Minisatellite Loci Research Articles

Increased band sharing in DNA fingerprints of an inbred human population

We have compared band sharing between the DNA fingerprints of members of an inbred human population with band sharing between members of an outbred population. It had not previously been determined whether the high rate of mutation at minisatellite loci is sufficient to prevent an increase in band sharing in moderately inbred populations. We have found that there is an increase in band sharing in the 2-kb to 9-kb size range, but not in the greater than 9-kb size range, in the inbred population. The difference was consistently observed using four different multi-locus probes, viz. 33.6, 33.15, (CAC)5 and M13. Thus, we have demonstrated that moderate but prolonged inbreeding can lead to increased similarity in human DNA fingerprints. This should be considered when analysing DNA fingerprints in forensic or paternity cases involving members of an inbred community.

Hypervariable minisatellite DNA sequences in the Indian peafowl Pavo cristatus

We report here for the first time the large-scale isolation of hypervariable minisatellite DNA sequences from a non-human species, the Indian peafowl ( Pavo cristatus). A size-selected genomic DNA fraction, rich in hypervariable minisatellites, was cloned into Charomid 9–36. This library was screened using two multilocus hypervariable probes, 33.6 and 33.15 and also, in a “probe-walking” approach, with five of the peafowl minisatellites initially isolated. Forty-eight positively hybridizing clones were characterized and found to originate from 30 different loci, 18 of which were polymorphic. Five of these variable minisatellite loci were studied further. They all showed Mendelian inheritance. The heterozygosities of these loci were relatively low (range 22–78%) in comparison with those of previously cloned human loci, as expected in view of inbreeding in our semicaptive study population. No new length allele mutations were observed in families and the mean mutation rate per locus is low (<0.004, 95% confidence maximum). These loci were also investigated by cross-species hybridization in related taxa. The ability of the probes to detect hypervariable sequences in other species within the same avian family was found to vary, from those probes that are species-specific to those that are apparently general to the family. We also illustrate the potential usefulness of these probes for paternity analysis in a study of sexual selection, and discuss the general application of specific hypervariable probes in behavioral and evolutionary studies.

Evolutionary transience of hypervariable minisatellites in man and the primates

Using PCR, two minisatellite loci showing extreme repeat-unit copy-number variation in humans have been characterized in great apes and monkeys. In contrast to humans, minisatellite locus MS32 is monomorphic with only 3-4 diverged repeat units in great apes, Old World and New World monkeys, this organization presumably representing the relatively stable ancestral precursor state of the human hypervariable locus. Similarly, minisatellite MS1 shows extreme repeat-copy-number variability in man compared with low copy number and minimal variability in great apes. Analysis of variant repeat units shows that the 5' and 3' regions of MS1 are relatively stable in great apes and man, and that variability in man is confined to the central region of the minisatellite. In contrast to the great apes, MS1 is highly variable in Old World monkeys. These results, as well as computer simulations of minisatellite evolution based on known mutation rates, show that short minisatellites are stable within the genome, and that the degree of polymorphism at a given locus can change dramatically over a short period of evolutionary time. The ability of hypervariable minisatellites to detect highly informative loci by cross-species hybridization is therefore largely unpredictable.

Analysis of Transforming Genes in Indirectly Induced Radiogenic Thymomas in Mice

The expression of oncogenes was studied in 12 types of 178 mouse tumors induced by radiations and chemicals. DNA was analyzed in tumors in which the overexpression of oncogenes was noted. Amplification of the myc oncogene was found in chemically induced sarcomas, but not in sarcomas induced by radiation. Activation of oncogenes by small mutations and the inactivation of tumor suppressor genes has to be taken in account in the radiation induction of mouse tumors. We therefore made further analyses of radiogenic thymomas. Loss of heterozygocity was revealed in directly induced thymomas by the deletions of allele specific minisatellite bands. Analysis of a hypervariable minisatellite locus also revealed that these thymoma cells suffered high recombinogenic activity during tumorigenesis. In addition, transfection of cellular DNA to normal Golden hamster cells identified the activated K-ras oncogene in the directly induced radiogenic thymomas. Indirectly induced radiogenic thymomas were tested similarly. Transformed cells from secondary transfection experiment were positive for the mouse-specific repetitious sequences, but devoid of mouse ras oncogenes. Indirectly induced radiogenic thymomas originate from unirradiated normal thymus cells transplanted in irradiated hosts. The spontaneous activation of oncogenes yet to be identified may therefore be involved in the development of this tumor.

