Mouse linkage cytogenetics (L-C) probes.

We have identified 149 hybridization probes at 10-cM intervals in the mouse and have confirmed their order and linkage by fluorescence in situ hybridization. These probes represent a new resource for mapping in the mouse and can be used to correlate linkage and cytogenetic maps, to map novel sequences to within a few centimorgans, to relate cytogenetic abnormalities to the genetic map, and to make cross-species comparisons.

Hybridization-based karyotyping of mouse chromosomes: hybridization-bands.

We have developed a method, which we have named hybridization-banding, to identify simultaneously all chromosomes in a mouse metaphase spread. The method uses a combination of hybridization probes labeled with a single fluor to yield a simple, unique, readily identifiable hybridization pattern on each chromosome. The method is superior to Giemsa- or fluorescence-based banding methods for chromosome identification because the hybridization patterns are simpler and easier to identify, and unique patterns can be designed at will for each chromosome. Analysis can be performed with a standard fluorescence microscope, and images can be recorded on film with an ordinary 35-mm camera, making the method useful to many investigators. The method can also be applied to any species for which chromosomes and probes can be prepared.

Analysis of large and small colony L5178Y tk-/- mouse lymphoma mutants by loss of heterozygosity (LOH) and by whole chromosome 11 painting: detection of recombination.

Analysis of 122 spontaneous large and small colony mutants derived from L5178Y tk +/- mouse lymphoma cells at 28 heteromorphic microsatellite loci on chromosome 11 showed that extensive loss of heterozygosity (LOH) is common in both large colony and small colony mutants, eliminating most chromosome 11 loci as candidates for a putative growth control locus. These results, in conjunction with historical cytogenetic data, suggest that a putative growth control locus lies distal to the thymidine kinase (Tk1) gene, near the telomere. Thirty seven mutants were hybridized with a chromosome 11-specific whole chromosome painting probe for analysis of rearrangements. Generally, painting confirmed earlier observations that large colony mutants are karyotypically normal, whereas small colony mutants frequently have detectable rearrangements. A point probe distal to Tk1 revealed no evidence of chromosome breakage in small colony mutants that appeared normal on whole 11 painting and had no LOH. Therefore, the molecular difference between large and small colony mutants remains unknown. Models to explain large and small colony mutants consistent with our findings are presented, including loss of a putative growth control gene, differential mechanisms of chromosome breakage/repair and second site mutations as explanations for small colony mutants. Painting revealed translocations and aneuploidy and showed that non-disjunction was not a common explanation for complete LOH. The most common finding was that large regions of LOH do not result from deletions, demonstrating that these cells can detect recombination events as well as previously observed chromosomal rearrangements, deletions and point mutations.

Differential destabilization of repetitive sequence hybrids in fluorescence in situ hybridization.

A method for painting a chromosome or chromosome region by fluorescence in situ hybridization (FISH) without blocking DNA is described. Both unique sequence and repetitive sequence components of a fluorescently labeled probe are hybridized under low-stringency conditions, but the chromosomes are washed in such a manner that repetitive sequences are differentially removed, while region-specific unique sequence fragments remain bound to the target chromosomes. We refer to this differential retention and removal of probe components as differential stability FISH.

Micronuclei containing whole chromosomes harbouring the selectable gene do not lead to mutagenesis.

Loss of heterozygosity is one genetic change observed in many tumours. We do not know whether the loss of chromosomal material through micronucleus formation is a viable mechanism associated with, and possibly leading to, genetic disease. Previously, we treated L5178Y mouse lymphoma cells with four aneugens. Although these aneugens induced micronuclei containing predominantly whole chromosomes, they did not induce mutations at Tk1, the selectable gene, under the same non-toxic conditions in which they induced micronuclei. This suggested that the induction of micronuclei containing whole chromosomes was not an early event leading to phenotypically expressed mutations in these cells under the conditions used. However, it is possible that chromosome 11, on which Tk1 resides, may be under-represented in the micronucleus population. To find out the frequency of induction of micronuclei containing chromosome 11, we applied fluorescence in situ hybridization using a chromosome 11 paint to micronuclei induced by colcemid and vinblastine. We found that the numbers of micronuclei containing chromosome 11 are more than sufficient to be detectable as mutations if these micronuclei lead to viable mutants. We conclude that the formation of micronuclei containing whole chromosomes does not lead to viable, dividing mutants in this system.

Identification of a heteromorphic microsatellite within the thymidine kinase gene in L5178Y mouse lymphoma cells.

