Genetic Structure of the Volga–Ural and Central Asian Populations Inferred from the Data on Alu Polymorphism

NineAlu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga–Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga–Ural population (F _st = 0.061) was higher than for the populations of Central Asia (F _st = 0.024), Europe (F _st = 0.02), and Southeastern Asia (F _st = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.     

Genetic structure of people from the Volga-Ural region and Central Asia from data of Alu-polymorphism

Nine Alu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga-Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga-Ural population (Fst = 0.061) was higher than for the populations of Central Asia (Fst = 0.024), Europe (Fst = 0.02), and Southeastern Asia (Fst = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.     

Analysis of Alu-insertion polymorphism in three subethnic groups of Kalmyks

Eight Alu insertions at the NBC27, TPA25, NBC148, NBC123, ACE, APOA1, NBC51, and PV92 locus were examined in three subethnic groups of Kalmyks (Torgouds, Derbets, and Buzava). In general, the pattern of allele frequencies in Kalmyks was consistent with that in Asian populations of the world, and was similar to the Alu insertion frequencies pattern in Turkic populations of the Volga-Ural region and Central Asia. Pairwise comparisons of three subpopulations of Kalmyks with respect to the frequency distributions of eight Alu insertions revealed the differences between the groups examined. The coefficient of gene differentiation, F _st, constituted 1.37%, pointing to the common origin of the groups of interest, as well as to the uniformity of the gene pools of subethnic groups of Kalmyks examined.     

Analysis of the AluPolymorphism in the Buryat Populations

Polymorphism of three populations of the Buryat Republic and a population from Aginskii Buryat Autonomous okrug of Chita oblast was examined using a set of five autosomal Aluinsertions at theACE, PLAT, PV92, APOA1,and F13Bloci. The allele frequency distribution patterns revealed in Buryat populations were typical to other Asian populations. Buryats were characterized by relatively low level of intrapopulation diversity (0.369 in the pooled population sample). Analysis of autosomal Aluinsertions suggests the uniformity of the Buryat gene pool. The coefficient of genetic differentiation in the four populations studied was 0.8%.     

Genetic Differentiation of the Tuva Population with Respect to the AluInsertions

Polymorphism of three rural populations of the Tuva Republic was examined using a set of five autosomal Aluinsertions at the ACE, PLAT, PV92, APOA1,and F13Bloci. The allele frequency distribution patterns revealed in Tuvinians were typical to Mongoloid populations of Asia and were characterized by relatively high frequency of the Alu-repeat insertion at the PV92and F13Bloci along with relatively low insertion frequency at the APOA1locus. With respect to the test systems used, Tuvinian populations examined displayed high levels of genetic diversity. The mean expected heterozygosity values in the populations of Kungurtug, Toora-Khem, and Teeli were 0.433, 0.407, and 0.437, respectively. The level of genetic diversity in the pooled Tuvinian sample was 0.432. The coefficient of genetic differentiation in the three populations studied was 1.4% pointing to relatively low level of genetic subdivision of the indigenous Tuvinian populations. However, estimates of genetic differentiation of the Tuvinian gene pool made by use of the Alu-repeat system were higher compared to those performed using classical protein systems, mtDNA, or Y-chromosomal haplotypes. Even though Tuvinian populations were characterized by common gene pool, some features specific to Western Tuvinian population could be distinguished. These features could be associated with higher contribution of the Caucasian component to the gene pool of this population. Phylogenetic analysis demonstrated close genetic relationships between the Tuvinian and Altaic ethnic populations.     

Genetic Differentiation of the Population of Central Asia Inferred from Autosomal Markers

The gene pool of five ethnic groups of the Central Asian population was characterized using nine human-specific polymorphic insertion/deletion loci (ACE, PLAT, APOA1, PV92, F13B, A25, B65, CD4, Mt-Nuc). It has been shown for the first time that at the CD4 locus, the frequency of Alu(–) is inversely related to the Mongoloid component of the population. For the Central Asian populations, the lowest and highest frequencies of the Alu deletion at locus CD4 were recorded respectively in Dungans (0.04), immigrants from China, and Tajiks (0.15). The coefficient of gene differentiation in the Central Asian populations for all the genes was 2.8%, which indicates a relatively low level of population genetic subdivision in this region. The unity of the gene pool of the Central Asian Caucasoids was shown.     

