Duplication/deletion polymorphism 5' - to the human beta globin gene.

DNA sequence analysis of the human beta globin locus has identified an array of simple tandem repeated sequences upstream from the beta globin structural gene. Comparison of several cloned human beta globin alleles demonstrated a high frequency of sequence heteromorphism at this site apparently due to duplication or deletion of single units of the repeat array. At least two such duplication/deletion events are necessary to account for the observed variation. No other sequence variation was observed, suggesting that duplication/deletion events within the tandem repeat array may be at least 13 to 14 times more frequent than nucleotide substitutions in the surrounding DNA.     

Characteristics of polymorphism at a VNTR locus 3' to the apolipoprotein B gene in five human populations.

We have analyzed the allele frequency distribution at the hypervariable locus 3' to the apolipoprotein B gene (ApoB 3' VNTR) in five well-defined human populations (Kacharis of northeast India, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, and a relatively homogeneous Caucasian population of northern German extraction) by using the PCR technique. A total of 12 segregating alleles were detected in the pooled sample of 319 individuals. A fairly consistent bimodal pattern of allele frequency distribution, apparent in most of these geographically and genetically diverse populations, suggests that the ApoB 3' VNTR polymorphism predates the geographic dispersal of ancestral human populations. In spite of the observed high degree of polymorphism at this locus (expected heterozygosity levels 55%-78%), the genotype distributions in all populations (irrespective of their tribal or cosmopolitan nature) conform to their respective Hardy-Weinberg predictions. Furthermore, analysis of the congruence between expected heterozygosity and the observed number of alleles reveals that, in general, the allele frequency distributions at this locus are in agreement with the predictions of the classical mutation-drift models. The data also show that alleles that are shared by all populations have the highest average frequency within populations. These findings demonstrate the potential utility of highly informative hypervariable loci such as the ApoB 3' VNTR locus in population genetic research, as well as in forensic medicine and determination of biological relatedness of individuals.     

A unique AT-rich hypervariable minisatellite 3' to the ApoB gene defines a high information restriction fragment length polymorphism

A DNA restriction fragment length polymorphism has been found immediately 3' to the human apoB gene. Digestion of many different human DNAs at sites flanking the region and Southern blotting analysis reveal that this region can vary in length by approximately 300 base pairs with five alleles readily distinguishable. The length polymorphism is due to a unique AT-rich minisatellite that consists primarily of a 30-base pair tandem repeat with two structurally related subunit sequences, x (ATAATTAAATATTTT) and y (ATAATTAAAATATTT). In general, the sequences repeat in an x-y order. The AT-rich region also contains variant x and y sequences that result from C or G for A substitution. Sequence analysis of one large allele revealed the expected increased number of xy repeats. In addition, similar analysis of three different smaller alleles with the same apparent size on Southern blotting analysis showed that all were of slightly different size due to minor differences in the number of xy repeats. The heterogeneity of this AT-rich minisatellite provides the basis for a highly informative restriction fragment length polymorphism of the apoB gene and should be very useful in association and linkage analysis studies of the contribution of this locus to atherosclerosis susceptibility.     

Nucleotide sequence of a transcriptional enhancer located 2.2 kb 3' of a human placental lactogen-encoding gene

The nucleotide sequence of the human placental lactogen-encoding gene enhancer was determined. This tissue-specific enhancer is contained in a region flanked by a 284-bp Alu repeat.     

In vivo generation of 3' and 5' truncated species in the process of c-myc mRNA decay.

It has been demonstrated that the half-life of c-myc mRNA is modulated in response to physiological agents. The elucidation of the decay process and the identification of the critical steps in the in vivo c-myc mRNA degradation pathway can be approached by following the fate of c-myc mRNA under the influence of such factors. IFN-alpha was the factor used to modulate c-myc mRNA half-life in HeLa 1C5 cells, a stable clone derived from HeLa cells. This cell line carries multiple copies of the c-myc gene, under the control of the dexamethasone inducible mouse mammary tumor virus-long terminal repeat (MMTV-LTR). Exposure of HeLa 1C5 cells to IFN-alpha resulted in a further 2-fold increase over the dexamethasone-induced c-myc mRNA. However, the c-myc mRNA in IFN-alpha treated cells was less stable than that in the control cells. RNase H mapping of the 3' untranslated region of c-myc mRNA revealed, in addition to the full length mRNA, three smaller fragments. These fragments were proven to be truncated, non-adenylated c-myc mRNA species generated in vivo. Exposure of HeLa 1C5 cells to Interferon-alpha before induction with dexamethasone resulted in the enhanced presence of these intermediates. RNase H analysis of c-myc mRNA after actinomycin D chase revealed that deadenylation led to the formation of a relatively more stable oligoadenylated c-myc mRNA population which did not appear to be precursor to the truncated intermediates. The detection of truncated 3' end c-myc mRNA adenylated fragments as well, implies that the c-myc mRNA degradation process may follow an alternative pathway possibly involving endonucleolytic cleavage.     

