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Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis.

BACKGROUND: The inability to efficiently repair DNA damage or remove cells with severely damaged genomes has been linked to several human cancers. Studies in yeasts and mammals have identified several genes that are required for proper activation of cell cycle checkpoints following various types of DNA damage. However, in metazoans, DNA damage can induce apoptosis as well. How DNA damage activates the apoptotic machinery is not fully understood. RESULTS: We demonstrate here that the Caenorhabditis elegans gene hus-1 is required for DNA damage-induced cell cycle arrest and apoptosis. Following DNA damage, HUS-1 relocalizes and forms distinct foci that overlap with chromatin. Relocalization does not require the novel checkpoint protein RAD-5; rather, relocalization appears more frequently in rad-5 mutants, suggesting that RAD-5 plays a role in repair. HUS-1 is required for genome stability, as demonstrated by increased frequency of spontaneous mutations, chromosome nondisjunction, and telomere shortening. Finally, we show that DNA damage increases expression of the proapoptotic gene egl-1, a response that requires hus-1 and the p53 homolog cep-1. CONCLUSIONS: Our findings suggest that the RAD-5 checkpoint protein is not required for HUS-1 to relocalize following DNA damage. Furthermore, our studies reveal a new function of HUS-1 in the prevention of telomere shortening and mortalization of germ cells. DNA damage-induced germ cell death is abrogated in hus-1 mutants, in part, due to the inability of these mutants to activate egl-1 transcription in a cep-1/p53-dependent manner. Thus, HUS-1 is required for p53-dependent activation of a BH3 domain protein in C. elegans.

Amino Acid Sequence↗

Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks.

The RecQ protein family is a highly conserved group of DNA helicases that play roles in maintaining genomic stability. In this study, we present biochemical and genetic evidence that Escherichia coli RecQ processes stalled replication forks and participates in SOS signaling. Cells that carry dnaE486, a mutation in the DNA polymerase III alpha-catalytic subunit, induce an RecA-dependent SOS response and become highly filamented at the semirestrictive temperature (38 degrees C). An recQ mutation suppresses the induction of SOS response and the filamentation in the dnaE486 mutant at 38 degrees C, causing appearance of a high proportion of anucleate cells. In vitro, RecQ binds and unwinds forked DNA substrates with a gap on the leading strand more efficiently than those with a gap on the lagging strand or Holliday junction DNA. RecQ unwinds the template duplex ahead of the fork, and then the lagging strand is unwound. Consequently, this process generates a single-stranded DNA (ssDNA) gap on the lagging strand adjacent to a replication fork. These results suggest that RecQ functions to generate an initiating signal that can recruit RecA for SOS induction and recombination at stalled replication forks, which are required for the cell cycle checkpoint and resumption of DNA replication.

Adenosine Triphosphatases↗

Role of mammalian Rad9 in genomic stability and ionizing radiation response.

Eukaryotic cells have evolved DNA damage response mechanisms utilizing proficient DNA repair and cell cycle checkpoints in order to maintain genomic stability. The Schizosaccharomyces pombe Rad9 gene was initially identified as encoding a cell cycle checkpoint protein. When the mammalian homologue of S. pombe Rad9 was inactivated, however, chromosomal instability was observed even in the absence of DNA damaging agents. Both an increase in chromosome end-to-end associations and telomere loss were observed in cells with inactivated mammalian Rad9. This telomere instability correlated with enhanced S- and G2-phase specific cell killing, delayed kinetics of gamma-H2AX foci appearance and disappearance, and reduced chromosomal repair after ionizing radiation (IR) exposure, suggesting that Rad9 plays a role in cell cycle phase specific DNA damage repair. Inactivation of mammalian Rad9 also resulted in decreased homologous recombinational (HR) repair, which occurs predominantly in the S- and G2-phase of the cell cycle. These newly defined functions of mammalian Rad9 are discussed in relation to telomere stability and HR repair as a mechanism for promoting cell survival after IR exposure.

Animals↗

Immune diversity and genomic stability: opposite goals but similar paths.