Endothelial Nitric Oxide Synthase (eNOS) gene polymorphisms in spontaneously aborted embryos

Endothelium-derived nitric oxide (NO) is synthesized from L-arginine by endothelial nitric oxide synthase (eNOS) encoded by the eNOS gene on chromosome 7. The effects of the eNOS polymorphisms with the risk of spontaneous pregnancy losses are conflicting. In this study, we investigated the association of the eNOS genotypes with spontaneously aborted embryos in Koreans. Case-control studies were performed to evaluate the association between endothelial nitric oxide synthase (eNOS) gene polymorphisms and spontaneously aborted embryos. Ninety-nine spontaneously aborted fetuses at <20 weeks of gestational age and 103 child controls and 282 adult controls. Genotype frequency of three eNOS gene polymorphisms, ?786T>C, VNTR in intron 4 (4a4b), and 894G>T in spontaneously aborted embryos was surveyed. The frequencies of ?786TC and CC genotypes in aborted embryos were significantly higher than in both child and adult controls. The frequencies of 4a4a homozygote of VNTR polymorphism in intron 4 and TT homozygote of 894G>T polymorphisms were also higher in aborted embryos than in adult controls. Haploptype analysis suggested that ?786T>C polymorphism was a possible risk factor for spontaneously aborted embryos. eNOS gene polymorphisms, ?786T>C, VNTR in intron 4 (4a4b), and 894G>T, are associated with the risk of spontaneously aborted fetuses.     

Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements

Background

VNTR (Variable Number of Tandem Repeats) composite retrotransposons - SVA (SINE-R-VNTR-Alu), LAVA (LINE-1-Alu-VNTR-Alu), PVA (PTGR2-VNTR-Alu) and FVA (FRAM-VNTR-Alu) - are specific to hominoid primates. Their assembly, the evolution of their 5’ and 3’ domains, and the functional significance of the shared 5’ Alu-like region are well understood. The central VNTR domain, by contrast, has long been assumed to represent a more or less random collection of 30-50 bp GC-rich repeats. It is only recently that it attracted attention in the context of regulation of SVA expression.

Results

Here we provide evidence that the organization of the VNTR is non-random, with conserved repeat unit (RU) arrays at both the 5’ and 3’ ends of the VNTRs of human, chimpanzee and orangutan SVA and gibbon LAVA. The younger SVA subfamilies harbour highly organized internal RU arrays. The composition of these arrays is specific to the human/chimpanzee and orangutan lineages, respectively. Tracing the development of the VNTR through evolution we show for the first time how tandem repeats evolve within the constraints set by a functional, non-autonomous non-LTR retrotransposon in two different families - LAVA and SVA - in different hominoid lineages. Our analysis revealed that a microhomology-driven mechanism mediates expansion/contraction of the VNTR domain at the DNA level.Elements of all four VNTR composite families have been shown to be mobilized by the autonomous LINE1 retrotransposon in trans. In case of SVA, key determinants of mobilization are found in the 5’ hexameric repeat/Alu-like region. We now demonstrate that in LAVA, by contrast, the VNTR domain determines mobilization efficiency in the context of domain swaps between active and inactive elements.

Conclusions

The central domain of VNTR composites evolves in a lineage-specific manner which gives rise to distinct structures in gibbon LAVA, orangutan SVA, and human/chimpanzee SVA. The differences observed between the families and lineages are likely to have an influence on the expression and mobilization of the elements.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1543-z) contains supplementary material, which is available to authorized users.     

Polymorphism of Y-Chromosomal Diallelic Loci in Populations of the Volga–Ural Region

