Evolutionary transience of hypervariable minisatellites in man and the primates

A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data

Motivation

The advent of Next Generation Sequencing (NGS) has led to the generation of enormous volumes of short read sequence data, cheaply and in reasonable time scales. Nevertheless, the quality of genome assemblies generated using NGS technologies has been greatly affected, compared to those generated using Sanger DNA sequencing. This is largely due to the inability of short read sequence data to scaffold repetitive structures, creating gaps, inversions and rearrangements and resulting in assemblies that are, at best, draft forms. Third generation single-molecule sequencing (SMS) technologies (e.g. Pacific Biosciences Single Molecule Real Time (SMRT) system) address this challenge by generating sequences with increased read lengths, offering the prospect to better recover these complex repetitive structures, concomitantly improving assembly quality.

Results

Here, we evaluate the ability of SMS data (specifically human genome Pacific Biosciences SMRT data) to recover poorly represented repetitive sequences (specifically, GC-rich human minisatellites). To do this we designed a pipeline for the collection, processing and local assembly of single-molecule sequence data to form accurate contiguous local reconstructions. Our results show the recovery of an allele of the non-coding minisatellite MS1 (located on chromosome 1 at 1p33-35) at greater than 97% identity to reference (GRCh38) from the unprocessed sequence data of a haploid complete hydatidiform mole (CHM1) cell line. Furthermore, our assembly revealed an allele of over 500 repeat units; much larger than the reference (GRCh38), but consistent in structure with naturally occurring alleles that are segregating in human populations. This local assembly's reconstruction was validated with the release of the whole genome assemblies GCA_001297185.1 and GCA_000772585.3, where this allele occurs. Additionally, application of this pipeline to coding minisatellites in the PRDM9 and ZNF93 genes enabled recovery of high identity allele structures for these sequence regions whose length was confirmed by PCR from cell line genomic DNA. The internal repeat structure of the PRDM9 allele recovered was consistent with common human-specific alleles.

Availability and Implementation

Code available at https://github.com/ndliberial/smrt_pipeline.

Contact

dno2@le.ac.uk.

DNA fingerprinting in zoology: past, present, future

In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic 'paradigm shifts' during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys' identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as 'DNA fingerprinting', also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys' invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys' pioneering work.

Mutation at the human D1S80 minisatellite locus

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of 1.04 × 10(-4) and a female mutation rate of 5.18 × 10(-5) with an overall mutation rate of approximately 7.77 × 10(-5). Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.

Heteroduplex analysis of minisatellite variability

Minisatellites are tandem repeat arrays of middle size (5-100 bp) repeat units widely distributed in eukaryotic genomes. They have been related to several important features of human genome biology, including gene regulation, chromosomal fragile sites, and imprinting. In this report, we have critically assessed and employed heteroduplex analysis (HA) for the identification of different human minisatellite MsH43 alleles. This minisatellite is organized as a repeat array of 5-6 bp units spanning 0.5 kbp. Our results demonstrate that this procedure is an easy, rapid, and reliable method to document allelic diversity for this locus. This work suggests that HA will also be a useful tool for studying the polymorphism of other minisatellites with small repeat units.

Advances in the application of germline tandem repeat instability for in situ monitoring

Alterations in tandem repetitive DNA sequences such as minisatellite DNA and expanded simple tandem repeats (ESTRs) may provide useful biomarkers of induced germline effects. In this review, I describe the differences between ESTRs and minisatellites with respect to their structure and mutational mechanisms, and discuss field applications measuring induced germline instability. It is evident that both types of loci have high rates of mutation that facilitate the measurement of induced mutation measured in relatively small numbers of samples following environmentally relevant exposures. Several research groups have used these loci to demonstrate a significant increase in germline mutation in humans and animals exposed to radioactive or chemical pollutants in their natural environment. Mutations are manifested as gains or losses in repeat units and are detected either by pedigree screening or by PCR amplification of sperm DNA. Mutations at both ESTRs and minisatellites appear to arise via indirect mechanisms rather than by direct damage to the repeat locus itself. Most interestingly, ESTR instability following radiation has been shown to be heritable and transmitted to subsequent generations. An understanding of the mechanisms involved in induced instability is required in order to begin to decipher the potential biological implications of increased germline tandem repeat mutation. Furthermore, relatively few studies have investigated the ability of different genotoxins to induce tandem repeat instability. Such laboratory-based experiments will be crucial in clarifying the particular environmental or occupational exposures that should be targeted for future studies and for isolating and subsequently identifying the putative mutagens in complex environmental matrices.

