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PubMed2006

Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori.

BACKGROUND: Population structures are normally determined using genes under minimal functional selection. In this study we have assessed genes that are not always essential, show differences in alleles between strains, and are involved in the directly host-selectable phenotype of LPS biosynthesis. RESULTS: Eight complete LPS biosynthesis genes, seven of which are associated with phase variation in some or all strains of Helicobacter pylori, have been sequenced and their divergence analyzed. The differences observed indicate that recombination within these genes largely reflects exchange between strains within the population lineages previously determined on the basis of MLST using housekeeping genes. This indicates that the differences that are used for MLST are likely to broadly associate with genes under functional selection, and differences in strain behaviour. However, instances of exchange between the subpopulations were identified, including the hpAfrica2 subpopulation. Further, there were other differences in gene complements and the chromosomal location of genes indicative of greater diversity within the population than is revealed by the available genome sequences and comparative genome hybridization studies. CONCLUSION: These results indicate that the described population structure based upon MLST is broadly a good basis for studying the biology of H. pylori, but that individual alleles may not follow these associations. As a consequence, when working in unsequenced strains, it is necessary to carefully check the presence, sequence, and distribution of any individual gene of interest.

Alleles↗
PubMed2001

Antigenic variation of Anaplasma marginale: major surface protein 2 diversity during cyclic transmission between ticks and cattle.

The rickettsial pathogen Anaplasma marginale expresses a variable immunodominant outer membrane protein, major surface protein 2 (MSP2), involved in antigenic variation and long-term persistence of the organism in carrier animals. MSP2 contains a central hypervariable region of about 100 amino acids that encodes immunogenic B-cell epitopes that induce variant-specific antibodies during infection. Previously, we have shown that MSP2 is encoded on a polycistronic mRNA transcript in erythrocyte stages of A. marginale and defined the structure of the genomic expression site for this transcript. In this study, we show that the same expression site is utilized in stages of A. marginale infecting tick salivary glands. We also analyzed the variability of this genomic expression site in Oklahoma strain A. marginale transmitted from in vitro cultures to cattle and between cattle and ticks. The structure of the expression site and flanking regions was conserved except for sequence that encoded the MSP2 hypervariable region. At least three different MSP2 variants were encoded in each A. marginale population. The major sequence variants did not change on passage of A. marginale between culture, acute erythrocyte stage infections, and tick salivary glands but did change during persistent infections of cattle. The variant types found in tick salivary glands most closely resembled those present in bovine blood at the time of acquisition of infection, whether infection was acquired from an acute or from a persistent rickettsemia. These variations in structure of an expression site for a major, immunoprotective outer membrane protein have important implications for vaccine development and for obtaining an improved understanding of the mechanisms of persistence of ehrlichial infections in humans, domestic animals, and reservoir hosts.

Anaplasma↗
PubMed1990

Repeat unit sequence variation in minisatellites: a novel source of DNA polymorphism for studying variation and mutation by single molecule analysis.

Variation in internal minisatellite structure can be analyzed by mapping variant repeat units within amplified alleles. A system capable of distinguishing greater than 10(70) allelic states at the human hypervariable locus D1S8 has been developed. Population surveys of internal allelic structure indicate that D1S8 alleles evolve rapidly along haploid chromosome lineages. Internal mapping of deletion mutant alleles physically selected from genomic DNA provides further evidence that germline and somatic mutations altering the number of allelic repeat units seldom if ever arise by unequal exchange between alleles. The existence of low level germline mosaicism for new mutants further indicates that many germline mutation events are premeiotic. Physical selection of new mutants also allows minisatellite mutation rates to be estimated directly in human DNA.

Alleles↗
PubMed2004

Phenotypic stability of the P-M system in wild populations of Drosophila melanogaster.

The P element appears to be one of the most recently invaded transposons of D. melanogaster. To study the dynamics and long-term fate of P elements in natural populations of D. melanogaster, 472 isofemale lines newly collected from 27 localities of Japan were examined for the P element-associated characteristics (abilities to induce and repress of P element transposition) and genomic P element composition (size classes and their numbers). There was variation in the P element-related phenotypes among local populations, but genomic P composition did not correlate strongly with the phenotype of each line: full-size P and KP elements predominated in their genomes (FP+ KP predominance). Comparison with previous results suggests a stability in the P-M system in local populations over about 15 years. In some populations, phenotypic stability for particularly long times was found: for 30 years or more Q strains predominated in Hikone and Tanushimaru, P or Q strains around Inakadate, and M' or Q strains around Tozukawa. There was no clear evidence of structural destruction underlying functional variation of P elements during this period. These results suggest that the current evolutionary status of P elements in the gene pool of D. melanogaster is not intermediary stage predicted by the original recent invasion hypothesis, and that several other factors such as the position effect play important roles.

