Detection of recombinational mutations in cultured human cells by Southern blot analysis with minisatellite DNA probes

Unfolding of quadruplex structure in the G-rich strand of the minisatellite repeat by the binding protein UP1

The mouse hypervariable minisatellite (MN) Pc-1 consists of tandem repeats of d(GGCAG) and flanked sequences. We have previously demonstrated that single-stranded d(GGCAG)(n) folds into the intramolecular folded-back quadruplex structure under physiological conditions. Because DNA polymerase progression in vitro is blocked at the repeat, the characteristic intramolecular quadruplex structure of the repeat, at least in part, could be responsible for the hypermutable feature of Pc-1 and other MNs with similar repetitive units. On the other hand, we have isolated six MN Pc-1 binding proteins (MNBPs) from nuclear extracts of NIH 3T3 cells. Here, we describe one of those MNBPs, MNBP-B, that binds to the single-stranded d(GGCAG)(n). Amino acid sequences of seven proteolytic peptide fragments of MNBP-B were determined, and the cDNA clones were isolated. MNBP-B was proven identical to the single-stranded DNA-binding protein, UP1. Recombinant UP1 bound to single-stranded d(GGCAG)(n) and other G-rich repetitive sequences, such as d(GTCAGG)(n) and d(GTTAGG)(n). In addition, UP1 was demonstrated by CD spectrum analysis to unfold the intramolecular quadruplex structure of d(GGCAG)(5) and d(TTAGGG)(4) and to abrogate the arrest of DNA synthesis at the d(GGG)(n) site. This ability of UP1 suggests that unfolding of quadruplex DNA is required for DNA synthesis processes.

LRP130, a protein containing nine pentatricopeptide repeat motifs, interacts with a single-stranded cytosine-rich sequence of mouse hypervariable minisatellite Pc-1

Recently, we have identified and purified minisatellite DNA binding proteins (MNBPs) that bind to the mouse hypervariable minisatellite Pc-1, from NIH3T3 cells. This study describes the isolation and characterization of a mouse leucine-rich protein (mLRP130) as one of the MNBPs that binds to the C-rich strand of Pc-1. The mLRP130 cDNA was demonstrated to encode a polypeptide of 1306 amino-acid residues with a deduced molecular mass of 137 kDa, and the mLRP130 mRNA is detected in various organs, including heart, brain, liver, skeletal muscle, kidneys and testes. The mLRP130 protein has nine copies of pentatricopeptide repeat (PPR) motifs that are considered to serve as protein-protein interactions. Two forms of the mLRP130 protein were detected in NIH3T3 cells with an approximate molecular mass of 140 kDa (mLRP130) and 100 kDa (mLRP130der), and were detected mainly in nuclear and cytoplasmic fractions, respectively. Immunofluorescence microscopic analysis demonstrated dominant localization of mLRP130 at the perinuclear region, and also in the nucleus and cytoplasm with dot- or squiggle-like staining. The immunoprecipitated mLRP130 bound to the single-stranded d(CTGCC)8, but not to its complementary G-rich strand of d(GGCAG)8 or double-stranded form. Possible biological roles of mLRP130 are discussed in association with the stability of minisatellite DNA sequences.

Detection and isolation of minisatellite Pc-1 binding proteins

Minisatellites (MNs) are arrays of 5-100 nucleotide repeats that are dispersed throughout the genome of vertebrates. They demonstrate alteration in tumors and in cells exposed to various carcinogens, but the molecular mechanisms underlying the induction of mutations at MNs are largely unknown. Hypervariable MN Pc-1 isolated from the mouse genome consists of tandem repeats of d(GGCAG) flanked with locus-specific sequences at both ends. We have found that MN mutations are induced in NIH3T3 cells by treatment with okadaic acid using a Pc-1 MN fragment as a probe. In order to shed light on the molecular mechanisms, we isolated six MN Pc-1 binding proteins, pA, pB, pD, pE, pF and pG, from nuclear extracts of NIH3T3 cells treated with okadaic acid. While pA and pB bound to the G-rich strand of Pc-1, pD, pE, pF and pG bound to the complementary C-rich strand. Sequence specificities for DNA binding were revealed and one base substitution and insertion into the Pc-1 repeat unit dramatically changed the affinity of each protein, suggesting that they bind to Pc-1 and Pc-1-like MNs in vivo.

Intramolecular quadruplex formation of the G-rich strand of the mouse hypervariable minisatellite Pc-1

The minisatellite Pc-1, isolated from the mouse genome consisting of a tandem repeat of d(GGCAG), is hypervariable with a mutation rate of 0.15/generation. Here we describe a structural characterization of the G-rich strand of Pc-1 by biochemical and physicochemical methods. It was found to be comparatively resistant to both single-stranded DNA-binding protein binding and digestion by single-stranded DNA-specific nuclease and to cause arrest of DNA synthesis. The guanine imino proton NMR signals observed on the Pc-1 G-rich strand and their slow (1)H/(2)H exchange profiles pointed to a quadruplex structure with guanine quartets. The melting temperature of the quadruplex determined by CD was not dependent on DNA concentration. These results indicate that the G-rich strand of Pc-1 forms an intramolecular folded-back quadruplex structure under physiological conditions. Possible mechanisms of the Pc-1 mutations implicated with the formation of the quadruplex structure are discussed.

