests that lpc is a point mutation. The lpc2 mutation was located within the interval 20-29.9 kb of the phage genome.

Alleles↗
PubMed2006

Identification of coding single nucleotide polymorphisms and mutations by combination of genome tiling arrays and enrichment/depletion of mismatch cDNAs.

Genome tiling array technology combined with a method for both enrichment and depletion of mismatch-containing cDNA fragments offers a useful approach for detecting coding single nucleotide polymorphisms (cSNPs) and mutations in pooled cDNA samples. Enriched mismatch and perfect match cDNA samples from human primary melanoma cells and normal melanocytes were obtained by selection using mismatch repair thymine DNA glycosylase-bound beads. These cDNA samples were then labeled and hybridized to Encyclopedia of DNA Elements genome tiling arrays. The results revealed that the hybridization intensity values of potential cDNA variation regions of the enriched mismatch samples increased, whereas the hybridization intensity values of corresponding regions of the enriched perfect match samples decreased. Six potential mutations were confirmed by polymerase chain reaction product sequencing, including two novel heterozygous mutations in melanoma cells. We suggest that this strategy should increase the efficiency of both cSNP and mutation detection throughout the entire human genome and decrease the cost and complexity of genomewide analysis of cDNA variations.

Base Pair Mismatch↗
PubMed2003

The evolution of mutator genes in bacterial populations: the roles of environmental change and timing.

Recent studies have found high frequencies of bacteria with increased genomic rates of mutation in both clinical and laboratory populations. These observations may seem surprising in light of earlier experimental and theoretical studies. Mutator genes (genes that elevate the genomic mutation rate) are likely to induce deleterious mutations and thus suffer an indirect selective disadvantage; at the same time, bacteria carrying them can increase in frequency only by generating beneficial mutations at other loci. When clones carrying mutator genes are rare, however, these beneficial mutations are far more likely to arise in members of the much larger nonmutator population. How then can mutators become prevalent? To address this question, we develop a model of the population dynamics of bacteria confronted with ever-changing environments. Using analytical and simulation procedures, we explore the process by which initially rare mutator alleles can rise in frequency. We demonstrate that subsequent to a shift in environmental conditions, there will be relatively long periods of time during which the mutator subpopulation can produce a beneficial mutation before the ancestral subpopulations are eliminated. If the beneficial mutation arises early enough, the overall frequency of mutators will climb to a point higher than when the process began. The probability of producing a subsequent beneficial mutation will then also increase. In this manner, mutators can increase in frequency over successive selective sweeps. We discuss the implications and predictions of these theoretical results in relation to antibiotic resistance and the evolution of mutation rates.

Bacteria↗
PubMed1978

[Gene relA function in the expression of amino acid operons. I. Effect of the allelic state of gene relA on phenotypic manifestations of auxotrophic threonine and isoleucine mutations in Escherichia coli K-12].

The substitution of the relA gene mutant allele with wild type allele of this gene in strictly auxotrophic strain of Escherichia coli K-12 GT25, carrying thr B1007 mitation, results in the appearance of the partial dependence of the bacterial growth upon threonine. On the other hand, the introduction of relA mutation into genome of incomplete threonine auxotroph, which was isolated as pseudorevertant from the strict threonine auxotroph CP78, recovered the strict dependency of the growth on the presence of threonine in the medium. The introduction of relA mutation into genome of partial isoleucine auxotroph, carrying a mutation in ilvA gene, reduces the residual activity of threonine deaminase under the conditions of derepression and results in the appearance of strict dependency of bacterial growth on the presence of isoleucine. These data indicate that operons, which control the biosynthesis of threonine and isoleucine, are positively regulated by the product of relA gene. The possibility of using leaky mutations, which lead to incomplete block of these amino acids synthesis, for testing allelic state of relA gene is discussed.

Alleles↗
PubMed1984

mlt Mutation in the polyomavirus genome impairing a function of the middle T protein.