Animals↗
PubMed1988

Toward a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S. choleraesuis, S. derby, S. dublin, S. enteritidis, S. heidelberg, S. infantis, S. newport, and S. typhimurium.

Variation in the chromosomal genomes of 1527 isolates of eight common serotypes (O and H antigen profiles) of Salmonella was assessed by analysis of electrophoretically demonstrable allelic polymorphism at 23 metabolic enzyme loci. Seventy-one distinctive electrophoretic types, representing multilocus genotypes, were identified. A basically clonal population structure was indicated by the presence of strong linkage disequilibrium among enzyme loci, the association of each serotype with a relatively small number of multilocus enzyme genotypes, and the global distribution of certain genotypes. For each of six of the serotypes, 83-96% of isolates were members of a single clone. The occurrence of each of four serotypes (S. derby, S. enteritidis, S. infantis, and S. newport) in isolates of clones belonging to several evolutionary lineages, some of which are distantly related, suggests that the horizontal transfer and recombination of chromosomal genes mediating expression of cell-surface antigens has been a significant process in the evolution of the salmonellae. Two divergent clone clusters of S. derby differ in the relative frequency with which they cause disease in birds versus mammals, and two major lineages of S. newport differ in the frequency with which their clones are associated with disease in humans versus animals.

Alleles↗
PubMed2026

Comparative genomics and phenotypic divergence of ERIC I and ERIC II genotypes of Paenibacillus larvae, the causative agent of American Foulbrood disease.

Honeybees of the species Apis mellifera are important pollinators of crops and wild plants. Paenibacillus larvae, a spore-forming bacterium, is a problematic pathogen that causes American foulbrood (AFB) in honeybee larvae worldwide. In many countries, AFB is a notifiable disease, requiring the destruction of diseased colonies, resulting in economic loss that impacts beekeeping and agriculture. Disease onset starts with larval ingestion of P. larvae spores, which germinate into growing cells that proliferate in the larval gut, leading to larval death and eventually bee colony collapse. As infection progresses, P. larvae produce spores, reinitiating the disease cycle. Thus, growth, sporulation and germination underlie AFB. In this study, using various microbiological assays, quantitative cell biology methods, transmission electron microscopy and genomics, we sought to identify genetic and phenotypic characteristics associated with the predominant ERIC I and ERIC II genotypes of P. larvae during growth, sporulation and germination. Extending previous findings, our data identify genetic differences between ERIC I and ERIC II strains and some genetic variation between strains of the same ERIC type. Furthermore, we describe significant differences in cellular morphology during growth, differences in spore envelope structure and differences in germination efficiency between ERIC I and ERIC II genotypes. Collectively, our findings improve understanding of P. larvae biology and provide a foundation for developing genotype-specific disease management strategies for AFB.

Animals↗
PubMed2026

The Charcot-Marie-Tooth Neuropathy (CMTX3) Complex Structural Variation Causes Differential SOX3 Spatiotemporal Expression.

Charcot-Marie-Tooth (CMT) neuropathy is a clinically and genetically heterogeneous group of diseases characterized by the length-dependent axonal degeneration of peripheral nerves. We previously mapped a rare form of X-linked CMT, CMTX3, to a 5.7-Mb interval on chromosome Xq26.3-q27.1 and excluded the coding region of all known genes in the linkage interval for mutations. Whole genome sequencing subsequently identified a 78-kb region of chromosome 8q24.3 that had been duplicated and inserted into the CMTX3 locus between the genes HAPSTR2 and SOX3. The 78-kb insertion, which contains a partial transcript of ARHGAP39, fully segregated in families with CMTX3 and was absent in neurologically normal controls. To retain the CMTX3 insertion and investigate its consequences in appropriate neuronal tissue, we generated induced pluripotent stem cells (iPSCs) from CMTX3 fibroblasts. Using bulk RNA sequencing of patient-derived spinal motor neurons, ARHGAP39 was deemed nonpathogenic by excluding both the formation of novel fusion transcripts and dosage effects from the partial duplication. Subsequent NanoString expression analyses of candidate genes within the CMTX3 locus, across different stages of neuronal differentiation, identified spatiotemporal dysregulation of SOX3. NanoString showed reduced SOX3 expression in patient iPSCs. RNA sequencing detected SOX3 downregulation in CMTX3 neuroepithelial progenitor cells, which was further confirmed by quantitative proteomics. Given the early onset and relatively rapid progression of CMTX3, these data prioritise SOX3 as a leading candidate gene, consistent with its role as one of the earliest transcription factors expressed in the developing nervous system and a key regulator of neuronal fate.