Three diallelic polymorphisms of human Y chromosome (DYS287(Y Alupolymorphism, YAP), T/C transition at the RBF5locus (Tat), and G/A transition at the LLY22locus) were studied in eight ethnic populations of the Volga–Ural region, representing Turkic branch of the Altai (Bashkirs, Tatars, and Chuvashes) and Finno-Ugric branch of the Uralic linguistic family (Maris, Mordovians, Udmurts, Komi-Zyryans, and Komi-Permyaks), and in the group of Slavic migrants, belonging to the Indo-European linguistic family (Russians). The Volga–Ural populations were characterized by a low frequency of the Y chromosome Aluinsertion. Examination of an association between the Alupolymorphism and Tatmutation revealed absolute YAP–/C linkage. Analysis of the haplotype frequency distribution patterns constructed from the data on the DYS287and RBF5polymorphisms revealed substantial differences between Udmurts and other populations. The differences were also observed between Komi-Zyryans and the populations of Bashkirs, Mordovians, Komi-Permyaks, and Russians. Analysis of the degree of genetic differentiation pointed to high level of genetic differentiation of the male lineages of the Finno–Ugric ethnic groups. The data on the linkage between the RBF5locus and the LLY22locus mutations indicated the common origin of the Tatmutationin Bashkirs, Mordovians, Udmurts, and Komi-Zyryans, and of a number of ancestralCallele-bearing Y chromosomes in Tatars, Maris, and Chuvashes.     

Distribution and frequency of a polymorphicAlu insertion at the plasminogen activator locus in humans

We have investigated the frequency distribution, across a broad range of geographically dispersed populations, of alleles of the polymorphic Alu insertion that occurs within the 8th intron of the tissue plasminogen activator gene (PLAT). This Alu is a member of a recently derived subfamily of Alu elements that has been expanding during human evolution and continues to be transpositionally active. We used a “population tube” approach to screen 10 chromosomes from each of 19 human populations for presence or absence of this Alu in the PLAT locus and found that all tested populations are dimorphic for presence/absence of this insertion. We show that the previously published EcoRI, HincII, PstI, TaqI, and XmnI polymorphisms at the PLAT locus all result from insertion of this Alu and we use both restriction fragment length polymorphism and polymerase chain reaction analysis to examine the frequency of Alu(+) and Alu(–) alleles in a sample of 1003 individuals from 27 human populations and in 38 nonhuman primates. Nonhuman primates are monomorphic for the Alu(–) allele. Human populations differ substantially in allele frequency, and in several populations both alleles are common. Our results date the insertion event prior to the spread and diversification of modern humans. Received: 10 July 1995 / Revised: 17 November 1995     

De novo insertion of an<Emphasis Type="Italic"> Alu</Emphasis> sequence in the coding region of the<Emphasis Type="Italic"> CLCN5</Emphasis> gene results in Dent's disease

Dent's disease is an X-linked renal tubular disorder characterized by low-molecular-weight proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis, and eventual renal failure. Various types of mutations in the renal chloride channel gene, CLCN5, have been identified in patients with this disease. We studied a Spanish patient with Dent's disease and found, by polymerase chain reaction amplification of the CLCN5 exons, an abnormally large exon 11. Sequencing analysis revealed that this was attributable to the insertion in codon 650 of an Alu element of the "young" Ya5 subfamily. The Alu element was inserted with the same orientation as the CLCN5 gene and arose de novo on the maternal chromosome. Polymorphism analysis indicated that the insertion occurred in the germline of the maternal grandfather. The presence of a long poly(A) tract and evidence for a 16-bp target-site duplication implied that the Alu element was integrated by retrotransposition. This mutation predicts a truncated ClC-5 protein that lacks part of the carboxy-terminus and is likely to result in loss of function of the chloride channel. Insertions of Alu sequences, which are rarely found in coding regions, have occasionally been reported to cause other genetic diseases. However, this is the first report of a retrotransposon insertion in the CLCN5 gene associated with Dent's disease.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Analysis of the VNTR Polymorphism at the PAH and eNOS Genes and the CCR5 Gene Deletion in Populations of Northern Caucasus