DNA damage response mechanisms serve to protect cells from exogenous and endogenous DNA damaging agents with the aim of maintaining genomic stability. In contrast, the generation of an efficient immune response requires the creation of a repertoire of distinct immunoglobulin and T cell receptor genes able to recognise the huge array of antigens that may be encountered in a lifetime. Surprisingly, cells have exploited the same mechanisms used to maintain genomic integrity to create genetic diversity during immune development. Here, we review the damage response mechanisms operating on DNA double strand breaks and their function during development of the immune response. We discuss disorders that are associated with immunodeficiency and defective responses to the presence of DNA double strand breaks.

Animals↗

Genomic stability of gibbon oncornavirus.

The 70S RNAs from several gibbon type C viruses were examined for sequence homology by molecular hybridization using complementary DNA probes. The sequence homology was found to vary with each virus isolate. The genome from one isolate was examined for genomic stability after the virus was experimentally passaged through three unrelated gibbons. The genomic homology remained unchanged after three passages, having greater than 93% homology based on complementary DNA-70S RNA hybridization and melting temperature analysis of the duplex. The genome from another isolate was similarly found to be unchanged after the virus was naturally transmitted in gibbons. The genomic variation found in the various isolates is not the consequence of recent horizontal transmission from a common virus.

Animals↗

The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations.

We have used spectral karyotyping to assess potential roles of three different components of the nonhomologous DNA end-joining pathway in the maintenance of genomic stability in mouse embryonic fibroblasts (MEFs). MEFs homozygous for mutations that inactivate either DNA ligase IV (Lig4) or Ku70 display dramatic genomic instability, even in the absence of exogenous DNA damaging agents. These aberrant events range from chromosomal fragmentation to nonreciprocal translocations that can involve several chromosomes. DNA-dependent protein kinase catalytic subunit deficiency also promotes genome instability. Deficiency for the p53 cell cycle checkpoint protein has little effect on spontaneous levels of chromosomal instability in Lig4-deficient fibroblasts. However, in the context of ionizing radiation treatment, p53 deficiency allowed visualization of massive acute chromosomal destruction in Lig4-deficient MEFs, which in surviving cells manifested as frequent nonreciprocal translocations. We conclude that nonhomologous DNA end-joining plays a crucial role as a caretaker of the mammalian genome, and that an alternative repair pathway exists that often leads to nonreciprocal translocations.

Animals↗

Methylenetetrahydrofolate reductase C677T polymorphism, folic acid and riboflavin are important determinants of genome stability in cultured human lymphocytes.

We tested the hypothesis that methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, folic acid deficiency and riboflavin deficiency, independently or interactively, are important determinants of genomic stability, cell death, cell proliferation and homocysteine (Hcy) concentration in 9-d human lymphocyte cultures. Lymphocytes of seven wild-type (CC) and seven mutant (TT) homozygotes were cultured under the four possible combinations of deficiency and sufficiency of riboflavin (0 and 500 nmol/L) and folic acid (20 and 100 nmol/L) at a constant L-methionine concentration of 50 micromol/L. Viable cell growth was 25% greater in TT than in CC cells (P<0.05) and 32% greater at 100 nmol/L folic acid than at 20 nmol/L folic acid (P=0.002). The comprehensive cytokinesis-block micronucleus assay was used to measure micronuclei (MNi; a marker for chromosome breakage and loss), nucleoplasmic bridges (NPB; a marker of chromosome rearrangement) and nuclear buds (NBUD, a marker of gene amplification). The MNi levels were 21% higher in TT cells than in CC cells (P<0.05) and 42% lower in the high folic acid medium than in the low folic acid medium (P<0.0001). The NBUD levels were 27% lower in TT cells than in CC cells (P<0.05) and 45% lower in the high folic acid medium than in the low folic acid medium (P<0.0001). High riboflavin concentration (500 nmol/L) increased NBUD levels by 25% (compared with 0 nmol/L riboflavin) in folate-deficient conditions (20 nmol/L folic acid medium; P<0.05), and there was an interaction between folic acid and riboflavin that affected NBUD levels (P=0.042). This preliminary investigation suggests that MTHFR C677T polymorphism and riboflavin affect genome instability; however, the effect is relatively small compared with that of folic acid.

Adult↗

Multiple but dissectible functions of FEN-1 nucleases in nucleic acid processing, genome stability and diseases.