Humans↗
PubMed2004

Genetic characterization of equine arteritis virus during persistent infection of stallions.

Equine arteritis virus (EAV) causes a persistent infection of the reproductive tract of carrier stallions. The authors determined the complete genome sequences of viruses (CW96 and CW01) that were present 5 years apart in the semen of a carrier stallion (CW). The CW96 and CW01 viruses respectively had only 85.6 % and 85.7 % nucleotide identity to the published sequence of EAV (EAV030). The CW96 and CW01 viruses had two 1 nt insertions and a single 1 nt deletion in the leader sequence, and a 3 nt coding insertion in ORF1a; thus their genomes included 12 708 nt as compared to the 12 704 nt in EAV030. Variation between viruses present in the semen of stallion CW and EAV030 was especially marked in the replicase gene (ORF1a and 1b), and the greatest variation occurred in the portion of ORF1a encoding the nsp2 protein. The ORFs 3 and 5, which respectively encode the GP3 and GP5 envelope proteins, showed greatest variation amongst ORFs encoding structural EAV proteins. Comparative sequence analyses of CW96 and CW01 indicated that ORFs 1a, 1b and 7 were highly conserved during persistent infection, whereas there was substantial variation in ORFs 3 and 5. Although the variation that occurs in ORF5 results in the emergence of novel phenotypic viral variants as determined by neutralization assay, all variants were neutralized by high-titre polyclonal equine antisera, suggesting that immune evasion is unlikely to be responsible for the establishment of persistent EAV infection of carrier stallions. Northern blot analyses of RNA extracted from cell culture propagated viruses isolated from 10 different persistently infected stallions failed to demonstrate any large genomic deletions, suggesting that defective interfering particles are also unlikely to be important in either the maintenance or clearance of persistent EAV infection of the reproductive tract of carrier stallions.

Amino Acid Sequence↗
PubMed2026

Tryptophan-driven metabolomic shift in Acidobacteriaceae reveals phytohormones and antifungal metabolites.

UNLABELLED: Acidobacteriota is one of the most abundant phyla in soils and has recently attracted attention for its potential role in promoting phytosanitary benefits. The metabolomic capabilities of this phylum remain poorly characterized, with few experimentally confirmed metabolites described. To address these gaps, we combined untargeted metabolomic profiling with comparative genomic analyses to explore the functional potential of newly isolated Acidobacteriaceae strains. Genome mining across the Acidobacteriota phylum revealed the presence and taxon-specific enrichment of genes associated with plant-related traits, including phytohormone biosynthesis. In parallel, metabolomic analyses of OSMAC-derived extracts uncovered pronounced condition-dependent metabolic variation. Tryptophan supplementation was associated with marked metabolomic reprogramming, including changes in indole-derived metabolites, such as indole-3-acetic acid. Subsequent analyses linked these metabolic shifts to the suppression of phytopathogenic fungi and enabled the identification of malassezindoles and pityriacitrins as active compounds, confirmed by structure elucidation using NMR spectroscopy. Overall, these findings shed light on the previously unexplored metabolic potential of the Acidobacteriota phylum, emphasizing its ecological importance for phytosanitary applications. IMPORTANCE: Despite their ubiquity and genomic diversity, the functional metabolism of members of the Acidobacteriota has largely remained uncharacterized. This study links genomic predictions to experimentally verified metabolomic outputs of Acidobacteriaceae, demonstrating tryptophan-responsive metabolic shifts translating to phytohormones and metabolites suppressing fungal growth. Our work underscores the emerging role of Acidobacteriota as important contributors to soil ecosystem functioning and plant-microbe interactions.

Acidobacteriota↗
PubMed2004

HIV-1 Vpr: genetic diversity and functional features from the perspective of structure.