The objective of this work is to identify a heteromorphism within the thymidine kinase (Tk1) gene which can be used to assay for allele loss by means of PCR. Intron F of mouse Tk1 contains two (CA)n microsatellite sequences separated by 107 bp of non-repetitive sequence. We tested this region for heteromorphism in L5178Y mouse lymphoma cells. A PCR primer pair designated Agl1 yielded products of 396 and 194 bp from L5178Y tk+/- genomic DNA. The 194-bp product resulted from a secondary binding site between the two (CA)n repeats for the forward Ag11 primer and was not produced from tk-/- mutants that had lost the functional Tk1b allele. Agl2 primers produced two PCR products of 523 and approximately 440 bp and Agl3 primers produced products of 579 and approximately 500 bp. In both these cases, the difference in product size was approximately equal, indicating that Intron F is approximately 80 bp shorter in the non-functional Tk1a allele than in Tk1b. This heteromorphism forms the basis for an assay for allele loss by means of PCR. Agl1 and Agl3 primers yielded additional products of 91 and 274 bp, respectively, consistent with sizes expected from the mouse Tk1 pseudogenes (Tk1-ps). Our conclusions drawn from an analysis of 122 mutants for Tk1b loss using Agl2 primers agreed with previous analysis of the NcoI heteromorphism. Thus, a simple PCR-based analysis can identify Tk1b loss in the L5178Y mouse lymphoma cells.

Induction of multilocus mutations at the Tk1 locus after X irradiation of L5178Y cells at different times in the mitotic cycle.

TK1+/- L5178Y-R16 cells were separated into G1, S and G2/M-phase populations by centrifugal elutriation and were treated with 1.5 Gy X radiation. Cells irradiated in the G1 and G2/M phases were most sensitive to the cytotoxic effects of radiation, while cells irradiated in the G2/M phase showed the highest mutant frequency at the thymidine kinase (Tk1) locus. DNA isolated from independent TK1-/- mutants was analyzed for loss of heterozygosity (LOH) at the Tk1 locus and two microsatellites, D11Mit48 and D11Nds7. Homogenates of each mutant were assayed for activity of galactokinase (GLK), the product of the galactokinase (Glk) gene neighboring the Tk1 gene on chromosome 11. Irradiated G1-phase cells had the highest percentage of mutants showing no LOH. The frequency of mutants with LOH at both Tk1 and D11Nds7 with no loss of GLK activity was high in all cell populations: There was no significant difference in the observed frequency of these mutants between the populations. The frequency of mutants losing GLK activity was low, particularly in cells irradiated in the S or G2/M phases. The possibility that the loss of GLK activity is not indicative of LOH at the Glk gene under the conditions of the present experiments is discussed.

Mouse chromosome-specific painting probes generated from microdissected chromosomes.

Using degenerate primer amplification of chromosomes microdissected from banded cytogenetic preparations, we constructed both whole chromosome painting probes for mouse Chromosomes (Chrs) 1, 2, 3, and 11 and a centromere probe that strongly paints most mouse centromeres. We also amplified a Robertsonian translocation chromosome microdissected from unstained preparations to construct a painting probe for Chrs 9 and 19. The chromosome probes uniformly painted the respective chromosomes of origin. We demonstrated the utility of the Chr 11 probe in aberration analysis by staining mutants that we had previously identified as containing a Chr 11 translocation, and in some mutant cell lines we observed chromosome rearrangements not previously detected in stained cytogenetic preparations. The technology of microdissection and amplification applies to all mouse chromosomes or to specific subchromosomal regions and will be useful in mouse genetics, in aberration analysis, and for chromosome identification.

Use of microsatellite DNA polymorphisms on mouse chromosome 11 for in vitro analysis of thymidine kinase gene mutations.

The mouse lymphoma (L5178Y tk+/- 3.7.2C) in vitro mutagenesis assay can measure the genotoxic effects of a wide variety of chemical agents by inactivation of a single functional thymidine kinase (tk-1) gene. We have previously demonstrated, using cytogenetic and molecular techniques, that the types of molecular lesions associated with tk-1 gene inactivation span a wide range similar to that seen in tumor cells at specific oncogene and tumor suppressor gene loci. We have identified, using polymerase chain reaction techniques, 21 microsatellite, or 'simple sequence repeat', polymorphisms between chromosomes 11a and 11b in 3.7.2C cells. These microsatellite polymorphisms span virtually the entire chromosome, from mapping positions of 3-78 centiMorgans (cM) from the centromere, thus providing landmarks to study loss of genetic material across the entire chromosome. Four of the microsatellite polymorphisms lie within 12 cM of tk-1, and provide a means of mapping loss of genetic material in the immediate vicinity of tk-1, a capability that we have not previously had in the mouse lymphoma assay. Loss of alleles (i.e. loss of heterozygosity) is an important feature of tumor development, having to do with tumor suppressor gene expression. Therefore, the ability to detect loss of heterozygosity in the mouse lymphoma assay will make the assay an extremely valuable tool in the detection of agents capable of inducing loss of heterozygosity.

Sequence analysis of tka(-)-1 and tkb(+)-1 alleles in L5178Y tk+/- mouse-lymphoma cells and spontaneous tk-/- mutants.