Two modes of germline instability at human minisatellite MS1 (locus D1S7): complex rearrangements and paradoxical hyperdeletion

Minisatellite MS1 (locus D1S7) is one of the most unstable minisatellites identified in humans. It is unusual in having a short repeat unit of 9 bp and in showing somatic instability in colorectal carcinomas, suggesting that mitotic replication or repair errors may contribute to repeat-DNA mutation. We have therefore used single-molecule polymerase chain reaction to characterize mutation events in sperm and somatic DNA. As with other minisatellites, high levels of instability are seen only in the germline and generate two distinct classes of structural change. The first involves large and frequently complex rearrangements that most likely arise by recombinational processes, as is seen at other minisatellites. The second pathway generates primarily, if not exclusively, single-repeat changes restricted to sequence-homogeneous regions of alleles. Their frequency is dependent on the length of uninterrupted repeats, with evidence of a hyperinstability threshold similar in length to that observed at triplet-repeat loci showing expansions driven by dynamic mutation. In contrast to triplet loci, however, the single-repeat changes at MS1 exclusively involve repeat deletion, and can be so frequent--as many as 0.7-1.3 mutation events per sperm cell for the longest homogeneous arrays--that alleles harboring these long arrays must be extremely ephemeral in human populations. The apparently impossible existence of alleles with deletion-prone uninterrupted repeats therefore presents a paradox with no obvious explanation.

Evolution of the cystatin B gene: implications for the origin of its variable dodecamer tandem repeat in humans

The human cystatin B gene contains a variable number of 12-bp tandem repeats in its promoter region, of which the common alleles contain two or three copies and unusual expansion causes progressive myoclonus epilepsy of the Unverricht-Lundborg type. We undertook a comprehensive analysis of the genomic sequence to address the evolutionary events of this variable repeat. By examination of a contiguous genome sequence spanning 5.0 kb and linkage analysis of detected polymorphic changes, we identified six major intragenic haplotypes in unrelated Japanese subjects. The number of normal repeats was closely correlated with these alleles, indicating that changes in the array should be comparatively rare events during human evolution. To examine the origin of the repeat array further, we also analyzed five primate genomes. Repetitive polymorphism was unlikely in hominoids, and the array originated with the dodecamer itself in the course of primate evolution. The variability conceivably developed after the separation to humans.

Evolutionary behavioral genetics in Drosophila

Behavioral genes have a special evolutionary interest because they are potentially involved in speciation and in many forms of adaptation. Dozens of loci affecting different aspects of behavior have been already identified and cloned in Drosophila. Some of these genes determine variation in such ethologically complex phenotypes as the male "love song" that is produced during courtship and the locomotor "sleep-wake" activity cycles that are controlled by the circadian clock. Although the evolutionary analysis of most behavioral genes in Drosophila is relatively new, it has already given important insights into the forces shaping the molecular variation at these loci and their functional consequences.

Microsatellite structures in the context of human evolution

Six microsatellite - or short tandem repeat (STR) - systems with uniform repetitive sequences (HumTH01, HumCD4, HumFES/FPS, HumF13B, HumTPO, HumLPL) and three compound repeat systems (HumVWA, HumFIBRA, D21S11) were used, including data from the literature, to determine genetic distances among eight populations worldwide. The TH01- and VWA homologous loci in nonhuman primates (chimpanzees, gorillas, orangutans, rhesus monkeys, ring-tailed lemurs) were compared and found to be shorter than in humans. Microsatellites of lower complexity were most efficient for the separation of major ethnic groups. The loci of higher complexity showed a leveling of the diversity differences among populations, which could be attributed to higher mutation rates.