VNTR allelic polymorphism at the phenylalanine hydroxilase (PAH) and endothelial constitutive nitric oxide synthase (eNOS) genes and the prevalence of the CCR5 chemokine receptor gene 32-bp deletion were examined in four populations of Northern Caucasus: Adygs, Kumyks, Karachais, and Nogais (Kuban and Karanogais). Population-specific features of the allele and genotype frequency distribution patterns of the polymorphisms examined were described. The data obtained were compared to those obtained from literature. The results of the study confirmed that the frequency and occurrence of the PAH polymorphic alleles exhibit substantial interpopulation differences. In the populations of Northern Caucasus, the eNOS minisatellite polymorphism alleles and genotypes frequency distribution patterns were close to those described earlier for populations of the Volga–Ural region (VUR), and also for the Australian Caucasoids, Japanese, and Turks. In the populations examined, the mean frequency of the CCR5 gene deletion was 0.055, which was somewhat lower than in the populations of VUR (0.070) and Europe (0.081), and practically identical to that in Asian populations (0.050). For each population observed and expected heterozygosities at each locus were calculated. In general, the gene pool of Northern Caucasian populations showed substantial differentiation at the loci examined: the G _ST value was 0.0274. The data for individual loci showed that the greater contribution to the interpopulation diversity was made by the differences in the PAH VNTR allele frequencies (G _ST = 0.04), while the differences at the eNOSand CCR5 loci were small (G _ST = 0.0025 and G _ST = 0.0039, respectively).     

Characteristic Sequence Pattern in the 5- to 20-bp Upstream Region of Primate Alu Elements

We conducted comprehensive sequence analysis of 5′ flanking regions of primate Alu elements. Information contents were computed and frequencies of 1024 pentanucleotides were measured to approximate the location of a characteristic sequence and to specify its pattern(s), which may be involved in the integration of Alu elements into their host genomes. A large number of samples was used, the wide region of the 5′ end of Alu elements was analyzed, and comparisons were made among different subfamilies. Through our analyses, ``TTTTAAAAA' or ``(T) _m (A) _n ' can be stated as a candidate for the characteristic sequence pattern, which resides around the region 5 to 20 base pairs upstream of the 5′ end of Alu elements. This characteristic sequence pattern was more prominent in the sequences of younger Alus, which is a strong indication that the sequence pattern has a role at the time of Alu integration. Received: 10 May 1999 / Accepted: 1 October 1999     

Complete Genomic Sequence of the Human Retinoblastoma Susceptibility Gene

A 180,388-bp contig encompassing the human retinoblastoma gene was sequenced in its entirety. Partial analysis of the sequence revealed (1) a high (A + T)/(G + C) ratio and a high density of Line-1 (L1) repeat sequences, suggesting that the locus maps to G-bands 13q14.12 or 13q14.2; (2) Alu repeats that are asymmetrically oriented over a region extending 87 kb; (3) an overabundance of non-Alu-associated poly(A) tracts 10 bp or larger oriented in the antisense rather than the sense direction (36 vs 6); (4) an Alu sequence nested within an L1 repeat, indicating that the expansion of L1 repeats predates at least some of the Alu expansions; (5) at least three newly discovered microsatellite polymorphisms, one of which was subsequently found to be identical to a polymorphism in a microsatellite-based linkage map of the human genome published by another group; and (6) the basis of previously discovered intragenic RFLPs. This sequence should enhance studies of this locus and of the organization of the human genome.     

Polymorphism of the (CTG)n Repeat of the Myotonin Protein Kinase Gene in Populations of the Sakha Republic (Yakutia) and Central Asia

The allele frequency distribution of the (CTG)_n repeat located in the 3′-terminal region of the myotonin protein kinase gene (DMPK) was compared for populations of Yakutia (three ethnogeographic groups of Yakuts, Evenks, Evens, Yukaghirs, and Dolgans) and Central Asia (Kazakhs, Uzbeks, and Uighurs) and other ethnic groups. The populations of the two regions proved to considerably differ from each other: features characteristic of Asian Mongoloids were more distinct in the populations of Yakutia, while the Central Asian populations were closer to European populations. The (CTG)_n allele spectrum of Yakuts was considered in connection with the high incidence of myotonic dystrophy in Yakutia. The results support the hypothesis of the founder effect for the spread of myotonic dystrophy in Yakuts. Data on the (CTG)_n polymorphism were used to estimate the phylogenetic relationships of the populations under study.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 3, 2005, pp. 385–393.Original Russian Text Copyright © 2005 by Fedorova, Khusainova, Kutuev, Sukhomyasova, Nikolaeva, Kulichkin, Akhmetova, Salimova, Svyatova, Berezina, Platonov, Khusnutdinova.     

