Induction of large DNA deletions by persistent nicks: a new hypothesis

Molecular Configuration of Human Genome Neighboring Megabase-Sized Large Deletions Induced by X-Ray Irradiation

The genomic landscape neighboring large deletions including the hypoxanthine-guanine phosphoribosyl transferase (HPRT) locus on human X chromosome in 6-thioguanine-resistant mutants originating from immortalized human fibroblast cells exposed to X rays was characterized by real-time quantitative PCR (qPCR)-based analyses. Among the 13 mutant clones with large deletions extending over several Mb, including the HPRT locus, revealed by 10 conventional sequence-tagged site (STS) markers, three clones bearing the largest deletions were selected for further qPCR analysis using another 21 STS markers and 15 newly designed PCR primer pairs. The results indicated that the major deletions were in very specific regions between the 130-Mb and 140-Mb positions containing the HPRT locus on the X chromosome and, contrary to our initial expectations, additional minor deletions were distributed in a patchwork pattern. These findings strongly indicate that the complex deletion patterns in the affected chromosome are related to the radiation track structure with spatially heterogeneous energy deposition and the specific structure of the chromatin-nuclear membrane complex. The uncovered complex deletion patterns are in agreement with the idea of complex chromatin damage, which is frequently associated with carcinogenesis.

Dose-dependent changes in the spectrum of mutations induced by ionizing radiation

We examined the influence of dose on the spectrum of mutations induced at the hypoxanthine guanine phosphoribosyltransferase (Hprt) locus in Chinese hamster ovary (CHO) cells. Independent CHO-K1 cell mutants at the Hprt locus were isolated from cells exposed to 0, 0.5, 1.5, 3.0 and 6.0 Gy (137)Cs gamma rays, and the genetic changes responsible for the mutations were determined by multiplex polymerase chain reaction (PCR)-based exon deletion analysis. We observed dose-dependent changes in mutation spectra. At low doses, the principal radiation-induced mutations were point mutations. With increasing dose, multibase deletion mutations became the predominant mutation type such that by 6.0 Gy, there were almost three times more deletion mutations than point mutations. The dose response for induction of point mutations was linear while that for multibase deletions fit a linear-quadratic response. There was a biphasic distribution of deletion sizes, and different dose responses for small compared to large deletions. The frequency of large (>36 kb) total gene deletions increased exponentially, implying that they develop from the interaction between two independent events. In contrast, the dose response for deletion mutations of less than 10 kb was nearly linear, suggesting that these types of mutations develop mostly from single events and not the interactions between two independently produced lesions. The observation of dose-dependent changes in radiation-induced mutation spectra suggests that the types of alterations and therefore the risks from low-dose radiation exposure cannot be easily extrapolated from high-dose effects.

Palindromic sequences and A+T-rich DNA elements promote illegitimate recombination in Nicotiana tabacum

Illegitimate recombination is the prevailing molecular mechanism for the integration of recombinant DNA into the genome of most eukaryotic systems and the generation of deletions by intrachromosomal recombination. We developed a ?selectable marker system to screen for intrachromosomal illegitimate recombination events in order to assess the sequence and structure-specific requirements for illegitimate recombination in tobacco. In 12 illegitimate recombination products analysed, we found that all deletion termini localise to sites of palindromic structures or to A+T-rich DNA elements. All deletion termini showed microhomologies of two to six nucleotides. In three plants, the recombination products contained filler-DNA or an inversion of an endogenous segment. Our data strongly suggest that illegitimate recombination in plants is mediated by a DNA synthesis-dependent process, and that this mechanism is promoted by DNA regions that can form palindromic structures or facilitate DNA unwinding.

Altered UV resistance and UV mutational spectrum in repair-proficient murine fibroblasts expressing endonuclease V

In previously reported studies, we transfected repair-proficient murine fibroblasts with the denV gene of bacteriophage T4 and showed that expression of encoded endonuclease V markedly enhanced cyclobutane pyrimidine dimer (CPD) repair and reduced the frequency of ultraviolet radiation (UV)-induced mutations. In the present studies, we compared the spectra of UV-induced mutations at the hprt locus in denV-transfected and control cells. A significant difference in mutation types was observed. While multiple base deletions and single base insertions were found in denV-transfected but not control cells, multiple tandem and non-tandem point mutations identified in control cells were absent in denV-transfected cells. When we compared colony survival following UV exposure in the two cell lines, it appeared that endonuclease V expression did not enhance UV resistance, instead denV-transfected cells had increased susceptibility to low fluences of UV. The effects of endonuclease V expression on UV resistance and on UV mutational spectrum are likely to be due both to the removal of CPDs and to the novel enzymatic activity of endonuclease V.