Flap EndoNuclease-1 (FEN-1) is a multifunctional and structure-specific nuclease involved in nucleic acid processing pathways. It plays a critical role in maintaining human genome stability through RNA primer removal, long-patch base excision repair and resolution of dinucleotide and trinucleotide repeat secondary structures. In addition to its flap endonuclease (FEN) and nick exonuclease (EXO) activities, a new gap endonuclease (GEN) activity has been characterized. This activity may be important in apoptotic DNA fragmentation and in resolving stalled DNA replication forks. The multiple functions of FEN-1 are regulated via several means, including formation of complexes with different protein partners, nuclear localization in response to cell cycle or DNA damage and post-translational modifications. Its functional deficiency is predicted to cause genetic diseases, including Huntington's disease, myotonic dystrophy and cancers. This review summarizes the knowledge gained through efforts in the past decade to define its structural elements for specific activities and possible pathological consequences of altered functions of this multirole player.

Amino Acid Motifs↗

The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability.

Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome assembly spanning 129.4 Mb across 12 chromosomes, encompassing 15,321 predicted protein-coding genes. Leveraging whole-genome sequencing of eight mutation accumulation (MA) lines propagated for an average of 482 generations (spanning over 20 years), we estimated a spontaneous single nucleotide mutation (SNM) rate of 2.23 &#xd7; 10-9 and an indel mutation rate of 2.75 &#xd7; 10-10 per site per generation. The SNM spectrum was strongly biased toward C:G > T:A transitions. Comparative analyses with natural population data revealed that exonic mutations observed in the MA lines were significantly less likely to be present in standing variation than intronic or intergenic mutations, suggesting that purifying selection in natural populations acts to remove deleterious alleles. We also identified 48 de novo loss-of-heterozygosity (LOH) events, comprising 8 heterozygous deletions and 40 gene conversion events. The genome-wide gene conversion rate was estimated at 2.62 &#xd7; 10-5 per heterozygous site per generation. These findings provide a comprehensive view of the mutation spectrum, selective pressures, and mechanisms underlying genome stability in D. obtusa.

Daphnia obtusa↗

Role of the error-free damage bypass postreplication repair pathway in the maintenance of genomic stability.

The postreplication repair pathway (PRR) is composed of error-free and error-prone sub-pathways that allow bypass of DNA damage-induced replication-blocking lesions. The error-free sub-pathway is also used for bypass of spontaneous DNA damage and functions in cooperation with recombination pathways. In diploid yeast cells, error-free PRR is needed to prevent genomic instability, which is manifest as loss of heterozygosity (LOH) events of increased chromosome loss and recombination. Homologous recombination acts synergistically with the error-free damage avoidance branch of PRR to prevent chromosome loss. The DNA damage checkpoint gene MEC1 acts synergistically with the PRR pathway in maintaining genomic stability. Integration of the PRR pathway with other cellular pathways for preventing genomic instability is discussed. In diploid strains, the most dramatic increase is in the abnormality of chromosome loss when a repair or damage detection pathway is defective.

Crossing Over, Genetic↗

Variations in gene expression and genomic stability of human hepatoma cells integrated with hepatitis B virus DNA.

The association of hepatitis B virus (HBV) infection with human hepatoma is well established. However, no consensus regarding the etiology of hepatocellular carcinoma was elucidated. In this paper, the genomic stability and gene expression of HBV DNA-integrated and non-integrated hepatoma cells by Transcript Profile (TP)-PCR and RT-PCR are characterized. The additional DNA bands generated from TP-PCR of HBV integrated genomes were not correlated with the sequence of HBV, suggesting that the variations may result from genomic instability of the host cells. Moreover, differential genes expressed in HBV DNA-integrated cells were sequenced. A cDNA generated from the integrated cells exhibited 99.3% homology with the sequences of ATP synthase 6 and cytochrome C oxidase III, but the sequences were abnormally linked together. Since HBV infection may alter the energy metabolism of the cell, the results suggest that the integration may cause mitochondriae defects in the ATP synthase 6 and cytochrome C oxidase III genes.

ATP Synthetase Complexes↗

Role of magnesium in genomic stability.