Analysis of Gene Complexes Predisposing to Coronary Atherosclerosis

The following seven polymorphic marker loci of genes responsible for predisposition to coronary atherosclerosis (CAS) were studied: the ACE locus responsible for angiotensin-converting enzyme insertion/deletion polymorphism for the presence or absence of the Alu insertion in the gene; the F13,PLAT, and APOA1 loci, controlling the clotting factor 13, plasminogen-activating tissue factor, and apolipoprotein A, respectively; the MTHFR and AGT polymorphic loci responsible for point mutations in methylenetetrahydrofolate reductase and those in angiotensinogen, respectively, and the NOS3 locus controlling the number of tandem repeats in the nitric oxide synthase gene. These loci are located on different chromosomes and encode products involved into various metabolic pathways leading to CAS. In the populations studied, significant differences between healthy subjects and patients predisposed to cardiovascular diseases were revealed with regard to the above seven markers. The 174M allele (T174M polymorphism in the AGT gene) was significantly associated with coronary atherosclerosis. It was found that specific gene combinations are involved in the CAS development and determine variation in the pathogenetically important quantitative traits.     

DNA multiallelic systems reveal gene/longevity associations not detected by diallelic systems. The APOB locus

To identify possible genetic factors affecting human longevity we compared allele pools at two candidate loci for longevity between a sample of 143 centenarians (S) and a control sample of 158 individuals (C). The candidate loci were APOB and TPO, which code for apolipoprotein B and thyroid peroxidase, respectively. Both restriction fragment length (RFL) (XbaI₂₄₈₈ and EcoRI₄₁₅₄) and variable number of tandem repeat (VNTR) (3′APOB-VNTR) polymorphisms were analysed at the APOB locus; the TPO-VNTR polymorphism (intron 10) was analysed at the TPO locus. The main result of the investigation was that there is an association between the APOB locus and longevity that is revealed only when multiallelic polymorphisms are considered. In particular: (i) the frequency of 3′APOB-VNTR alleles with fewer than 35 repeats is significantly lower in cases than in controls; (ii) the linkage disequilibrium between the XbaI-RFLP and the EcoRI-RFLP is significantly different from 0 in cases but not in controls; (iii) the EcoRI-RFLP and XbaI-RFLP allele frequencies do not discriminate between cases and controls. The differences observed between case and control allele pools are specific to the APOB locus, since no significant difference was observed at the TPO locus. Received: 27 November 1995 / Revised: 24 July 1996     

Comparative Analysis of <Emphasis Type="Italic">Alu</Emphasis> Insertion Sequences in the APP 5′ FlankingRegion in Humans and Other Primates

Overexpression of the amyloid precursor protein gene (APP) may play a role in the neuropathology of Alzheimers disease. Therefore, elucidating the mechanisms involved in APP gene regulation is of primary importance, and various cis-acting regulatory elements located in 5 distal regions are known to play a main role. Some of them lie within Alu elements, one of which (Alu1) is only found in humans and apes while the other (Alu2) has a much older history and is also found in rhesus. These Alu insertions harbor sequence motifs that may act as cis-regulatory elements, which may cause differences in APP regulation among primate species and whose functionality may be ascertained through their conservation in a comparative analysis. We have performed a comparative analysis of the region comprising the two Alu elements of the APP promoter in several primates, including humans. We have found a significant decrease in nucleotide diversity in the Alu2 element (inserted in all the species analyzed) compared to the Alu1 (inserted only in apes). This finding can be interpreted as a constriction in the Alu2 sequence variation as a consequence of a functional role of this element in the APP expression. The present results suggest a wider extension of the regulatory elements than the known short consensus regulatory sequences. Moreover, the different conservation of two highly similar and neighboring sequences suggests that, besides the importance of the sequence motifs, their position in relation to the gene suggests that they have played a role in being recruited as regulatory elements.     

Restriction fragment polymorphism in the sex-determining region of the Y chromosomal DNA of European wild mice

Summary Using ³²P-labeled probe consisting mainly of (GATA)_n we have shown that a male specific Alu1 DNA blot pattern which defines the Y chromosome sex-determining locus in inbred mice is highly polymorphic in wild mice, indicating substantial sequence evolution in this region under field conditions. In all cases examined by in situ hybridization, the region concerned is paracentromeric. In contrast, the blot pattern of another probe (M 34) which detects repeated sequences specific to the mouse Y chromosome but outside the sex-determining locus, remains constant between different isolates.Deceased