Denaturing gradient gel electrophoretic analysis of minisatellite alleles

By two-dimensional DNA fingerprinting, an electrophoretic method which combines separation according to size with separation in a denaturing gradient, virtually all minisatellite sequences detected with a minisatellite core probe can be resolved (Uitterlinden et al., Proc. Natl. Acad. Sci. USA 1989, 86, 2742-2746). To investigate the electrophoretic behavior in denaturing gradient gels of allelic restriction fragments containing minisatellite sequences, we analyzed alleles of the two highly polymorphic minisatellite loci D7S22 and D2S44. The results obtained indicate that for these loci, depending on the restriction enzyme used to digest genomic DNA, alleles of different sizes migrate to regions of similar denaturant concentration, i.e. to isothermal positions in the denaturing gradient. Denaturing gradient gel electrophoresis also allows for the discrimination of restriction fragments which are the result of the presence of internal recognition sites in the minisatellite and, therefore, to distinguish between VNTR and restriction site polymorphisms.

DNA fingerprinting in schistosome-vector snails

The planorbid snail Bulinus is an intermediate host for trematodes of the genus Schis tosoma. A knowledge of snail reproductive biology is necessary to understand the genetically based susceptibility and/or resistance to various strains of schistosomes (Richards, 1973; Rollinson, 1984). Despite this need, the reproductive biology has been investigated in only a few species (Larambergue, 1939; Rudolph, 1983; Rudolph and Bailey, 1985; Rollinson et al., 1989). Bul inus snails are hermaphroditic and can self-fertilize, but crossfertilize when paired. Foreign sperm from multiple partners can be stored and remain viable for several months after copulation (Larambergue, 1939; Rudolph, 1983; Rollinson et al., 1989). In order to investigate the mating system, genetic markers are needed. Most Bul inus snails have little protein variability seen by electrophoresis (Jelnes, 1986). Pigment markers (Larambergue, 1939; Rudolph, 1983) restrict the analysis to pairs of individuals. Therefore, these techniques cannot be used in Bulinus. Jeffreys et al. (1985) have isolated human minisatellite probes which, when hybridized to other minisatellite loci, produce an individual-specific pattern called a fingerprint. Moreover, the alleles are inherited in a standard Mendelian fashion. These probes have been widely used in numerous species

Systematic cloning of human minisatellites from ordered array charomid libraries

We present a rapid and efficient method for the isolation of minisatellite loci from human DNA. The method combines cloning a size-selected fraction of human MboI DNA fragments in a charomid vector with hybridization screening of the library in ordered array. Size-selection of large MboI fragments enriches for the longer, more variable minisatellites and reduces the size of the library required. The library was screened with a series of multi-locus probes known to detect a large number of hypervariable loci in human DNA. The gridded library allowed both the rapid processing of positive clones and the comparative evaluation of the different multi-locus probes used, in terms of both the relative success in detecting hypervariable loci and the degree of overlap between the sets of loci detected. We report 23 new human minisatellite loci isolated by this method, which map to 14 autosomes and the sex chromosomes.

Minisatellite DNA fingerprints of salmonid fishes

The human minisatellite probes 33.6 and 33.15 cross-hybridized to DNA digests of Atlantic salmon, brown trout and rainbow trout revealing complex multi-banded patterns. These DNA fingerprints (in excess of 40 resolvable fragments in some cases) were highly polymorphic, individual specific and found to be stable, both somatically and in the germline. Pedigree analysis of an Atlantic salmon family confirmed that the minisatellite fragments showed Mendelian inheritance. With only a single occurrence of linkage and allelism being observed it is likely the minisatellite loci are widely distributed throughout the salmonid genome. The potential applications for both multi- and single locus minisatellite probes in salmonid research are discussed.

“Major minisatellite loci” detected by minisatellite clones 33.6 and 33.15 correspond to the cognate loci D1S111 and D7S437

G. Chimini et al. (1989, Genomics 5:316–324) have recently reported that the two multilocus DNA fingerprinting probes 33.6 and 33.15 each detect a single major site in the human genome, at 1q23 and 7q35–q36, respectively, and speculate that these sites represent particularly large loci homologous to these probes. However, the human minisatellite loci cloned in 33.6 and 33.15 can themselves be assigned by somatic cell hybrid analysis to 1cen-q24 and 7q31.3-qter, respectively, corresponding to the “major loci” of Chimini et al. Furthermore, under their hybridization conditions, both 33.6 and 33.15 act largely as locus-specific minisatellite probes. The “major minisatellite loci” postulated by Chimini et al. do not therefore appear to represent major localized clusters of minisatellites in the human genome, but rather the loci cloned in 33.6 and 33.15.

A novel human DNA polymorphism resulting from transfer of DNA from chromosome 6 to chromosome 16

A cloned minisatellite, termed λMS29, that is unusual because it detects two variable loci in human DNA has been isolated. One locus, DNF21S1, located in the terminal region of the short arm of human chromosome 6, is also present in great apes. The second minisatellite locus, DNF21S2, is located interstitially on chromosome 16p11 and is absent both from non-human primates and from some humans. Physical mapping and sequencing show that the second locus has arisen recently in evolution by duplication of a large (> 15 kb) segment of chromosome 6 DNA containing a minisatellite and transposition onto chromosome 16 into a member of a novel low-copy-number repetitive DNA family. This unusual duplication/transposition event appears to represent the first example of a human DNA polymorphism arising through DNA-mediated, rather than RNA-mediated, transfer between autosomes.