Distribution of the 3' VNTR polymorphism in the human dopamine transporter gene in world populations

A polymorphism with a variable number of tandem repeats (VNTR) found in the 3' untranslated region of the human dopamine transporter gene (DAT1) was scored in unrelated individuals drawn from 10 geographically widely dispersed populations in order to assess this marker's usefulness in human population genetics. The populations that were analyzed in this study included 4 indigenous groups of Siberia, natives of North and South America, as well as Caucasian and Oceanic groups, most of which represented small-scale societies. A total of 5 DAT1 alleles were seen overall, but only in one Siberian population, the Altai-Kizhi, were all 5 present, and in the Native Americans of Colombia the locus was monomorphic. The most common allele, DAT1*10, ranged in frequency from 52% in Greeks to 100% in South Americans. The high frequency of the DAT1*10 allele (approximately 90%) among Mongoloid groups of north and east Asia distinguishes them from most Caucasian groups. The presence of the rare DAT1*7 allele in relatively high frequency (approximately 5%) among all Siberian groups suggests a close affinity with north Asian groups, especially Mongolians. The presence of the even rarer DAT1*13 allele in one Siberian population, the Altai-Kizhi, reflects this group's long historical contact with Mongolians. The results demonstrated that the DAT1 VNTR polymorphism is useful in investigating population relationships, and that rare alleles at this locus may be particularly valuable in understanding the extent of genetic affinity between neighboring groups and in situations where admixture is suspected. However, because of both the association and linkage of this VNTR locus with attention-deficit hyperactivity disorder (ADHD) in children, and its highly restricted polymorphism (usually 3 alleles) in most human groups, the possibility of selection constraints on the DAT1 gene cannot be ignored.     

Diabetic hypertriglyceridaemia and related 5' flanking polymorphism of the human insulin gene.

A polymorphic DNA sequence was studied on the 5'' flanking region of the human insulin gene in relation to diabetic lipaemia. The genotype frequencies in a control population (n = 52) were homozygous L 6%, heterozygous 54%, and homozygous S 40%. Corresponding genotype frequencies in a hypertriglyceridaemic group (n = 74) were 18%, 66%, and 16% (p less than 0.01; chi 2 test). When the hypertriglyceridaemic patients were divided on the basis of glucose tolerance the corresponding genotype frequencies in the diabetic subgroup (n = 23) were 39%, 52%, and 9% compared with 0%, 74%, and 26% in the non-diabetics (n = 34) (p less than 0.001; chi 2 test). These findings suggest that the homozygous L genotype may confer susceptibility to diabetic hypertriglyceridaemia.     

A locus control region at -12 kb of the tyrosinase gene.

We have shown previously that the tyrosinase gene encompassed in a 250 kb yeast artificial chromosome (YAC) is expressed faithfully in transgenic mice. To define the sequences important for this qualitatively and quantitatively correct expression pattern, we have generated transgenic mice with YACs carrying several deletions in the mouse tyrosinase locus. In particular, we wanted to address the in vivo relevance of a regulatory element indicated by a cell-specific DNase I hypersensitive site (HS) located -12 kb upstream of the gene. Wild-type level expression was observed only when the YACs transferred contained this HS. Constructs in which the HS was deleted gave rise to much weaker expression and variable patterns of expression. In conclusion, this HS region appears to harbour the essential regulatory element for the correct expression of the tyrosinase gene. Moreover, it behaves as a locus control region in that it commands the functional status of this expression domain, protecting it from position effects.