p53 polymorphisms in Russia and Belarus: correlation of the 2-1-1 haplotype frequency with longitude

Four different polymorphisms in the human p53 gene (a 16-bp duplication in intron 3, and three RFLPs: for Bsh1236I at codon 72, for MspI in intron 6 and for BamHI in the 3 flanking region) and extended haplotypes were studied in nine geographically diverse populations from Russia and Belarus. The Yakuts differed from all other populations, as they had a significantly higher frequency of the BamHI A1 allele. Most populations did not differ significantly from each other in the frequency of the Bsh1236I polymorphism. The 16-bp duplication A1 allele and MspI A2 allele frequencies were significantly higher in the Yakut and Khant populations. Linkage disequilibrium values (D) between BamHI and other polymorphic sites were not significant in many cases; for this reason we have used the 16 bp–Bsh1236I–MspI haplotype frequencies only. Of eight possible haplotypes, five were observed in the populations investigated. Haplotype 1-2-2 was the most frequent in all populations. The next most common haplotype, 1-1-2, was present at very similar frequencies among the Byelorussians and Russians from Smolensk, but was more frequent in other populations. The frequency of haplotype 2-1-1 showed a nearly continuous decrease from West to East (from 17.857% among the Byelorussians to 0.685% in the Yakuts from the Verkhoyansk) and correlated with longitude (Spearmans r=–0.8667, P=0.0025), which may be due to natural selection and adaptation. The relationships among populations were evaluated by means of Neis D_A distances for the 16 bp–Bsh1236I–MspI haplotype frequencies. Based on the multidimensional scaling analysis a correlation between p53 haplotype frequencies and ethnicity is supposed.     

haplotypes identified by DNA polymorphisms at the apolipoprotein A-1 and C-III loci and hypertriglyceridaemia

Summary A Japanese group comprising 40 hypertriglyceridaemic and 35 normolipidaemic subjects were genotyped for two intragenic DNA restriction fragment length polymorphisms (RFLPs) at the A-1 and C-III gene loci. An Sst-1 polymorphism is located at the 3 end of the C-III gene and a Msp-1 polymorphism in the third intron of the A-1 gene. The polymorphic restriction sites are 3.8kb apart. The polymorphism with Sst-1 was present at allelic frequencies of 0.67 (S1 allele) and 0.33 (S2 allele), and the polymorphism with Msp-1 was present at allelic frequencies of 0.55 (M1 allele) and 0.45 (M2 allele). The alleles S1, S2, M1, and M2 are in linkage disequilibrium and three haplotypes were identified S1-M1, S1-M2, and S2-M2. Unlike the previously reported association of the S2 allele with hypertriglyceridaemia found in Caucasians there was no difference in the frequency of S2 allele between normolipidaemic and hyperlipidaemic Japanese. However one of the haplotypes S1-M2 was significantly increased in the hypertriglyceridaemic subjects (32% versus 11% P>0.025). Thus in Japanese there is an association with genotypes at this locus and hypertriglyceridaemia but with a different haplotype than in Caucasians.     

DNA polymorphic patterns and haplotype arrangements of the apo A-1, apo C-III,apo A-IV gene cluster in different ethnic groups

Summary The allelic frequency of five different restriction fragment length polymorphisms (RFLPs) in the A-1, C-III, A-IV gene region has been determined in Caucasians, Negroes, Indian Asians, and Japanese. The polymorphic sites are with Taq-1 at the 5 end of the A-1 gene, with Msp-1 in the third intron of the A-1 gene, with Pst-1 in the intergenic sequence between the A-1 and C-III genes, with Sst-1 in the 3 non-coding region of the C-III gene, and with Pvu-II in the third intron of the C-III gene. The alleles identified by three of the RFLPs showed large differences in frequency amongst the races, especially between Caucasians and non-Caucasians. Alleles of the Msp-1 polymorphism and Sst-1 polymorphism, which were rare in Caucasians (frequencies 0.03 and 0.01), were more common in Japanese (frequencies 0.37 and 0.35), Indian Asians (frequencies 0.37 and 0.26), and Negroes (frequencies 0.31 and 0.31). In contrast with a Pvu-II polymorphism one allele was rare in Japanese and in Indian Asians (frequency 0.01) but more common in Caucasians (frequency 0.11). Linkage disequilibrium was evident between some of the alleles and a total of seven haplotypes were identified among the different races.     