The variability of DNA fingerprints in three species of swan

The genetic variation in three species of swans was examined by DNA fingerprinting. Human minisatellite probes detected a number of highly variable fragments in the restriction digests of total nuclear DNA. Assuming bands to be independent, the average allele frequency for minisatellite loci was 0·154, 0·154 and 0·109 for Mute, Whooper and Bewick's Swans, respectively. The pattern of band-distribution showed a certain degree of species-specificity, so that the fingerprints may reflect taxonomic affinities of the species. Pedigree analysis of a single family of Mute Swans showed that most of the variable fragments were inherited in a simple Mendelian fashion, allowing the relatedness of the individuals to be determined. DNA fingerprinting potentially provides a large number of genetic markers for studying the behavioural ecology, population genetics and evolution of swans.

DNA fingerprinting: a new dimension

They've done it again! Those friendly people who brought you DNA fingerprinting have now revealed genetic variation on an extraordinarily fine scale. Not only that: in a recent paper describing DNA sequence differences between alleles at a minisatellite (fingerprint) locus, Alec Jeffreys, Rita Neumann and Victoria Wilson of Leicester University have also answered fundamental questions about the rate and mode of generation of this variation I. DNA fingerprints-',.*, those unevenly spaced ladders of bands, which in many species are unique for an individual, are the result of screening several extremely variable loci simultaneously. Each band represents an allele at a particular locus and is thus one of a pair. Its partner is usually elsewhere in the fingerprint profile (heterozygous state) but may occasionally occur at the same point (homozygous state). The DNA sequences detected by fingerprint probes are very short (e.g. 16 base pairs for the Jeffreys probe X33.15) and often occur in strings, known as tandem repeat arrays or minisatellite DNA. Variation in allele position on a fingerprint profile is due to differences in the length of the DNA fragments detected, which in turn result from variation ,7:~ the number of repeats within an array. At minisatellite loci, repeat units appear to be easily gained or lost and different alleles can have anything from a handful to hundreds of repeats. Although DNA fingerprints are useful for de termining close kin, for many other purposes (e.g. population surveys) it is useful to have locus-specific information. Unfortunately, sorting out which bands

Highly polymorphic minisatellite DNA probes. Further evaluation for individual identification and paternity testing

Reliable and reproducible protocols have been developed for the routine DNA fingerprinting of individuals using the highly polymorphic minisatellite DNA probes 33.15 and 33.6. Comparison of DNA fingerprinting from 50 individuals has generated further data on the level of band sharing in the DNA fingerprints of unrelated individuals, as well as the number of bands scorable in individuals. These results are consistent with previous studies. The occurrence of mutant bands in offspring has been examined in over 100 families. Further support is presented for the Mendelian inheritance of minisatellite loci and for lack of significant allelism and linkage between different variable DNA fragments detected in a human DNA fingerprint.

Characterization of a highly unstable mouse minisatellite locus: Evidence for somatic mutation during early development

A highly unstable mouse minisatellite locus, Ms6-hm, has been identified in mouse DNA fingerprints produced by cross-hybridization with human minisatellite probe 33.6. A 7-kb allele of Ms6-hm was cloned from a C57BL 6J mouse and collapsed to a 400-bp plasmid insert on propagation in Escherichia coli due to loss of the majority of minisatellite repeat units. Sequence analysis revealed that Ms6-hm has evolved by amplification within a member of the MT (mouse transcript) family of interspersed repetitive elements. Linkage analysis localized Ms6-hm near the brown coat color gene ( b) on chromosome 4. Multiallelism and heterozygosity at this locus within inbred strains result from a high germline mutation rate to newlength alleles (2.5% per gamete). Mice mosaic for cells carrying a nonparental allele in somatic tissue, and in some cases also in the germline, provide evidence for additional, somatic, mutation events at Ms6-hm. In two mosaic mice the fraction of cells containing the nonparental allele has been shown to be indistinguishable in different adult tissues. These somatic mutation events at Ms6-hm must therefore occur very early in development, preceding the allocation of somatic lineages, and the same pool of primitive ectoderm cells must contribute equally to all somatic tissues. Under low-stringency hybridization conditions the collapsed subclone of Ms6-hm cross-hybridizes to other unstable loci in the mouse genome to generate a novel and highly individual specific mouse DNA fingerprint.