Deletions at stalled replication forks occur by two different pathways

Replication blockage induces non-homologous deletions in Escherichia coli. The mechanism of the formation of these deletions was investigated. A pBR322-mini-oriC hybrid plasmid carrying two E. coli replication terminators (Ter sites) in opposite orientations was used. Deletions which remove at least the pBR322 blocking site (named Ter1) occurred at a frequency of 2 x 10(-6) per generation. They fall into two equally large classes: deletions that join sequences with no homology, and others that join sequences of 3-10 bp of homology. Some 95% of the deletions in the former class resulted from the fusion of sequences immediately preceding the two Ter sites, indicating a direct role for blocked replication forks in their formation. These deletions were not found in a topA10 mutant, suggesting a topoisomerase I-mediated process. In contrast, deletions joining short homologous sequences were not affected by the topA10 mutation. However, the incidence of this second class of deletions increased 10-fold in a recD mutant, devoid of exonuclease V activity. This indicates that linear molecules are intermediates in their formation. In addition, approximately 50% of these deletions were clustered in the region flanking the Ter1 site. We propose that they are produced by repair of molecules broken at the blocked replication forks.

Molecular spectrum of mutations induced by 5-hydroxymethyl-2'-deoxyuridine in (CHO)-PL61 cells

We have utilized (CHO)-PL61 cells to characterize the mutations produced in mammalian cells by exogenous treatment with the nucleoside 5-hydroxymethyl-2'-deoxyuridine (hmdUrd). HmdUrd is incorporated into DNA as a thymidine analogue and is removed by the repair enzyme hmUra-DNA glycosylase. PL61 cells are hprt(-) and contain adjacent single copies of the Escherichia coli gpt and neo genes (gpt+, neo+) separated by 2 kb, rendering the cells thioguanine sensitive (TGs) and geneticin resistant (G418r). Cells were exposed to hmdUrd and the colonies resistant to thioguanine or thioguanine and G418 were selected. Selection in thioguanine alone (TGr/gpt(-)) allows the growth of all gpt(-) mutants (small, intermediate and large deletions/insertions and point mutations) while selection in thioguanine and G418 (TGr/gpt(-), G418r/neo+) prevents survival of colonies containing vary large deletions of the gpt gene that include the neo gene. To confirm the types of mutation at the molecular level, the gpt gene was amplified from mutants' genomic DNA by PCR, and the amplified DNA was sequenced directly by the dideoxy method. Our study showed that 4 microM hmdUrd induced mutations to TGr/gpt(-) at a rate 3-4 times that of control, but showed no marked increase in mutation to TGr/gpt(-), G418r/neo+. The predominant type of hmdUrd induced mutation in the thioguanine resistant cells at the gpt locus was complete loss of the gpt gene resulting from a large deletion. Background mutations were generally point mutations or small insertion/deletion mutations. We propose that hmdUrd induces large/intermediate deletions as a major type of mutations in mammalian cells as a consequence of DNA repair, and not as a result of misincorporation or mispairing, suggesting that base excision repair by itself can lead to large deletion mutagenesis.

The molecular nature of spontaneous mutations at the hprt locus in the radiosensitive CHO mutant xrs-5

The radiosensitive mutant xrs-5, a derivative of the Chinese hamster ovary (CHO) K1 cell, is defective in DNA double-strand break rejoining ability and in V(D)J recombination. The radiosensitivity and defective repair phenotype are complemented by the 80-kDa subunit of the Ku protein. We determined the nature of the mutations that develop spontaneously at the hprt locus in this cell line using both multiplex PCR deletion screening and DNA sequencing. Ninety-two independent spontaneous mutants were analyzed and the results were compared to the mutation spectrum of 64 previously analyzed hprt spontaneous mutants isolated from the parental CHO-K1 cell line. More than 50% of the spontaneous xrs-5 mutants had lost one or more exons while less than 25% of spontaneous CHO-K1 mutants had lost one or more exons. Most of the deletions in xrs-5 cells involved the loss of multiple exons while single exon deletions predominated in CHO-K1. There was also a nonrandom distribution of breakpoints in both CHO-K1 and xrs-5. Most of the deletion breakpoints were 3' to exon 9, around exons 4-6, or near exon 1. Although the frequency of base substitutions was lower in xrs-5, the spectrum of base substitutions was qualitatively similar to that of CHO-K1. There was no significant difference in the spontaneous mutant frequency in xrs-5 and CHO-K1. The results suggest that in certain regions of the hprt gene, base alterations can be converted to large deletions, and that alterations in the Ku protein complex can influence this process.