RNA viruses are well known for the enormous genetic variation. Retroviruses share this feature with other RNA viruses, and human immunodeficiency virus type 1 (HIV-1) has been extensively investigated in this regard. Based on the DNA sequence analysis, HIV-1 has been classified into three groups; M, N, and O, with viral subtypes in each group. While the genetic variation between viral isolates has been documented throughout the genome, specifically, the env gene exhibits high variation. Analysis of the env gene from the sequential samples from HIV-1-infected patients reveals variation in the range of 1% per year. The variation observed in individual HIV-1 genes in the form of changes at the nucleotide level, as expected, should result in one of the possible scenarios: (1) no change in the amino acid, (2) conservative change in the amino acid, (3) nonconservative change in the amino acid, and (4) premature stop codon resulting in a truncated protein. Hence, it is likely that the variation may impact on the function of the protein, depending on the nature of the mutation. The goal of this review is to summarize the polymorphisms in Vpr using the available sequence information and discuss their effects on the functions of Vpr from the point of view of its structure. The data generated by several groups provide a base for understanding the consequences of natural polymorphisms in specific regions of the Vpr molecule. However, it is also clear that secondary changes (second site or compensatory mutations) may modify the effect of a specific mutation and a comprehensive analysis is needed to delineate the role of specific residues in Vpr molecule. This is an area which, we hope, will attract investigators for further studies, and may provide information for understanding the molecular basis of Vpr functions.

Acquired Immunodeficiency Syndrome↗
PubMed2026

Mitochondrial genome-derived microsatellites reveal genetic diversity and population structure in Callery pear populations.

Callery pear (Pyrus calleryana Decne.; PC) possesses many desirable characteristics valued in managed landscapes. This has driven the release of numerous cultivars, including both hybrids and selections derived from native populations. The extensive planting of PC cultivars in managed areas has contributed to the widespread occurrence of invasive individuals across a broad range of habitats in the eastern United States (US). Self-incompatibility, tolerance to various environmental conditions, pathogen and pest resistance, intraspecific hybridization among the cultivars, possible interspecific hybridization with other Pyrus species, and seed dispersal by various vertebrates have contributed to the spread and persistence of PC across diverse environments. Because effective and environmentally appropriate management options remain limited, improved understanding of PC genetics may help inform management strategies. Previous studies have characterized PC diversity using nuclear genomic short sequence repeats (gSSRs), however, neither a mitochondrial genome resource nor mitochondrial short sequence repeats (mtSSRs) have been developed for this purpose. Here, we assembled a mitochondrial genome of 485,892 bp and used five mtSSRs to characterize mitochondrial diversity and population structure among accessions from the species' native range in Asia (n = 72), southeastern US escapees (SNesc; n = 90), Tennessee escapees (TNesc; n = 90), and US-released commercial cultivars (UScult; n = 69 representing 14 unique cultivars). We found a high genetic diversity (He = 0.728) and evidence of genetic structure in PC. In distance-based and multivariate analyses, UScult occupied an intermediate position between the Asian populations and the US escapees. The observed mitochondrial diversity among samples assigned to PC cultivars is consistent with a complex genetic landscape and may reflect distinct maternal lineages, cultivar-labeling or record-keeping discrepancies, and/or technical variation. This study underscores the need for broader genomic investigations using authenticated cultivar reference material and high-resolution nuclear markers to resolve cultivar ancestry, validate true-to-name identity, and inform species management.

Genetic Variation↗
PubMed1992

Marked variation in the size of genomic plasmids among members of a family of related Epstein-Barr viruses.

Epstein-Barr virus (EBV) genomes in the P3J-HR-1 (HR-1) Burkitt lymphoma cell line rearrange at a high rate. Previously described deletions and rearrangements in HR-1 cells have been found at sites of EBV replication in vivo, suggesting that DNA rearrangement may be an integral aspect of EBV biology and pathogenesis. We examined the structure of linear EBV genomes in subcultures of HR-1 cells using contour-clamped homogenous electric field gel electrophoresis. We developed a second pulsed electrophoretic technique to separate intracellular circular EBV plasmids. The standard, linear HR-1 EBV genome was approximately 155 kilobases in length. Linear molecules of less than unit length, presumably defective genomes, were seen in numerous subcultures. Linear intracellular genomes greater than 155 kilobases were also detected, but only linear genomes of 155 kilobases or less were packaged into virions. The size of circular EBV plasmids also varied greatly among HR-1 subcultures, some of which contained two plasmids of different size. The progeny of the unusual circular plasmids could be either standard or nonstandard linear genomes. No aberrant linear or circular form was detected in a subculture carrying the previously described het fragments. Pulsed-gel electrophoresis has provided two additional characteristics of mutant EBVs: abnormal linear and circular genome configurations.