DNA fingerprint analysis reveals differences in mutational patterns in experimentally induced rat peritoneal tumors, depending on the type of environmental mutagen

We performed tumor DNA fingerprint analysis using the synthetic minisatellite probe S3315x2 based on the 33.15-repeat unit. The aim of the study was to investigate fingerprinting patterns of peritoneal tumors induced experimentally in Wistar rats by two carcinogens with unknown mechanism of action (crocidolite asbestos and nickel powder) and, as a positive control, benzo[a]pyrene. The carcinogens were administered intraperitoneally into rats. The banding patterns obtained with DNA from 71 peritoneal tumors were compared to the corresponding normal tissues. DNA derived from peritoneal tumors induced by the three carcinogens differed with respect to mutation frequencies and mutation patterns. The mutation frequencies in these tumors, revealed by DNA fingerprinting, were 18.2% for benzo[a]pyrene, 14.8% for crocidolite asbestos, and 40.9% for nickel powder. The alterations detected in the banding pattern of benzo[a]pyrene-induced peritoneal tumors were exclusively additional bands. On the contrary, in the DNA from asbestos-induced peritoneal tumors, only deletions of bands were observed on the autoradiographs. In the DNA from nickel-induced peritoneal tumors, both types of mutations occurred. The different mutation frequencies and mutation patterns appear to discriminate between benzo[a]pyrene, crocidolite asbestos, and nickel powder, and may be related to the mechanisms of action of these compounds.

Monitoring for induced heritable mutations in natural populations: application of minisatellite DNA screening

The need to understand the role that anthropogenic chemicals play in generating germline mutations is critical, both from an ecological and a human health perspective. Exposure to complex mixtures of urban and industrial chemicals is widespread and we have little understanding of the long-term implications to populations and gene pools. It has recently been suggested that minisatellite DNA mutations may be sensitive biomarkers for induced heritable mutations in populations exposed to radioactive and non-radioactive contamination in their environments. Minisatellite loci are attractive targets for mutational analyses because they undergo a rate of mutation much greater than unique sequence DNA and with DNA fingerprinting many loci can be scanned simultaneously. As a result, the technique is statistically powerful requiring relatively small sample sizes (compared to other in situ mutation assays) and is reasonably cost and time efficient. This paper will review the application of minisatellite mutation screening to the field of genetic toxicology.

DNA fingerprint analysis in chemically mutagenized Chinese hamster lung cells

Using a multi-locus minisatellite Per-6 DNA probe, we performed DNA fingerprint analysis. Chinese hamster lung (CHL) cells were treated with six model chemicals: N-methyl-N'-nitro-N-nitrosoguanidine, mitomycin C, methyl methanesulfonate, furylfuramide, 2-acetylamino-fluorene, and cyclophosphamide, with or without S9 mix. 771 hypoxanthine phosphoribosyltransferase deficient clones (749 from mutagen-treated cells and 22 from untreated cells) and 90 unselected clones from untreated cells were isolated and analyzed. The spontaneous mutation frequency at CHL cell minisatellite loci was 0.31-0.63%. All the chemicals increased mutation frequencies. Almost all mutations localized to the three specific minisatellite loci corresponding to 4.2, 3.8, and 2.4 kb bands, suggesting that these regions are more unstable and susceptible to mutation. DNA fingerprint analysis is a promising technique for detecting mutations at neutral DNA regions, especially recombinational mutations, and may be useful for surveying genetic instability related to heritable defects or aging.

Establishment and characterization of a new cell line from human bladder cancer (JMSU1)

A new human bladder cancer cell line designated JMSU1 has been established from malignant ascitic fluid of a 75-year-old Japanese man with bladder cancer, and maintained in culture for more than 7 years and over 240 passages. Inverted phase-contrast microscopy revealed that JMSU1 was composed of morphologically distinct cells (polygonal to spindle-shaped cells), showing morphological heterogeneity in vitro. Histological examination of xenografts showed poorly differentiated transitional cell carcinoma, resembling the original tumor. Immunohistochemical staining for cytokeratin and electron microscopic examination suggested that JMSU1 was of epithelial origin. Chromosome analysis gave a modal number of 69 with no Y chromosome. Isozyme analysis (LDH, G6PD, and NP) showed the mobility pattern of human type B. DNA fingerprint analysis demonstrated that there was no cross-culture contamination of JMSU1 during the passages. In conclusion, a newly established and well-characterized cell line, JMSU1, offers promising material for the investigation of the biological properties of bladder cancer.

Demonstration by DNA fingerprint analysis of genomic instability in mouse BALB 3T3 cells during cell transformation

We employed DNA fingerprint analysis to monitor DNA rearrangements in BALB 3T3 cells transformed spontaneously or by treatment with 3-methylcholanthrene (MCA) and UV-C. The effect of 12-O-tetradecanoyl-phorbol-13-acetate (TPA) in combination with MCA was also examined. Twenty-three spontaneously transformed cells, 28 induced transformed cells (18 by 1 microgram/ml MCA, six by 5 micrograms/ml MCA, and four by UV-C), and 31 non-transformed subclones were isolated from parental BALB 3T3 A31-1-1 cells. The DNAs were digested with HinfI and subjected to DNA fingerprint analysis with three multi-locus minisatellite probes, Per-6, Core, and Ins. Per-6 was the most effective probe for detecting DNA rearrangements. Rearranged bands detected by the Per-6 probe were observed in 9/31 (29%) of non-transformed subclones, 14/23 (61%) of spontaneously transformed cells, 16/18 (89%) of cells transformed by 1 microgram/ml of MCA, 6/6 (100%) of cells transformed by 5 micrograms/ml MCA, and 4/4 (100%) of UV-C-transformed cells. Higher numbers of DNA rearrangements (> or = 3) occurred most frequently in the induced transformed cells. TPA enhanced the frequency of DNA rearrangements in cells transformed by MCA. These data indicate that (1) genomic DNA in BALB 3T3 cells is unstable and susceptible to rearrangement, (2) its instability is elevated during cell transformation, and (3) MCA and UV-C induce DNA rearrangements, and TPA enhances the effect of the former, probably via the recombination process. DNA fingerprint analysis is valuable for monitoring genomic instability during cell transformation.