The mouse-lymphoma mutagenesis assay detects forward mutations at the heterozygous thymidine kinase (tk-1) locus in L5178Y tk+/- 3.7.2C cells. This assay of genotoxicity is widely used to quantitate the mutagenic potential of a variety of chemical and physical agents. A NcoI heteromorphism between the tka- and tkb+ alleles allows the use of Southern blotting to broadly detect two major categories of mutations. These consist of deletions of the functional allele, characterized by absence of a 6.3-kb tk-hybridizing band, and apparent point mutations, indistinguishable from wild-type on blots. Rarely, Southern blots reveal a partial deletion of tkb. The variety of lesions recorded at the heterozygous tk-1 locus may be representative of events important in mammalian carcinogenesis and may include a greater range of mutagenic events than can be observed at hemizygous test loci. To further assess the ability of the mouse-lymphoma assay to detect a variety of mutations and to allow identification of point mutations, we have sequenced the entire tk-1 coding region from both tka- and tkb+ alleles of L5178Y 3.7.2C mouse-lymphoma cells. Sequences were obtained using PCR amplified double-stranded DNA templates prepared from cytoplasmic RNA from the heterozygous cell line. The two alleles were found to differ by a single TA to GC transversion, altering one amino acid in the deduced amino acid sequence. 4 spontaneous mutants were also sequenced and demonstrated a variety of mutations, including a 6-base pair in-frame deletion, a CG to GC transversion upstream of the start codon, a mutant apparently lacking expression of the tkb allele, and a mutant with apparent wild-type coding sequence for both tka- and tkb+ alleles. The diverse nature of the mutants isolated from L5178Y cells suggests that the mouse-lymphoma mutagenesis assay is capable of detecting a number of mutation types, enhancing the utility of the assay in studying the range of genetic lesions important in human disease. The lesions produced are readily analyzed using a combination of Southern blotting and sequence analysis.

Use of DNA purified in situ from cells embedded in agarose plugs for the molecular analysis of tk-/- mutants recovered in the L5178Y tk+/- 3.7.2C mutagen assay system.

We have reported that tk-/- mutants recovered in the mouse L5178Y tk+/- 3.7.2C mutagen assay have often lost the tk+ allele. Allele loss in the tk-/- mutants is documented on Southern blots as the absence of a 6.3-kb Nco I fragment seen in both tk+/+ and tk+/- cell DNAs. For the routine screening of large- and small-colony tk-/- mutants DNAs for the absence of this genomic fragment, we have found that cells can be lysed in agarose plugs, and DNA of cells embedded in plugs can be purified, restricted with Nco I, electrophoresed, and analyzed on Southern blots without significant band distortion or diffusional loss of tk- specific fragments in the 2-7-kb range. Purification and restriction analysis of DNA in agarose plugs, originally developed to allow pulsed-field gel electrophoresis of very large DNA fragments, represents a convenient alternative to conventional DNA purification methods, allowing quantitative recovery of DNA from small numbers of cells, eliminating centrifugation, phenol extraction, and ethanol precipitation steps, and requiring smaller quantities of reagents.

Genetics of clindamycin resistance in Bacteroides.

Results presented in this paper have shown that a widely distributed LM-resistance determinant is present on at least 3 distinct Bacteroides R-plasmids. In fact these plasmids bear no homology outside of the defined regions implicated in the LM resistance. This resistance determinant on pBF4, pBFTM10, and pBI136 is located within DNA segments bounded on each side by a directly repeated sequence of more than 500 bp. The intervening sequences of these 3 elements are variable, and range in size from about 3.7 kb to 7.2 kb (Fig. 7). Apart from the EcoRI/AvaI restriction sites which characterize the repeated sequence, there is a notable lack of common restriction sites within these elements. These results suggest that the elements do possess a certain degree of structural similarity but significant evolutionary divergence has occurred. The presence and location of the directly repeated sequences, their association with specific deletions, and their association with an antibiotic-resistance determinant, are features common to many antibiotic-resistance transposons described for other prokaryotes. In addition, these elements are highly mobile, being found on a number of R-plasmids. The unique relationship between pBF4, pBI106, and pBI136 described here is a clear indication of the potential for these DNA sequences to move from one molecule to another. Given the extensive dissemination and the genetic and structural characteristics described above, it seems likely that the LM-resistance determinant is carried on transposon-like elements present in pBF4, pBFTM10, and pBI136. However, further experimentation will be necessary to document the transposition event. Bacteroides strains such as B. fragilis V503, possess a transmissible LM-resistance determinant which does not appear to be associated with detectable extrachromosomal elements (5,9,10). Presently, a number of strains of this type have been found over a wide geographic area. The LM-resistance genes associated with these strains are apparently similar to the one carried on the Bacteroides R-plasmids because homology between the 2 has been observed. However, it is important to note that within the limits of Southern filter blot hybridization, neither V503 nor its transconjugants possess the directly repeated sequence found on the LM-resistance plasmids (Fig. 8). The elusive nature of the V503 LM-resistance elements presents an intriguing problem. One model that has been proposed is that these resistance determinants reside on a conjugative transposon similar to Tn916 of Streptococcus faecalis (3).(ABSTRACT TRUNCATED AT 400 WORDS)