Identification of restriction fragment length polymorphisms linked to genes controlling soluble solids content in tomato fruit

Summary Gene(s) conferring high soluble solids (SS) in tomato fruit had been backcrossed previously from a wild tomato species, Lycopersicon chmielewskii LA1028 ( 10% SS), into a L. esculentum cultivar, VF36 ( 5% SS), to derive a BC₅S₅ line, LA1563, similar to VF 36 but with 7–8% SS. DNAs from these lines and a tomato breeding line, H2038, were screened for restriction fragment length polymorphisms (RFLPs) using four restriction endonucleases and sixty clones chosen at random from a tomato cDNA library. Most of the cDNA clones (56) identified the same RFLP in VF 36 and LA1563 and a different RFLP in LA1028. However, two cDNA clones identified the same RFLP in LA1563 and LA1028 and a different RFLP in VF36. To determine whether RFLPs identified by these two cDNA clones were linked to SS genes, a H2038 x LA1563 F₂ population was screened for segregation of the RFLPs and for SS content. The segregation ratios of these RFLPs were consistent with ratios expected for codominant alleles at unlinked loci. Analysis of variance of SS content for different RFLP genotypic classes indicated that RFLP alleles at one of the loci were linked to genes controlling SS content. The RFLP allele from the high SS tomato line, LA1563, was associated with significantly higher SS content and, therefore, could be useful in selecting for high SS gene(s) in a tomato breeding program.     

A novel mosaic Bantu/Benin/Bantu βs haplotype found in several African populations

In a survey of the chromosomal backgrounds associated with the sickle cell gene in Portuguese-speaking populations from Europe and Africa, a discordance between the classical haplotype and the predicted allele at theRsaI polymorphism 5 to the globin gene was observed in four patients. Extensive typing of the corresponding s chromosomes at simple polymorphic repeat motifs revealed a novel extended haplotype that appeared to be a mosaic of (1) a Bantu-type DNase I hypersensitive site 2 within the globin gene cluster locus control region, (2) a Benin 5 subhaplotype, and (3) a Bantu 3 subhaplotype. We propose two alternative schedules for the generation of yet another chromosomal background of the sickle cell gene.     

A pentanucleotide tandem duplication polymorphism in the 3′ untranslated region of the HLA-linked heat-shock protein 70-2 (HSP70-2) gene

A novel two-allele pentanucleotide tandem duplication polymorphism is described within the 3 untranslated region of the HLA-linked HSP70-2 gene, for which a PstI polymorphism is known. All four haplotype combinations were found.     

A PvuII polymorphism in the 5′ flanking region of the apolipoprotein AIV gene: its use to study genetic variation determining serum lipid and apolipoprotein concentration

Summary We have used a 1.05-kb unique genomic fragment from the 5 end of the apolipoprotein (apo) CIII gene to identify a restriction fragment length polymorphism (RFLP) detected with the restriction enzyme PvuII, in the apoCIII-apoAIV intergenic region. In a sample of 220 normolipidaemic individuals from the UK population, the frequency of the rare allele, VB2 is 0.054. The PvuII polymorphism is in apparent linkage equilibrium with three other RFLPs of this gene cluster, detected with the restriction enzymes XmnI, PstI and SstI, but in linkage disequilibrium with an RFLP in the apoCIII gene also detected with PvuII. Taken together, these five RFLPs have a PIC (polymorphism information content) value of 0.8, and therefore are informative for genetic studies. Individuals with the genotype VB1VB2 had lower mean concentrations of apoAI, and HDL-cholesterol than individuals with the genotype VB1VB1. However these differences were not statistically significant.     

TaqI polymorphism in the LDL receptor gene and a TaqI 1.5-kb band associated with familial hypercholesterolemia

Summary The low density lipoprotein (LDL) receptor gene was analyzed in 67 unrelated healthy Japanese and 38 members of six consecutive families with familial hypercholesterolemia (FH) by Southern blot hybridization with TaqI, an LDL receptor cDNA fragment containing exons 1 to 8 being used as a probe. A new TaqI RFLP at the LDL receptor locus was detected with allele frequencies of 0.67 and 0.33. The data obtained with smaller cDNA subfragment probes revealed that the TaqI RFLP site is located within 1.1 kb of the 5 side of the EcoRI site of exon 5. The TaqI RFLP was in linkage disequilibrium with the PstI RFLP but showed no significant linkage disequilibrium with the RFLPs for AvaII, ApaLI/I15, PvuII, NcoI, and ApaLI/3. Among the seven RFLPs at the LDL receptor locus, the TaqI RFLP was the only useful genetic marker in one of the six families with FH. Furthermore, the association of an additional TaqI 1.5-kb band with a mutant LDL receptor gene was observed in another family with FH in which the proband was homozygous for all of the seven RFLPs. The data obtained with various restriction enzymes and smaller cDNA subfragments probes suggested that a minor change in nucleotide sequences in the region including exons 5 to 8 is present in the mutant gene. These data suggest that the TaqI RFLP is a useful genetic marker at the LDL receptor locus and that TaqI serves for the analysis of some mutant LDL receptor genes, when used with small LDL receptor cDNA probes.     