In cellular systems, magnesium is the second most abundant element and is involved in basically all metabolic pathways. At physiologically relevant concentrations, magnesium itself is not genotoxic, but is highly required to maintain genomic stability. Besides its stabilizing effect on DNA and chromatin structure, magnesium is an essential cofactor in almost all enzymatic systems involved in DNA processing. Most obvious in studies on DNA replication, its function is not only charge-related, but very specific with respect to the high fidelity of DNA synthesis. Furthermore, as essential cofactor in nucleotide excision repair, base excision repair and mismatch repair magnesium is required for the removal of DNA damage generated by environmental mutagens, endogenous processes, and DNA replication. Intracellular magnesium concentrations are highly regulated and magnesium acts as an intracellular regulator of cell cycle control and apoptosis. As evident from animal experiments and epidemiological studies, magnesium deficiency may decrease membrane integrity and membrane function and increase the susceptibility to oxidative stress, cardiovascular heart diseases as well as accelerated aging. The relationship to tumor formation is more complex; magnesium appears to be protective at early stages but promotes the growth of existing tumors. With respect to the magnesium status in humans, the daily intake in most industrialized countries does not reach the current recommended daily dietary allowances (RDA) values, and thus marginal magnesium deficiencies are very common.

Animals↗

H2AX haploinsufficiency modifies genomic stability and tumor susceptibility.

Histone H2AX becomes phosphorylated in chromatin domains flanking sites of DNA double-strand breakage associated with gamma-irradiation, meiotic recombination, DNA replication, and antigen receptor rearrangements. Here, we show that loss of a single H2AX allele compromises genomic integrity and enhances the susceptibility to cancer in the absence of p53. In comparison with heterozygotes, tumors arise earlier in the H2AX homozygous null background, and H2AX(-/-) p53(-/-) lymphomas harbor an increased frequency of clonal nonreciprocal translocations and amplifications. These include complex rearrangements that juxtapose the c-myc oncogene to antigen receptor loci. Restoration of the H2AX null allele with wild-type H2AX restores genomic stability and radiation resistance, but this effect is abolished by substitution of the conserved serine phosphorylation sites in H2AX with alanine or glutamic acid residues. Our results establish H2AX as genomic caretaker that requires the function of both gene alleles for optimal protection against tumorigenesis.

Animals↗

The Fanconi anaemia genome stability and tumour suppressor network.

Fanconi anaemia (FA) is a rare autosomal recessive disease characterized by increased spontaneous and DNA crosslinker-induced chromosome instability, progressive pancytopenia and cancer susceptibility. An increasing number of genes are involved in FA, including the breast cancer susceptibility gene BRCA2. Five of the FA proteins (FANCA, FANCC, FANCE, FANCF and FANCG) assemble in a complex that is required for FANCD2 activation in response to DNA crosslinks. Active FANCD2 then interacts with BRCA1 and forms discrete nuclear foci. FANCD2 is independently phosphorylated by ATM (the protein whose gene is mutated in ataxia telangiectasia) in response to ionizing radiation. In addition, the FA proteins are interconnected with other nuclear and cytoplasmic factors all related to cellular responses to carcinogenic stress and to caretaker and gatekeeper functions. In this review, the most recently published data on the molecular biology of the FA pathway and its molecular crosstalk with ATM, BRCA1 and BRCA2, proteins involved in xenobiotic and reactive oxygen species metabolism, apoptosis, cell cycle control and telomere stability, are summarized. The currently available data indicate that FA is a central node in a complex nuclear and cytoplasmic network of tumour suppressor and genome stability pathways fully committed to prevent cancer.

Apoptosis↗

Alternative splicing and genomic stability.

Alternative splicing allows an organism to make different proteins in different cells at different times, all from the same gene. In a cell that uses alternative splicing, the total length of all the exons is much shorter than in a cell that encodes the same set of proteins without alternative splicing. This economical use of exons makes genes more stable during reproduction and development because a genome with a shorter exon length is more resistant to harmful mutations. Genomic stability may be the reason why higher vertebrates splice alternatively. For a broad class of alternatively spliced genes, a formula is given for the increase in their stability.

Alternative Splicing↗

DDX37 and DDX50 Maintain Genome Stability by Preventing Transcription-dependent R-loop Formation.