MSY2: a slowly evolving minisatellite on the human Y chromosome which provides a useful polymorphic marker in Chinese populations

We present the second human Y-specific minisatellite, MSY2 (DYS440). It consists of three or four copies of a 99-110bp repeat unit and is located about 1kb upstream of the DBY gene. The most common allele contains four units, but a three-unit allele has arisen on at least four occasions; in chimpanzees and orangutans, MSY2 contains only two units. It is therefore evolving slowly and provides a particularly useful polymorphic marker for Chinese populations.

High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot

Little is known about the fine-scale distribution of meiotic crossovers in human chromosomes. Methods have therefore been developed for detecting and mapping recombination products directly in human sperm DNA. Analysis of crossovers adjacent to the GC-rich minisatellite MS32, which is known to mutate by conversion and crossover within the repeat array, revealed an intense and highly localized recombination hotspot centered upstream of the locus and extending into the beginning of the minisatellite. Allele-specific cosuppression of crossovers and repeat instability suggests that the hotspot is responsible for driving repeat turnover at MS32 and thus that minisatellites might evolve as by-products of localized meiotic recombination in the human genome.

A minisatellite sequence within the propeptide region of the vacuolar carboxypeptidase Y gene of Schizosaccharomyces pombe

We describe the presence of a minisatellite sequence that displays length polymorphisms in the fission yeast Schizosaccharomyces pombe. The minisatellite sequence was found to reside within the propeptide region of the vacuolar carboxypeptidase Y gene. The minisatellite sequence, which was found only at a single locus, was mitotically stable and displayed length polymorphisms between the two varieties of S. pombe (S. pombe var. pombe and S. pombe var. malidevorans). The minisatellite sequence, however, appeared to be species specific and was absent in other members of the Schizosaccharomyces genus. This report constitutes the first experimental demonstration of the presence of such sequences in yeasts.

Isolation and characterization of mouse minisatellites

Minisatellites provide the most informative system for analyzing processes of tandem repeat turnover in humans. However, little is known about minisatellites and the mechanisms by which they mutate in other species. To this end, we have isolated and characterized 76 endogenous mouse VNTRs. Fifty-one loci have been localized on mouse chromosomes and, unlike in humans, show no clustering in proterminal regions. Sequence analysis of 25 loci revealed the majority to be authentic minisatellites with GC-rich repeat units ranging from 14 to 47 bp in length. We have further characterized 3 of the most polymorphic loci both in Mus musculus subspecies and in inbred strains by using minisatellite variant repeat mapping (MVR) by PCR to gain insight into allelic diversity and turnover processes. MVR data suggest that mouse minisatellites mutate mainly by intra-allelic nonpolar events at a rate well below 10(-3) per gamete, in contrast to the high-frequency complex meiotic gene conversion-like events seen in humans. These results may indicate a fundamental difference in mechanisms of minisatellite mutation and genome turnover between mice and humans.

Factors affecting levels of genetic diversity in natural populations

Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered 'normal', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be envisioned in which the process could provide intrinsic impetus to speciation.

Proceedings of the 4th International DNA Fingerprinting Conference. Melbourne, Australia, December 2-7, 1996

Minisatellites provide not only the basis for DNA fingerprinting and DNA profiling but also extremely informative systems for analysing processes of tandem repeat turnover in the human genome. Minisatellite instability appears to involve distinct mutation processes in somatic and germline cells; in the germline, mutation is frequently dominated by inter-allelic conversion-like events most likely occurring at meiosis and apparently regulated by cis-acting mutation initiator elements. Attempts to define these initiators in transgenic mice have so far been thwarted by what appears to be a major human/mouse barrier to the inter-species transfer of repeat instability. Minisatellites not only show high frequency spontaneous mutation in the germline, but also appear to be very sensitive to mutation induction by ionizing radiation, both in experimentally irradiated mice and in human populations exposed following the Chernobyl disaster; the mechanisms of mutation induction by radiation remain enigmatic.