DNA polymorphism in the 5′ flanking region of the human carbonic anhydrase II gene on chromosome 8

Summary A restriction-fragment-length polymorphism (RFLP) is described which is associated with the human carbonic anhydrase II gene (CA2) that codes for one of the three genetically distinct carbonic anhydrase isozymes, CA I, CA II, and CA III. The isolated DNA was cleaved with several restriction enzymes and subjected to Southern blot hybridization analysis using a DNA probe containing the 5 end of the human CA II gene. A two allele RFLP which was detected with the restriction endonuclease, Taq I, is expressed phenotypically on Southern blots as either a 5.4 kilobase (kb) fragment or as 4.0 and 1.4 kb fragments. These fragments result from the presence or absence of a Taq I recognition site in the 5 flanking region approximately 1.0kb from the initiation codon of the CA II gene. Segregation analysis showed that the alleles are inherited in a Mendelian fashion, with a frequency of 50%.     

Excision and transposition of two Ds transposons from the bronze mutable 4 derivative 6856 allele of Zea mays L

Summary The regulatory mutation bronze mutable 4 Derivative 6856 (bz-m4 D6856) contains a complex 6.7 kb Dissociation (Ds) element tagged with a duplication of low copy bz 3 flanking sequences (Klein et al. 1988). This creates a unique opportunity to study the transposition of a single member of the repetitive family of Ds elements. Eighteen full purple revertants (Bz alleles) of bz-m4 were characterized enzymatically and by genomic mapping. For 17 of the Bz alleles, reversion to a wild-type phenotype was caused by excision of the 6.7 kb Ds transposon. Nine of these Bz alleles retained the transposon somewhere in their genome. In this study we show that like Ac (Schwartz 1989; Dooner and Belachew 1989), the 6.7 kb Ds element can transpose within a short physical distance, both proximal and distal to its original position. Additional bz sequences have been mapped immediately distal to the mutant locus in bz-m4 D6856; genetic evidence suggests these are flanked by two additional Ds elements. The remaining Bz revertant, Bz :107, arose from excision of a more complex 13 kb Ds element.     

3′ creatine kinase (M-type) polymorphisms linked to myotonic dystrophy in Italian and Spanish populations

Summary Linkage analysis and haplotype characterization for the allelic system detected at the 3 creatine kinase muscle type (CKMM) locus were carried out in 59 myotonic dystrophy (DM) families from Italy and Spain. A maximum lod score (z _max) of 21.26 at a recombination frequency () of 0.00 was found. No statistically significant linkage disequilibrium was observed between DM and the RFLPs examined. However, a substantial linkage disequilibrium was found between CKMM-TaqI and CKMM-NcoI sites in these two populations.     

Restriction fragment length polymorphism of the human T cell receptor alpha gene

Previous studies have demonstrated restriction fragment length polymorphisms (RFLP) in the vicinity of the alpha and beta genes of the human T-cell receptor. In the course of experiments designed to discover additional polymorphic restriction sites, we found a new RFLP of the T-cell alpha gene recognized by the restriction enzyme Taq I. The site was localized to the interval between the most 3 joining (J) exon and the most 5 constant (C) region exon, about 7 kb distant from the previously described Bgl II polymorphic site which mapped to the vicinity of the 3 untranslated exon. With the use of these two polymorphic markers, four Ti-alpha alleles could be identified, allowing unambiguous assignment of all Ti-alpha genes in some families. These markers may be useful in identifying possible immune response genes or disease predisposition genes associated with the genes of the T-cell receptor for antigen.Abbreviations used in this paper RFLP restriction fragment length polymorphism - Ti-alpha alpha gene of the T-cell receptor for antigen     

A new XmnI polymorphism in the regulatory region of the corticotropin releasing hormone gene

We describe the first polymorphism in the 5 flanking region of the corticotropin releasing hormone (CRH) gene. DNA sequencing analysis identified a T G base substitution in the 5 flanking region of the gene. This substitution leads to the loss of anXmnI site at position 255 of the Genbank entry X67661. The frequency analysis in 32 Caucasians revealed that it is a rare polymorphism, with only three observed heterozygous individiuals for this polymorphism.     

DNA polymorphism of the C2 locus

The extent of the C2 locus in the HLA class III region has been determined by Southern blotting techniques and by DNA sequence analysis. The gene is 18 kb in length and therefore provides a marked contrast to the adjacent factor B gene of 6 kb. A novel restriction fragment length polymorphism (RFLP) has been identified using the endonuclease Sst I and a genomic probe derived from the 5 region of the C2 gene. Four variants have been detected in a sample of unrelated individuals with haplotypes carrying the C2C allele. Further analysis using C2 and factor B cDNA probes has determined the relationship between this and the other RFLPs previously identified in this region of the genome. Together, the three polymorphisms identified so far make the subdivision of previously indistinguishable haplotypes possible. They therefore constitute a series of markers which increase the resolution of genetic variation in the C2 locus and they may be important in studies of diseases associated with this region of the major histocompatibility complex.     