The DNA from polyomavirus mlt mutant P155 transforms cells in culture as efficiently as wild-type DNA but has a much lower tumorigenic potential when injected into newborn rodents. The mutant has a 12-base-pair deletion between nucleotides 1347 and 1360, i.e., in a region which encodes parts of the middle and large T antigens (G elinas et al., J. Virol. 43:1072-1081, 1982). To determine which of the two viral gene functions was affected by the mutation, we transferred the latter into a modified polyomavirus genome encoding exclusively the middle T protein. Our results show that the P155 mutation alters a function of the polyomavirus middle T protein required for the induction of the tumorigenic process in vivo. Beside the 12-base-pair deletion at 96.3 map units, there is no other alteration in the coding sequence of P155 middle T with respect to that of P16, the wild-type parental strain. We conclude, therefore, that the deletion is the lesion affecting the tumorigenic potential of mutant P155 .

Amino Acid Sequence↗
PubMed1994

[Mutations of the mitochondria genome. Diagnosis and pathogenetic significance].

The mitochondrial respiratory chain, which consists of five enzyme complexes, plays a central part in cellular energy metabolism. Thirteen of the protein sub-units are encoded by the mitochondrial genome, a circular DNA molecule of about 16,500 base pairs. Knowledge of the mitochondrial genome and alterations to it is essential to reveal functional defects of the respiratory chain. Point mutations, deletions and duplications of this DNA are associated with a growing number of diseases, whose clinical presentations vary quite widely.

Chromosome Aberrations↗
PubMed2004

CpG mutation rates in the human genome are highly dependent on local GC content.

CpG dinucleotides mutate at a high rate because cytosine is vulnerable to deamination, cytosines in CpG dinucleotides are often methylated, and deamination of 5-methylcytosine (5mC) produces thymidine. Previous experiments have shown that DNA melting is the rate-limiting step in cytosine deamination. Here we show, through the analysis of human single-nucleotide polymorphisms (SNPs), that the mutation rate produced by 5mC deamination is highly dependent on local GC content. In fact, linear regression analysis showed that the log(10) of the 5mC mutation rates (inferred from SNP frequencies) had slopes of -3 when graphed with respect to the GC content of neighboring sequences. This is the ideal slope that would be expected if the correlation between CpG underrepresentation and GC content had been solely caused by DNA melting. Moreover, this same result was obtained regardless of the SNP locations (all SNPs versus only SNPs in noncoding intergenic regions, excluding CpG islands) and regardless of the lengths over which GC content was calculated (SNP sequences with a modal length of 564 bp versus genomic contigs with a modal length of 163 kb). Several alternative interpretations are discussed.

Animals↗
PubMed2006

Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms.

So far, there is no genome-wide estimation of the mutational spectrum in humans. In this study, we systematically examined the directionality of the point mutations and maintenance of GC content in the human genome using approximately 1.8 million high-quality human single nucleotide polymorphisms and their ancestral sequences in chimpanzees. The frequency of C-->T (G-->A) changes was the highest among all mutation types and the frequency of each type of transition was approximately fourfold that of each type of transversion. In intergenic regions, when the GC content increased, the frequency of changes from G or C increased. In exons, the frequency of G:C-->A:T was the highest among the genomic categories and contributed mainly by the frequent mutations at the CpG sites. In contrast, mutations at the CpG sites, or CpG-->TpG/CpA mutations, occurred less frequently in the CpG islands relative to intergenic regions with similar GC content. Our results suggest that the GC content is overall not in equilibrium in the human genome, with a trend toward shifting the human genome to be AT rich and shifting the GC content of a region to approach the genome average. Our results, which differ from previous estimates based on limited loci or on the rodent lineage, provide the first representative and reliable mutational spectrum in the recent human genome and categorized genomic regions.

Animals↗
PubMed1982

Extrachromosomal mutator inducing point mutations and deletions in mitochondrial genome of fission yeast.

We report the isolation and characterization of a mutator mutant in the fission yeast Schizosaccharomyces pombe. This mutator is of extrachromosomal, very likely mitochondrial, inheritance and acts exclusively on mitochondrial mtDNA. It greatly enhances the frequency of spontaneous mitochondrial drug-resistance mutants compared to the wild type, but it is not obligatory for their occurrence. In contrast, mitochondrial respiratory deficient mutants can only be isolated from mutator strains. It could be shown that this mutator induces point mutations as well as deletions in the mitochondrial genome which lead to respiratory deficiency. This mutator might prove to have a novel function encoded by the mtDNA.