Blotting, Southern↗
PubMed2000

Heterogeneity of chicken slow skeletal muscle troponin T mRNA.

The troponin T (TnT) transcripts in chicken slow skeletal muscle were characterized by S1 nuclease mapping and nucleotide sequencing of cDNA produced by RT-PCR and 5'-RACE. We found two kinds of transcripts in the 5'-region, one having the codon for alanine (position 135-137), C (258), and A (262) and the other lacking the codon and having T (258) and G (262) instead of C and A. In the 3'-region, we found four single base substitutions at 703 (T or C), 774 or T), 797 or T), and 827 (G or A). Four of the six substitutions lead to amino acid changes in chicken sTnT isoforms. We determined the genomic structure of the 3'-region of the chicken sTnT gene. The region includes 7 exons corresponding to position 249-891 of the chicken sTnT cDNA and no alternative exon, showing that the 3'-heterogeneity in sTnT transcripts was due to allelic variation. J. Exp. Zool. 286:149-156, 2000.

Amino Acid Sequence↗
PubMed2006

Genetic variation among isolates of Sarcocystis neurona, the agent of protozoal myeloencephalitis, as revealed by amplified fragment length polymorphism markers.

Sarcocystis neurona causes serious neurological disease in horses and other vertebrates in the Americas. Based on epidemiological data, this parasite has recently emerged. Here, the genetic diversity of Sarcocystis neurona was evaluated using the amplified fragment length polymorphism (AFLP) method. Fifteen S. neurona taxa from different regions collected over the last 10 years were used; six isolates were from clinically diseased horses, eight isolates were from wild-caught opossums (Didelphis virginiana), and one isolate was from a cowbird (Molothrus ater). Additionally, four outgroup taxa were also fingerprinted. Nine primer pairs were used to generate AFLP patterns, with a total number of amplified fragments ranging from 30 to 60, depending on the isolate and primers tested. Based on the presence/absence of amplified AFLP fragments and pairwise similarity values, all the S. neurona isolates tested were clustered in one monophyletic group. No significant correlation could be found between genomic similarity and host origin of the S. neurona isolates. AFLP revealed significant intraspecific genetic variations, and S. neurona appeared as a highly variable species. Furthermore, linkage disequilibrium analysis suggested that S. neurona populations within Michigan have an intermediate type of population structure that includes characteristics of both clonal and panamictic population structures. AFLP is a reliable molecular technique that has provided one of the most informative approaches to ascertain phylogenetic relationships in S. neurona and its closest relatives, allowing them to be clustered by relative similarity using band matching and unweighted pair group method with arithmetic mean analysis, which may be applicable to other related protozoal species.

Animals↗
PubMed1994

The regulatory complex of HLA class I promoters exhibits locus-specific conservation with limited allelic variation.

The extensive genetic polymorphism of the classical MHC class I molecules provides an important distinguishing feature of the host's immune system. They influence the selection and function of effector cells against tumor and virally infected cells. In these cells, class I molecules are often selectively suppressed. This suppression is locus specific and, in certain cases, allele specific. We analyzed the HLA class I promoter sequences that include class I regulatory complex (CRC) in a total of 41 well-characterized HLA homozygous B lymphoblastoid cell lines, using locus-specific oligonucleotide probes complementary to the overlapping CRC elements. These include kappa B1, kappa B2, IFN response sequence, the putative negative regulatory element, and the HLA counterpart of the H-2RII region that contains the retinoid x receptor beta binding motif. The CRC of HLA promoters displayed locus-specific conservation; however, limited allelic variation was observed in each of the cis elements. In some, variations were apparently generated by gene conversion. The palindromic kappa B1 site, which has an active role in enhancing promoter activity, was found to be conserved in almost all HLA-A and -B alleles, but not in HLA-C. The core DNA binding motif for retinoid x receptor beta was absent within the HLA CRC region. Sequence analysis of promoters from HLA-A31, -B13, and -Cw1 genomic clones, as well as pairwise interallelic and intra-allelic comparison with those of published alleles, showed that locus-specific conservation extended throughout the promoter sequences. Locus specificity and the allelic variation seen in the CRC regions may provide a structural basis for the selective modulation of HLA class I genes.

Alleles↗
PubMed2024

Activity, structure, and diversity of Type II proline-rich antimicrobial peptides from insects.