R-loops consist of an RNA-DNA hybrid and a displaced single-stranded DNA strand that play a central role in several biological processes. However, as the presence of aberrant R-loops forms a significant threat to genome stability, R-loop formation and resolution is strictly controlled by RNAse H and helicases. In a screening for RNA helicases, previously described as RNA-DNA hybrid interactors, that control genome integrity, we identified for the first time DDX37 and DDX50. Depletion of DDX37 and DDX50 promotes DNA damage, as demonstrated by H2AX phosphorylation and increased comet tail length. In addition, knock down of these RNA helicases decreases the DNA replication track length and leads to RPA focus formation, results that are indicative of replication stress. Downregulation of DDX37 and DDX50 triggers an increase in RNA-DNA hybrids, that can be reverted by the overexpression of RNase H1. Interestingly, inhibition of transcription prevented the increased RNA-DNA hybrid formation and DNA damage upon DDX37 or DDX50 depletion. Together these results demonstrate that DDX37 and DDX50 are important for resolving RNA-DNA hybrids appearing during transcription and thereby preventing DNA damage by replication stress.

DEAD-box RNA Helicases↗

Does a vegetarian diet influence genomic stability?

BACKGROUND: The vegetarian lifestyle is supposedly healthy, and differences between vegetarians and non-vegetarians in biomarkers related to diseases such as cancer might be expected. AIM OF THE STUDY: To investigate the possible role of different diets in maintaining genomic stability. METHODS: The vegetarian group, consisting of 24 volunteers (13 women and 11 men), were matched for age and sex with 24 volunteers (12 women and 12 men) with a traditional dietary habit. Among vegetarians there were 13 lacto-ovo-vegetarians (8 women, 5 men) with average length of vegetarian diet 10.8 years (ranging from 5 to 26) and 11 lacto-vegetarians (5 women, 6 men) with average length of vegetarian diet 8.2 years (ranging from 3 to15). All volunteers were nonsmokers, non-consumers of alcohol and had similar education and patterns of physical activity. Chromosome aberrations, micronuclei and DNA damage (strand breaks, oxidised bases and H(2)O(2)-sensitivity) were examined in peripheral blood lymphocytes of vegetarians and non-vegetarians. Plasma antioxidant status was assessed with the FRAP assay. RESULTS: We did not find any differences in percentage of cells with chromosome aberrations or in the frequency of micronuclei between vegetarians and non-vegetarians or between lacto-ovo and lacto-vegetarians. There was no statistically significant difference in total antioxidant capacity between the groups. The group with traditional dietary habits had significantly higher levels of oxidative DNA damage (strand breaks and oxidised purines, P = 0.005) compared with vegetarians. A significant positive correlation between age and oxidative DNA damage (net FPG-sensitive sites) was found in non-vegetarians, while there was an opposite trend towards a negative association in vegetarians. On the other hand chromosome aberrations correlated with age in vegetarians (r = 0.48, P = 0.017) but not in non-vegetarians. CONCLUSIONS: Our results indicate that a vegetarian diet can lead to a slight decrease in oxidative DNA damage in lymphocytes, but other markers of genetic stability are not affected. The lowest level of DNA damage was found in lymphocytes of lactovegetarians, (especially oxidised pyrimidines, P = 0.0017), suggesting that this diet provides some protection against oxidative stress.

Adult↗

Conserved Wat1/Pop3 WD-repeat protein of fission yeast secures genome stability through microtubule integrity and may be involved in mRNA maturation.

Accurate chromosome segregation is dependent upon the integrity of mitotic spindles, which pull each pair of sister chromatids towards opposite poles. In this study, we have characterised fission yeast pop3-5235, a diploidising mutant that is impaired in genome stability. Pop3 is the same as Wat1, a conserved protein containing 7 WD repeats. Pop3/Wat1 has also been isolated from a two-hybrid screen as a binding partner to Prp2, the large subunit of the essential splicing factor U2AF. In wat1 mutants, the cellular amount of alpha-tubulin is decreased to very low levels, which results in compromised microtubules and spindles, consequently leading to unequal chromosome separation. Further analysis shows that, in spite of the binding between Wat1 and Prp2, Wat1 may not be involved directly in splicing reactions per se. Instead, we find that Wat1 is required for the maintenance of alpha-tubulin mRNA levels; moreover, transcript levels of genes other than the alpha-tubulin gene are also equally decreased in this mutant. Wild-type Wat1, but not the mutant protein, forms a large complex in the cell with several other proteins, suggesting that Wat1 functions as a structural linker in the complex. The results suggest that Wat1 plays a role in mRNA maturation as a coupling protein between splicing and synthesis and/or stabilisation.

Amino Acid Motifs↗