Mini- and microsatellites

While the faithful transmission of genetic information requires a fidelity and stability of DNA that is involved in translation into proteins, it has become evident that a large part of noncoding DNA is organized in repeated sequences, which often exhibit a pronounced instability and dynamics. This applies both to longer repeated sequences, minisatellites (about 10-100 base pairs), and microsatellites (mostly 2-4 base pairs). Although these satellite DNAs are abundantly distributed in all kinds of organisms, no clear function has been discerned for them. However, extension of trinucleotide microsatellite sequences has been associated with several severe human disorders, such as Fragile X syndrome and Huntington's disease. Rare alleles of a minisatellite sequence have been reported to be associated with the ras oncogene leading to an increased risk for several human cancers. A dynamic behavior of repeated DNA sequences also applies to telomeres, constituting the ends of the chromosomes. Repeated DNA sequences protect the chromosome ends from losing coding sequences at cell divisions. The telomeres are maintained by the enzyme telomerase. Somatic cells, however, lose telomerase function and gradually die. Cancer cells have activated telomerase and therefore they acquire immortality.

Length and sequence variation in D7S22 (g3) alleles studied by high resolution length measurements and nucleotide sequencing

In a study of DNA sequence and length variation in the repeat array of small D7S22 alleles, 100 alleles typed as the common 14 repeat allele (14R) and 92 rare ones were selected for further characterization. A polymerase chain reaction (PCR) based allele length measurement method revealed a discontinuous distribution of alleles. The 92 rare alleles were grouped by their number of repeats. All, except four 6R alleles were distributed within the 11R-19R allele groups. The 14Rs revealed no further length variation while 7 out of the 92 rare alleles showed small length deviations from the other alleles within their respective groups. Nucleotide sequencing of the repeat array was performed in 17 alleles selected from each of the nine allele groups. The micro length variation within allele groups was caused by the presence of either 33, 36 or 37 bp repeats in given positions. A comparison of three 14Rs revealed no further sequence variation between these. Nine out of the fourteen repeats in the 14R differed in sequence and/or size. Based on this difference the repeat array sequence was converted into a code of different variant repeats. The 6R showed a variant repeat code quite unlike that of the 14R, while the encoded allele structure of the other rare alleles suggested that most of them may have evolved from a 14R allele by deletion or duplication of repeat units. Nucleotide sequencing of progenitor and mutant in a D7S22 de novo mutation as well as typing in a polymorphic site near the repeat array suggested that the event was an intra-allelic deletion of exactly three repeats. The present findings indicate that the 14R is ancestral to most rare small alleles, and that mutations in small alleles most often are intra-allelic events leading to a change in bp size equal to an integer number of repeats.

PCR amplification of a polymorphic minisatellite VNTR locus in whiting (Merlangius merlangus L.)

An approach has been developed for the screening of allelic variation of minisatellite DNA loci that substantially reduces the time and hazards involved. Primers were designed for a minisatellite region isolated from a gadoid fish species (Merlangius merlangus L.), enabling amplification by polymerase chain reaction, so that differences in the number of minisatellite repeat units (allelic variability) were detectable by ethidium bromide fluorescence (over UV light) following separation by agarose gel electrophoresis. This amplifiable minisatellite variable number tandem repeat region, the first non-primate marker of its kind can be used successfully with DNA extracted by a rapid Chelex protocol. From a sample of 97 individuals, 24 alleles were resolved (750-2200 kb) and heterozygosity was estimated at 0.94.

Distribution of tandem repeat polymorphism within minisatellite MS621 (D5S110)

The minisatellite MS621 (D5S110) is a highly polymorphic tandem repeat locus which maps to the distal region of human chromosome 5p. Major repeat unit variants at D5S110 differ not by base substitutions but by differences in the repetition of an 11 bp sequence motif found within each repeat. The two major classes of repeat unit thus contain two ('dimeric' = D-type) or three ('trimeric' = T-type) copies of this short motif. Mapping the distribution of these D- and T-type repeat units within alleles has allowed the analysis of the structural basis of allelic variation and of one de novo mutation. In contrast to previous studies of some other highly polymorphic minisatellites, this analysis provided no clear evidence for polarized variability at D5S110.

Population study of 3 STR loci in the Basque Country (northern Spain)

The tetrameric STRs, HUMTH01, HUMVWA31A and HUMFES/FPS, were studied in a population from the Basque Country (northern Spain) for their frequency distribution and applicability to identity and paternity testing. All systems conformed to Hardy-Weinberg equilibrium; pairwise comparisons demonstrated the allelic independence between loci, and furthermore, all systems seemed to be in agreement with expectations from the Stepwise Mutation Model (SMM) of the mutation-drift theory, which indicates the homogeneity of the population and suggests a replication slippage mechanism as a possible model for generating alleles. A comparison with other population groups appeared to indicate that frequencies are well conserved in Caucasians, but differ from other racial groups. The calculated parameters "a priori probability of exclusion" (PEX) and "index of discrimination" (ID), show the informativeness of these loci for the determination of identity and relatedness of individuals.