Anti-Bacterial Agents↗
PubMed2006

Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways.

A large majority of bacterial genomes show strand asymmetry, such that G and T preferentially accumulate on the leading strand. The mechanisms are unknown, but cytosine deaminations are thought to play an important role. Here, we have examined DNA strand asymmetry in three strains of the aphid endosymbiont Buchnera aphidicola. These are phylogenetically related, have similar genomic GC contents, and conserved gene order structures, yet B. aphidicola (Bp) shows a fourfold higher replication-induced strand bias than B. aphidicola (Sg) and (Ap). We rule out an increase in the overall substitution frequency as the major cause of the stronger strand bias in B. aphidicola (Bp). Instead, the results suggest that the higher GC skew in this species is caused by a different spectrum of mutations, including a relatively higher frequency of C to T mutations on the leading strand and/or of G to A mutations on the lagging strand. A comparative analysis of 20 gamma-proteobacterial genomes revealed that endosymbiont genomes lacking recA and other genes involved in replication restart processes, such as priA, which codes for primosomal helicase PriA, displayed the strongest strand bias. We hypothesize that cytosine deaminations accumulate during single-strand exposure at arrested replication forks and that inefficient restart mechanisms may lead to high DNA strand asymmetry in bacterial genomes.

Buchnera↗
PubMed2006

Methods for studying mutagenesis and checkpoints in Schizosaccharomyces pombe.

Mutations in genome caretaker genes can induce genomic instability, which are potentially early events in tumorigenesis. Cells have evolved biological processes to cope with the genomic insults. One is a multifaceted response, termed checkpoint, which is a network of signaling pathways to coordinate cell cycle transition with DNA repair, activation of transcriptional programs, and induction of tolerance of the genomic perturbations. When genomic perturbations are beyond repair, checkpoint responses can also induce apoptosis or senescence to eliminate those deleterious damaged cells. Fission yeast, Schizosaccharomyces pombe (S. pombe) has served as a valuable model organism for studies of the checkpoint signaling pathways. In this chapter, we describe methods used to analyze mutagenesis and recombinational repair induced by genomic perturbations, and methods used to detect the checkpoint responses to replication stress and DNA damage in fission yeast cells. In the first section, we present methods used to analyze the mutation rate, mutation spectra, and recombinational repair in fission yeast when replication is perturbed by either genotoxic agents or mutations in genomic caretaker gene such as DNA replication genes. In the second section, we describe methods used to examine checkpoint activation in response to chromosome replication stress and DNA damage. In the final section, we comment on how checkpoint activation regulates mutagenic synthesis by a translesion DNA polymerase in generating a mutator phenotype of small sequence alterations in cells, and how a checkpoint kinase appropriately regulates an endonuclease complex to either prevent or allow deletion of genomic sequences and recombinational repair when fission yeast cells experience genomic perturbation in order to avoid deleterious mutations and maintain cell growth.

DNA Damage↗
PubMed1989

Searching for pattern and mutation in the Drosophila genome with a P-lacZ vector.

A P-element vector has been constructed and used to generate lines of flies with single autosomal P-element insertions. The lines were analyzed in two ways: (1) the identification of cis-acting patterning information within the Drosophila genome, as revealed by a lacZ reporter gene within the P element, and (2) the isolation of lethal mutations. We examined 3768 independent lines for the expression of lacZ in embryos and looked among these lines for lethal mutations affecting embryonic neurogenesis. This type of screen appears to be an effective way to find new loci that may play a role in the development of the Drosophila nervous system.

Animals↗
PubMed1995

Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?

It is well known that when s, the selection coefficient against a deleterious mutation, is below approximately 1/4Ne, where Ne is the effective population size, the expected frequency of this mutation is approximately 0.5, if forward and backward mutation rates are similar. Thus, if the genome size, G, in nucleotides substantially exceeds the Ne of the whole species, there is a dangerous range of selection coefficients, 1/G < s < 1/4Ne. Mutations with s within this range are neutral enough to accumulate almost freely, but are still deleterious enough to make an impact at the level of the whole genome. In many vertebrates Ne approximately 10(4), while G approximately 10(9), so that the dangerous range includes more than four orders of magnitude. If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.

Animals↗