The isolation of a genomic clone containing the apolipoprotein CII gene and the detection of linkage disequilibrium between two common DNA polymorphisms around the gene

Summary We report the isolation of a genomic clone containing the apolipoprotein CII (apo CII) gene and 5 and 3 flanking sequences. A detailed restriction map of the gene has been constructed and DNA fragments that are unique, or low copy number sequences in the genome have been identified. One of these detects a common restriction fragment length polymorphism (RFLP) with the enzyme BglI. Marked linkage disequilibrium is observed between this RFLP and that detected with the apo CII cDNA clone, even though the two variable restriction enzyme sites are approximately 12 kb apart. However, the usefulness of the apo CII gene as a marker for linkage studies is increased by the use of both RFLPs.     

Human α-globin maps to pter-p13.3 in chromosome 16 distal to PGP

Summary Fibroblasts from a fetus with an unbalanced karyotype 46(XY),-16,+(16qter-16p13.3::4q31.1-4qter) were found to possess only one allele at the 3 hypervariable region (3HVR) close to the -globin locus and two alleles at the PGP locus. This places the -globin locus at the very tip of 16p, distal to PGP.     

The human apolipoprotein B 3′ hypervariable region: detection of eight new alleles and comparisons of allele frequencies in blacks and whites

We investigated common length polymorphisms in the hypervariable region located 3 to the human gene encoding apolipoprotein B (APOB 3 HVR) as part of the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study. PDAY is a multicenter study of young persons who died of external causes (accident, homicide, and suicide). The APOB 3 HVR contains multiple copies of AT-rich tandem repeats (15bp) called hypervariable elements (HVE). Using polymerase chain reaction (PCR) to amplify APOB sequences in hepatic DNA samples, we identified 22 different HVR alleles among 232 PDAY cases. In addition to 14 previously identified alleles, we detected 8 new alleles that had not been observed in population surveys. Of these new alleles, 7 were present only in black cases. We also examined distributions of HVR allele frequencies for blacks and whites. The frequency distributions for whites did not differ from those from previous studies of French populations (P=0.3811) and Austrian populations (P= 0.1885). In contrast, the allele frequency distribution for blacks differed from whites (P<0.001). Blacks had higher frequencies of smaller alleles (33 repeats) and larger alleles (37 repeats) than whites. We also sequenced specific HVR alleles to identify differences responsible for size variation. The most frequent alleles were identical in sequence to HVR alleles described in previous studies. However, one allele was not identical in sequence to an equivalent-sized allele from a previous study. In all likelihood, detection of sequence substitutions in the APOB 3 HVR would result in an even greater amount of allelic variability than detected by size differences alone.     

Relationship between cyclic AMP level and accumulation of carotenoid pigments in Neurospora crassa

Dark grown mycelial cells of Neurospora crassa bearing mutant genes crisp-I or frost and having a decreased level of cyclic adenosine 3,5-monophosphate contained more carotenoid pigments than the cells with wild alleles of these genes. A transient decrease of the cyclic AMP occurred following photoinduction of carotenoid synthesis during its lag-period. Its intensity correlated with the increase of carotenoid pigment level due to photoinduction. No correlation in the content of cyclic guanosine 5-phosphate with both constitutive level of carotenoids and its photoinduced increase was observed.     

Ribosomal RNA evolution by fragmentation of the 23S progenitor: Maturation pathway parallels evolutionary emergence

Summary The eukaryotic 5.8S and the chloroplast 4.5S ribosomal RNAs were proposed to have arisen from the 5 and 3 ends respectively of prokaryotic 23S ribosomal RNA by the introduction of new processing sites during evolution. This hypothesis was supported by comparison of previously published primary sequences; in addition we can draw models of secondary structure in accord with this notion. Finally, we further noted that the sequence of processing cuts in the maturation pathway of ribosomal RNA reflects the probable order in which they arose during evolution.     

Identification of a PstI polymorphism in the p21Cip1/Waf1 cyclin-dependent kinase inhibitor gene

A PstI polymorphism in the 3 flanking region of the p21^CiP1/Waf1 cyclin-dependent kinase inhibitor gene is described. DNA sequencing analysis identified a CT base substitution in the 3 flanking region of the gene. This substitution leads to the destruction of a PstI site and results in a biallelic DNA polymorphism. This restriction fragment length polymorphism (RFLP) provides the first known genetic marker for this cell cycle regulatory gene.