PCR amplification of intergenic spacers in the ribosomal DNA of Drosophila melanogaster reveals high levels of turnover in length and copy-number of spacers in geographically separated populations

A recently described PCR-based method for the analysis of intergenic spacer (IGS) length variation in the ribosomal (r) DNA of Drosophila melanogaster was used to analyse the distribution of IGS length variants in the rDNA of a number of recently collected D. melanogaster populations. One group of populations, from Europe and North Africa, was shown to have low intrapopulation IGS length variation following maintenance of massed populations in the laboratory for an extended period. However, a greater degree of IGS profile variability was detected at a number of levels in the majority of laboratory-maintained isofemale lines from two of these populations plus a second group of populations which were collected more recently from the eastern coast of Australia; all of which were immediately divided into isofemale lines following collection. Interestingly, PCR analysis of pooled DNA extracts from 30 individuals of either sex showed almost identical PCR profiles from each of the Australian populations. These preliminary results are discussed with regard to the possible combinations of forces (natural selection, neutral drift and genomic molecular drive) on the patterns of IGS length variation.

Recent observations in human DNA-minisatellite mutations

We report maternal and paternal mutation rates at loci D1S7 (MS1), D7S21 (MS31), D12S11 (MS43A), and D7S22 (G3). The respective mutation rates were as follows: [table: see text] At loci D7S21, D12S11, and D7S22 statistically significant differences in mutation rates exist between the sexes. No such difference was observed at locus D1S7. However inspection of the latter data reveals that by mutation at spermiogenesis approximately two-thirds of the fragments showed an addition of repetitive units, while a 50: 50 ratio was encountered in the series of maternal mutations. We also report the observation of naturally occurring 3-fragment patterns.

Microsatellite polymorphisms reveal phylogenetic relationships in primates

We amplified, via PCR, DNA segments from intron 1 of the tyrosine hydroxylase gene (TH01) and intron 40 of the von Willebrand factor gene (VWA) in ten nonhuman primate genera. In humans both introns contain polymorphic microsatellites with tetrameric repeats. Compared to the allelic ranges in human populations relatively short repeat arrays could be detected for the nonhuman primates typed, presumably reflecting an ancient precursor state at both microsatellite loci. Furthermore, our results provide evidence for an association of the average number of repeats present in different primate genera and their divergence time from man. DNA sequencing of VWA orthologues revealed a relatively high variability in the arrangement of repeats in the 5'-repeat arrays, the generation of which could probably be explained by polar mutational events.

Microsatellite evolution--evidence for directionality and variation in rate between species

Microsatellite DNA sequences are rapidly becoming the dominant source of nuclear genetic markers for a wide range of applications, from genome mapping to forensic testing to population studies. If misinterpretation is to be avoided, it is vital that we understand fully the way in which microsatellite sequences evolve. We have therefore compared allele length distributions for 42 microsatellites in humans with their homologues in a range of related primates. We find a highly significant trend for the loci to be longer in humans, showing that microsatellites can evolve directionally and at different rates in closely related species.

Characterisation of a novel minisatellite that provides multiple splice donor sites in an interferon-induced transcript

Nucleotide sequence features of the human interferon-inducible gene 6-16 are described and include, within a CpG island, a partially expressed minisatellite consisting of 26 tandemly repeated dodecanucleotides. The repeat unit consensus sequence (CAGGTAAGGGTG) is similar to the mammalian splice donor consensus sequence [(A/C)AGGT(A/G)AGT]. The splice donor site of exon 2, as determined previously, forms part of the most upstream of the repeat units. We show that the two neighbouring repeat units also provide functional splice donor sites effectively extending exon 2 by 12 or 24 nt and inserting four or eight amino acids respectively into the predicted gene product. A similar pattern of differently spliced transcripts is detected in several human cell types. Both the number of repeat units per allele and the nucleotide sequence itself show limited polymorphism within the human population. Similar minisatellites from nonhuman primates are described and also appear to modulate splicing of a 6-16 transcript. The 6-16 minisatellite is therefore an example of tandemly repeated DNA that has a role in gene expression and may provide a useful in vivo system for the analysis of 5' splice site choice and minisatellite biology.