Simultaneous genetic mapping of multiple human minisatellite sequences using DNA fingerprinting

We have used several DNA probes which simultaneously recognize multiple loci to follow the segregation of a large number of minisatellite loci through two large reference pedigrees. The segregation data were analyzed for linkage to previously characterized marker loci using RFLP mapping data for these pedigrees from a previous study and from the Centre d'Etude du Polymorphisme Humain data bank. In this way we have mapped 31 separate minisatellite alleles of a total of 146 studied. The results of these analyses suggest that the distribution of minisatellites in the human genome is skewed toward telomeres and is highly clustered in character. A group of at least five separate minisatellites was found at 7qter, and smaller clusters are present in several other regions. We detected a smaller than expected number of linkages, perhaps because of the clustering of minisatellite loci. The 7qter minisatellite cluster is in a region of excess male meiotic recombination, and in this respect is similar to minisatellite clusters at 16pter and in the X-Y pseudoautosomal region.

Population bottlenecks in Polynesia revealed by minisatellites.

Tandem-repetitive highly variable loci in the human genome (minisatellites) have been used in gene mapping and as DNA "fingerprints", but they have not yet found much application in population genetics. We have investigate the capacity of six minisatellites to discriminate between four populations in Oceania. We find that in comparison to Melanesians, Polynesians have a significant loss of heterozygosity (or gene diversity), not noted using more traditional markers. We show also that the number of alleles, the allele distribution and the mutation rates at the Polynesian minisatellite loci do not deviate from those predicted by the neutral mutation/infinite allele model. The low gene diversity is therefore likely to be a result of the maintenance of small population sizes and bottleneck effects during the colonization of the Pacific.

Analysis of somatic mutations at human minisatellite loci in tumors and cell lines

Hypervariable human minisatellite loci show a substantial level of germline instability, and spontaneous mutation rates to new length alleles have been measured directly by pedigree analysis. We now show that mutation events altering the number of minisatellite repeat units are not restricted to the germline, but also arise in other tissues. Mutant alleles can be detected at a very low frequency in lymphoblastoid cell lines and at much higher frequencies in clonal tumor cell populations, most particularly in gastrointestinal adenocarcinomas. Mutant alleles in these tumors are usually present at a dosage equal to or greater than that of the progenitor allele, indicating that most or all of the tumor cells carry the same clonally derived mutant allele. As with germline mutation, the incidence of somatic mutations in tumors varies from locus to locus, with the same locus showing the highest level of germline and somatic instability. Most length changes, as those in the germline, are of only a few repeat units; however, very large changes are also observed, implying that such mutations can occur in the absence of meiosis.

Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells.

Hypervariable minisatellites can be amplified from human DNA by the polymerase chain reaction, using primers from DNA flanking the minisatellite to amplify the entire block of tandem repeat units. Minisatellite alleles up to 5-10 kb long can be faithfully amplified. At least six minisatellite loci can be co-amplified from the same DNA sample and simultaneously detected to provide a reproducible and highly variable DNA fingerprint which can be obtained from nanogram quantities of human DNA. The polymerase chain reaction can also be used to analyse single target minisatellite molecules and single human cells, despite the appearance of spurious PCR products from some hypervariable loci. DNA fingerprinting at the level of one or a few cells therefore appears possible.

The human apolipoprotein C-II gene sequence contains a novel chromosome 19-specific minisatellite in its third intron.

The human apolipoprotein C-II gene was sequenced and found to contain four exons and three introns, with a major transcription initiation site located 26 base pairs downstream from a TATA sequence element. The third intron was found to be composed almost entirely of a novel 37-base pair minisatellite that is repeated six times. The minisatellite sequence was found to be present in approximately 60 different genomic locations. The minisatellite DNA sequence at three of these loci were compared and found to be highly conserved. In situ hybridization indicated that the minisatellite loci were clustered in the q13.3 band of chromosome 19. This is the first example of a chromosome- and band-specific repetitive element in the mammalian genome.

Minisatellite mapping in manic depression

Hypervariable regions of DNA exist at many discrete loci in the human genome. Variations in the length of specific classes of hypervariable DNA termed “minisatellite” sequences may be detected by hybridisation of radioactive probes composed of a common10–15 base pair repeat or “core” sequence which is shared by each of the minisatellite loci. Such a procedure was used to perform linkage analysis on a kindred in which a disease allele causing manic depression appeared to be segregating as an autosomal dominant. Results indicate no apparent linkage between a manic depression allele and at least 20 hypervariable genetic loci which acted as markers. However, because of the hypervariability of the minisatellite loci these results do not preclude similar analyses of other manic depressive pedigrees being productive because each such family will have distinct observable minisatellite alleles at loci specific to that family. The method could be usefully applied to the genetic analysis of other psychiatric disorders where heterogeneity is suspected and where a single autosomal major gene locus appears to be responsible for causing multiple cases within a single kindred.