Mutations induced by dacarbazine activated with cytochrome P-450

The mutagenicity of the antitumor drug dacarbazine (DTIC) is due to alkylation of cellular DNA by metabolites resulting from the metabolism of this drug by the mixed function oxidase system. In the present study, we used an in vitro shuttle vector assay to study the base and sequence specificity of mutagenesis by DTIC. The shuttle vector plasmid pSP189 was treated with DTIC (1-2.5 mM) in vitro in a reconstituted cytochrome P-450 system at 37 degrees C for either 30 or 60 min. SupF tRNA gene insert contained in the plasmid was sequenced after replication of the drug-treated plasmid in human Ad 293 cells followed by amplification in indicator bacteria. Mutagenesis of DTIC in this system was dependent upon the presence of the cytochrome P-450 reconstituted system and NADPH. Mutations induced by DTIC included single base substitutions (35%), single base deletions (30.5%), single base insertions (19.4%) and large deletions (13.8%). Among the substitutions, transversions and transitions were in the ratio of 1:0.7. Base pairs 108 and 127 in the SupF tRNA of the pSP189 were identified as mutational hot spots.

When replication forks stop

DNA synthesis is an accurate and very processive phenomenon, yet chromosome replication does not proceed at a constant rate and progression of the replication fork can be impeded. Several structural and functional features of the template can modulate the rate of progress of the replication fork. These include DNA secondary structures, DNA damage and occupied protein-binding sites. In addition, prokaryotes contain sites where replication is specifically arrested. DNA regions at which the replication machinery is blocked or transiently slowed could be particularly susceptible to genome rearrangements. Illegitimate recombination, a ubiquitous phenomenon which may have dramatic consequences, occurs by a variety of mechanisms. The observation that some rearrangements might be facilitated by a pause in replication could provide a clue in elucidating these processes. In support of this, some homologous and illegitimate recombination events have already been correlated with replication pauses or arrest sites.

Radiation-induced point mutations, deletions and micronuclei in lacI transgenic mice

Ionizing radiation induces gene mutations (point mutations, deletions and insertions) as well as chromosome damage in mammalian cells. Although these effects have been studied extensively in cells in culture, until recently it has not been possible to analyze the mutagenic potential of ionizing radiation in vivo, especially at the molecular level. The development of transgenic mutagenesis systems has now made it possible to study the effects of ionizing radiation at both the molecular and chromosomal levels in the same animal. In this report we present preliminary data on the response of Big Blue lacI transgenic mice to ionizing radiation as measured by lacI mutations and micronuclei. C57Bl/6 transgenic mice were irradiated with 137Cs gamma-rays at doses ranging from 0.1 to 14 Gy, and expression times ranging from 2 to 14 days. Dose-related increases in the mutant frequency were observed after irradiations with longer expression times. Mutant plaques were analyzed by restriction enzyme digestion to detect large structural changes in the target sequence. Of 34 gamma-ray-induced mutations analyzed, 4 were large-scale rearrangements. 3 of these rearrangements were deletions within the lacI gene characterized by the presence of short regions of homology at the breakpoint junctions. The fourth rearrangement was a deletion that extended from within the alpha lacZ gene into downstream sequences and that had 43 bp of homology at the junction. These data indicate that the Big Blue lacI transgenic mouse system in sensitive to the types of mutations induced by ionizing radiation. To determine whether the presence of the transgene affects micronucleus induction we compared the response of nontransgenic to hemizygous transgenic B6C3F1 mice and the response of nontransgenic to hemizygous and homozygous transgenic C57Bl/6 mice. The presence or absence of the lacI transgene had no effect on spontaneous micronucleus frequencies for either strain. However, radiation-induced micronucleus frequencies were significantly higher in hemizygous lacI B6C3F1 mice than in nontransgenic litter mates; the converse was true in C57Bl/6 mice. These data suggest that the lacI transgene does not cause chromosome instability as measured by spontaneous micronucleus levels. However, the response of these transgenic mice to a variety of clastogenic agents needs to be investigated before they are integrated into standard in vivo assays for chromosome damage.