Apidaecin 1b (Api), the first characterized Type II Proline-rich antimicrobial peptide (PrAMP), is encoded in the honey bee genome. It inhibits bacterial growth by binding in the nascent peptide exit tunnel of the ribosome after the release of the completed protein and trapping the release factors. By genome mining, we have identified 71 PrAMPs encoded in insect genomes as pre-pro-polyproteins. Having chemically synthesized and tested the activity of 26 peptides, we demonstrate that despite significant sequence variation in the N-terminal sequence, the majority of the PrAMPs that retain the conserved C-terminal sequence of Api are able to trap the ribosome at the stop codons and induce stop codon readthrough-all hallmarks of Type II PrAMP mode of action. Some of the characterized PrAMPs exhibit superior antibacterial activity in comparison with Api. The newly solved crystallographic structures of the ribosome complexed with Api and with the more active peptide Fva1 from the stingless bee demonstrate the universal placement of the PrAMPs' C-terminal pharmacophore in the post-release ribosome despite variations in their N-terminal sequence.

Animals↗
PubMed1991

Regulation of elastin gene expression.

Recent isolation and characterization of cDNAs encompassing the full length of chicken, cow, and human elastin mRNA have led to the elucidation of the primary structure of the respective tropoelastins. Comparison of the tropoelastin from the different species has revealed that large segments of the sequence are conserved, but considerable variation also exists, ranging in extent from relatively small alterations, such as conservative amino acid substitutions, to large-scale deletions and insertions. Several distinct approaches have yielded compelling evidence of a single elastin gene per haploid genome. Analysis of the bovine and human elastin genes revealed that functionally distinct hydrophobic and cross-link domains of the protein are encoded in separate exons which alternate in the genes. The human gene contains 34 exons, the intron/exon ratio is unusually large (20:1), and the introns contain large amounts of repetitive sequences that may predispose to genetic instability. Comparison of the cDNA and genomic sequences has demonstrated that the primary transcript of both species is subject to considerable alternative splicing, which can account for the presence of multiple tropoelastin isoforms. It is likely that the conformation of elastin is, at least in part, that of a random coil, and therefore it might be expected that the stringency for conservation of the amino acid sequence would be less than that for other proteins with unique conformations. This suggests that functional elastin molecules that vary in their sequence and fitness may exist in the human population and be compatible with a normal life. Potentially though, these variations could have profound consequences on the properties of vital tissues found in the cardiovascular and pulmonary systems over the lifetime of the individual. Consequently, analysis of the structure of the elastin gene and its variation in what is regarded as the normal human population, rather than in those individuals with clearly heritable diseases, assumes greater importance. The 5'-flanking region of the gene is G + C rich and contains several SP-1 and AP2 binding sites, as well as putative glucocorticoid, cAMP, and TPA responsive elements, but no consensus TATA box or functional CAAT box. Primer extension and S1 mapping of the elastin mRNA indicated that transcription was initiated at multiple sites. Transfection experiments using promoter elements/reporter gene constructs demonstrated that the basic promoter element was found within region -128 to -1. In addition, three distinct up-regulatory and two down-regulatory regions were delineated. Taken together, these findings suggest that the regulation of elastin gene expression is complex and takes place at several levels.

Amino Acid Sequence↗
PubMed2002

Hypervariable locus of the 3'-flanking region of the neurotensin receptor gene: an effective region for personal identification in forensic practice.

We examined the complex short tandem repeat (STR) locus at the 3'-flanking region of the neurotensin receptor (NTR) gene. The polymorphism of this locus was first reported as a simple tetranucleotide repeat variation by Le et al., but it also offers a surprisingly informative variation, that permits reliable individual identification by two complementary strategies: fluorescent-labelled polymerase chain reaction (PCR)/electrophoresis and direct sequencing of the PCR products. We determined the alleles in 203 Japanese by fluorescent-labelled PCR/electrophoresis. Determination was based on their length with a reliability of +/-1 bp, and the frequency of each allele was very low. Sequencing analysis further grouped these alleles in detail. Sequencing demonstrated that the locus varied by six repetitive units and three insertion/deletion positions of nucleotide fragments. We detected multiple alleles having different structures even in the same allele length. We found structural differences in homozygous alleles having the same base pair size. We also determined that apparently homozygous alleles were heterozygous from sequencing electropherograms showing an overlap of nucleotides or +/-1 bp difference. These results indicate that this locus is structurally hypervariable in addition to having allelic length variations, promising a great advance in individual identification in forensic practice.

Alleles↗