Evolution of a repeat sequence in the parathyroid hormone-related peptide gene in primates

A polymorphism of the variable number of tandem repeat (VNTR) type is located 97 bp downstream of exon VI of the parathyroid hormone-related peptide (PTHrP) gene in humans. The repeat unit has the general sequence G(TA)nC, where n equals 4-11. In order to characterize the evolutionary history of this VNTR, we initially tested for its presence in 13 different species representing four main groups of living primates. The sequence is present in the human, great apes, and Old World monkeys, but not in New World monkeys; and this region failed to PCR amplify in the Loris group. Thus, the evolution of the sequence as part of the PTHrP gene started at least 25-35 millions years ago, after divergence of the Old World and New World monkeys, but before divergence of Old World monkeys and great apes and humans. The structural changes occurring during evolution are characterized by a relatively high degree of sequence divergence. In general, the tandem repeat region tends to be longer and more complex in higher primates with the repeat unit motifs all being based on a TA-dinucleotide repeat sequence. Intra-species variability of the locus was demonstrated only in humans and gorilla. The divergence of the TA-dinucleotide repeat sequence and the variable mutation rates observed in different primate species are in contrast to the relative conservation of the flanking sequences during primate evolution. This suggests that the nature of the TA-dinucleotide repeat sequence, rather than its flanking sequences, is responsible for generating variability.(ABSTRACT TRUNCATED AT 250 WORDS)

Association of the alpha-adducin locus with essential hypertension

Previous studies on genetic rat hypertension have shown that polymorphism within the alpha-adducin gene may regulate blood pressure. Adducin is a cytoskeletal protein that may be involved in cellular signal transduction and interacts with other membrane-skeleton proteins that affect ion transport across the cell membrane. There is a high homology between rat and human adducin and pathophysiological similarities between the Milan hypertensive rat strain and a subgroup of patients with essential hypertension. Thus, we designed a case-control study to test the possible association between the alpha-adducin locus and hypertension. One hundred ninety primary hypertensive patients were compared with 126 control subjects. All subjects were white and unrelated. Four multiallelic markers surrounding the alpha-adducin locus located in 4p16.3 were selected: D4S125 and D4S95 mapping at 680 and 20 kb centromeric, and D4S43 and D4S228/E24 mapping at 660 and 2500 kb telomeric. Alleles for each marker were pooled into groups. Comparisons between control subjects and hypertensive patients were carried out by testing the allele-disease association relative to the marker genotype. The maximal association occurred for D4S95 (chi 2(1) 13.33), which maps closest to alpha-adducin. These data suggest that a polymorphism within the alpha-adducin gene may affect blood pressure in humans.

Human (Homo sapiens) and chimpanzee (Pan troglodytes) share similar ancestral centromeric alpha satellite DNA sequences but other fractions of heterochromatin differ considerably

The euchromatic regions of chimpanzee (Pan troglodytes) genome share approximately 98% sequence similarity with the human (Homo sapiens), while the heterochromatic regions display considerable divergence. Positive heterochromatic regions revealed by the CBG-technique are confined to pericentromeric areas in humans, while in chimpanzees, these regions are pericentromeric, telomeric, and intercalary. When human chromosomes are digested with restriction endonuclease AluI and stained by Giemsa (AluI/Giemsa), positive heterochromatin is detected only in the pericentromeric regions, while in chimpanzee, telomeric, pericentromeric, and in some chromosomes both telomeric and centromeric, regions are positive. The DA/DAPI technique further revealed extensive cytochemical heterogeneity of heterochromatin in both species. Nevertheless, the fluorescence in situ hybridization technique (FISH) using a centromeric alpha satellite cocktail probe revealed that both primates share similar pericentromeric alpha satellite DNA sequences. Furthermore, cross-hybridization experiments using chromosomes of gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) suggest that the alphoid repeats of human and great apes are highly conserved, implying that these repeat families were present in their common ancestor. Nevertheless, the orangutan's chromosome 9 did not cross-hybridize with human probe.

The evolutionary dynamics of repetitive DNA in eukaryotes

Repetitive DNA sequences form a large portion of the genomes of eukaryotes. The 'selfish DNA' hypothesis proposes that they are maintained by their ability to replicate within the genome. The behaviour of repetitive sequences can result in mutations that cause genetic diseases, and confer significant fitness losses on the organism. Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA.

Minisatellite isoalleles can be distinguished by single-stranded conformational polymorphism analysis in agarose gels

Minisatellite isoallelism, i.e. the occurrence of minisatellite alleles with different internal sequence composition but indistinguishable length, is a common limitation of minisatellite allele length analysis. Internal sequence variation can be used to distinguish such isoalleles, provided that detailed sequence knowledge of its basis is available. We now show that minisatellite isoalleles can also be simply resolved by single-stranded conformational polymorphisms (SSCP) arising during agarose gel electrophoresis. SSCP on agarose gels can be used to distinguish minisatellite isoalleles either after PCR amplification, or by standard Southern blot analysis of genomic DNA.

Structure of the smallest salivary-gland secretory protein gene in Chironomus tentans

The salivary gland secretion in the dipteran Chironomus tentans is composed of approximately 15 different secretory proteins. The most well known of the corresponding genes are the four closely related Balbiani ring (BR) genes, in which the main part of each approximately 40-kb gene is composed of tandemly arranged repetitive units. Six of the seven additional secretory protein genes described share structural similarities with the BR genes and are members of the same BR multigene family. Here we report the identification of a new secretory protein gene, the sp12 gene, encoding the smallest component of the C. tentans salivary gland secretion. The gene has a corresponding mRNA length of approximately 0.7 kb and codes for a protein with a calculated molecular weight of 7,619 Da. The sp12 gene was characterized in seven Chironomus species. Based on a comparison of the orthologous gene sequences, we conclude that the sp12 gene has a repetitive structure consisting of diverged 21-bp-long repeats. The repeat structure and the codon composition are similar to the so-called SR regions of the BR genes and the sp12 gene may represent a diverged member of the BR multigene family.

Complex gene conversion events in germline mutation at human minisatellites

Mutation at the human minisatellites MS32, MS205 and MS31A has been investigated by characterizing mutant alleles in pedigrees and in the case of MS32 by direct analysis of mutant molecules in single sperm. Most mutations at all three loci are polar, involving the preferential gain of a few repeat units at one end of the tandem repeat array. Incoming repeats can be derived from the same allele or the homologous chromosome, through they are frequently rearranged during mutation. Lack of exchange of flanking markers suggests the involvement of complex conversion-like events in the generation of mutant alleles. At MS32, high frequency mutation processes in sperm appear to be largely germline specific and to occur at a constant rate irrespective of allele size. Together with mutational polarity, this implies that germline instability is controlled by elements outside the tandem repeat array.

A subterminal satellite located adjacent to telomeres in chimpanzees is absent from the human genome

One of the significant unresolved differences between the karyotypes of humans and African apes is the presence of positively staining G-bands at the ends of many chromosome arms in the chimpanzee and gorilla but absent from human chromosomes. Using a telomere anchored PCR strategy, we have isolated DNA from a subterminal satellite, composed of a 32 basepair A-T rich repeat, from the chimpanzee genome that hybridizes to all the additional terminal bands and at two interstitial sites. The satellite is more abundant in gorillas and is not detected in humans or orangutans. Furthermore, there is no similarity between other chimpanzee telomere-junction clones and human subterminal sequences, and therefore the organization of sequences adjacent to telomeres is very different between these closely related primates.

Origins of polymorphism at a polypurine hypervariable locus

We present characterisation of a hypervariable locus, D8S210, mapped to the telomeric region of the short arm of chromosome 8. The locus is highly polymorphic with alleles varying in size from 1.8 kb to 24 kb. Sequence data from 7 alleles shows that the variable region is entirely polypurine on one strand with a tetranucleotide repeating unit GGAA at the margins and diverged versions of this motif internally. The margins are conserved between alleles; polymorphism occurring in the internal regions of the repeat. Alleles are inherited in a Mendelian manner and one new mutation has been observed in analysis of 51 meioses. Use of single copy flanking sequences to elaborate the polymorphism revealed loss of single copy DNA in 3 unrelated families and in 2 other unrelated individuals. Restriction mapping shows that this loss is similar for different sized alleles in all three families suggesting that it was an early event that may have involved a flanking Alu sequence. We present evidence that the polypurine region can adopt triplex conformations in vitro. Such structures may facilitate loss or gain of unique sequences in the genome, contribute to mutation at conformation transition points and drive the hypervariability (> 99% heterozygosity) of this locus.

Analysis of apoB, HLADQ alpha, and D1S80 polymorphisms in the Italian population using the polymerase chain reaction

Allele and genotype frequencies of three highly polymorphic loci (apoB, HLADQ alpha, D1S80) have been determined in an Italian sample using the polymerase chain reaction (PCR) amplification and non-radioactive detection. The allele frequencies ranged from 0.1% to 39%, with an average heterozygosity of 0.74 and a power of discrimination ranging from 0.90 to 0.98. These results are of value for forensic and genetic studies. © 1992 Wiley-Liss, Inc.

Minisatellite binding protein Msbp-1 is a sequence-specific single-stranded DNA-binding protein

Msbp-1 is a minisatellite-specific DNA-binding protein. Using synthetic binding substrates, we now show that Msbp-1 binds not to double-stranded DNA, but exclusively to single-stranded DNA. Binding is specific to the guanine-rich strand of the minisatellite duplex, interactions with the cytosine-rich strand being undetectable by southwestern analysis. Furthermore, the binding site required for successful DNA-protein interactions appears to be two or more minisatellite repeat units. We have also isolated, by whole-genome PCR and cloning, one Msbp-1 binding site from the human genome. Again, the binding strand of this molecule contains a repetitive G-rich structure equivalent to that of a small minisatellite. These observations are discussed with respect to other single-stranded DNA-binding proteins known to play a role in recombination processes.

Minisatellite repeat coding as a digital approach to DNA typing

Most DNA typing systems used in forensic and legal medicine assay allelic length variation at tandem repetitive DNA regions such as minisatellites. A simple alternative approach that displays patterns of variant repeat units along minisatellite alleles is described here. This produces DNA profiles as extraordinarily variable digital sequences appropriate for forensic investigations, including computer databasing, and for analysing allele diversity and the role of recombination in minisatellite instability.

Spontaneous mutation at the hypervariable mouse minisatellite locus Ms6-hm: flanking DNA sequence and analysis of germline and early somatic mutation events

Hypervariability at minisatellite loci is maintained by spontaneous mutation to new-length alleles. At the most variable loci, mutation rate is directly measurable by pedigree analysis. The mouse minisatellite locus Ms6-hm has a germline mutation rate of 2.5% per gamete and is therefore one of the most unstable loci yet identified in the mouse genome. Mutation events at this locus also occur during early mouse development, resulting in mice mosaic for cells carrying a common non-parental allele in different somatic tissues and the germline. The DNA sequence flanking Ms6-hm is rich in dispersed repetitive elements; the minisatellite array has expanded from within a member of the Mouse Transcript family which is flanked by two additional Mouse Transcript elements, and a B2 element lies further 3' to the minisatellite. To define the characteristics of mutation events at Ms6-hm we have analysed 19 germline and 13 somatic length-change events. Germline mutation events at Ms6-hm are not accompanied by the exchange of flanking markers in three informative mutant alleles analysed.

Multilocus and single locus minisatellite analysis in population biological studies

In this review we describe the situations in which minisatellite analysis is of value to studies of population and evolutionary biology. Evolutionary and population biologists need to be able to quantify genetic relationships among individual organisms at many different levels, from close familial relationships to evolutionarily distant phylogenetic ones. The use of minisatellite markers is put into this context and compared with the other molecular biological techniques. Examples of the use of multilocus minisatellite analysis in population biology are described. The limitations of multilocus fingerprinting are presented, together with the potential advantages of locus-specific probes. The use of locus-specific probes in population biology is now often feasible due to the recent development of a cloning system which allows their efficient isolation. The availability of locus-specific probes should significantly expand the role of minisatellite markers in population biology.