Analysis of a 1963-bp polymorphic region flanking the human insulin gene

Both polymorphic variable number of tandem repeats and autoimmune regulator modulate differential expression of insulin in human thymic epithelial cells

OBJECTIVE

Polymorphic INS-VNTR plays an important role in regulating insulin transcript expression in the human thymus that leads to either insulin autoimmunity or tolerance. The molecular mechanisms underlying the INS-VNTR haplotype-dependent insulin expression are still unclear. In this study, we determined the mechanistic components underlying the differential insulin gene expression in human thymic epithelial cells, which should have profound effects on the insulin autoimmune tolerance induction.

RESEARCH DESIGN AND METHODS

A repetitive DNA region designated as a variable number of tandem repeats (VNTR) is located upstream of the human insulin gene and correlates with the incidence of type 1 diabetes. We generated six class I and two class III VNTR constructs linked to the human insulin basal promoter or SV40 heterologous promoter/enhancer and demonstrated that AIRE protein modulates the insulin promoter activities differentially through binding to the VNTR region.

RESULTS

Here we show that in the presence of the autoimmune regulator (AIRE), the class III VNTR haplotype is responsible for an average of three-fold higher insulin expression than class I VNTR in thymic epithelial cells. In a protein-DNA pull-down experiment, AIRE protein is capable of binding to VNTR class I and III probes. Further, the transcriptional activation of the INS-VNTR by AIRE requires the insulin basal promoter. The VNTR sequence loses its activation activity when linked to a heterologous promoter and/or enhancer.

CONCLUSIONS

These findings demonstrate a type 1 diabetes predisposition encoded by the INS-VNTR locus and a critical function played by AIRE, which constitute a dual control mechanisms regulating quantitative expression of insulin in human thymic epithelial cells.

The insulin gene in type 1 diabetes

Insulin is a key autoantigen in the autoimmune process leading to the development of type 1 diabetes. Recent studies in both humans and mice have shown that variation in the expression of the insulin gene, in the thymus rather than the pancreas, contributes to disease susceptibility by affecting self-tolerance to insulin. These findings have brought about a paradigm-shift in our understanding of self-tolerance and autoimmunity to molecules with tissue-restricted expression, which are often the target of autoimmune disease.

Solution conformation of d(C4ACAC4TGT)2; an intramolecularly folded i-motif from the insulin minisatellite

A 28-mer sequence taken from the insulin minisatellite is shown, through NMR and UV thermal melting studies, to form an intramolecular i-motif with two ACA and one TGT loop that persists to near neutral pH and room temperature.

Mechanisms of genetic susceptibility to type I diabetes: beyond HLA

An individual's predisposition to Type I diabetes (T1D) is largely determined by complex interactions between several genetic loci and other, nonheritable factors. In T1D, the HLA locus has been known for decades to contribute 50% of the inherited risk. Outside the HLA are many proposed candidate loci with smaller effects, but only two confirmed candidate genes, the INS-VNTR and the CTLA-4 genes, which together do not contribute more than 15% of the risk. Because of the high frequency of the disease-associated DNA variants of these genes, understanding the biological mechanisms of such DNA variation in the context of T1D can have tremendous impact on the development of preventive therapeutics. However, establishing a causal relationship between common DNA variations and disease-predisposing functional effects is not trivial and remains difficult, as the effects are expected to be subtle. The variable-number tandem-repeat (VNTR) region upstream of the insulin gene is known to mediate expression in the thymus and pancreas, whereas various polymorphisms in the 5' and 3' regulatory regions of CTLA-4 are thought to alter gene expression and a coding A49G polymorphism exerts effects on post-translational processing. This review details the latest efforts in elucidating the functional mechanisms that explain the genetic association of the INS-VNTR and CTLA-4 genes with T1D.

The insulin gene in diabetes

Lack of insulin production or abnormalities affecting insulin secretion are key to the development of almost all forms of diabetes, including the common type 1 (insulin-dependent) and type 2 (non-insulin-dependent) diabetes and the more rare forms of maturity-onset diabetes of the young (MODY). Because insulin has such a central role in the pathogenesis of both forms of diabetes, the insulin gene (INS) has always been considered a candidate susceptibility gene. A number of studies have shown that the allelic variation and parent-of-origin effects affect the transmission and expression of the insulin gene in pancreatic beta-cells and extra-pancreatic tissues. These observations have led to the formulation of new hypotheses to explain the biological mechanisms by which functional differences in the expression of the insulin gene may contribute to diabetes susceptibility.

Cystosine-rich strands of the insulin minisatellite adopt hairpins with intercalated cytosine+.cytosine pairs

Previously, we reported the high resolution NMR structure of the hairpin G-quartet structure formed by the G-rich strand of the insulin minisatellite of repeat sequence, (ACAG4TGTG4/TGTC4ACAC4) located upstream of the human insulin gene. Here, we report structural studies on the C-rich strand of this insulin minisatellite. First, we show by high resolution NMR that (C4TGTC4) forms a hairpin dimer with intercalated C+.C pairs (referred to as the hairpin i-motif); 340 NOE distance constraints uniquely define the nature of hairpin folding and the pattern of C+.C intercalation. Second, we show by one-dimensional NMR spectroscopy and molecular modeling studies that (C4TGTC4ACA4TGTC4) forms an intramolecularly folded hairpin with intercalated C+.C pairs. Third, we demonstrate by in vitro replication studies that several such hairpin i-motifs are present in long (C4TGTC4ACA)n (n>/=6) sequences, even in the presence of their complementary strands. Finally, we discuss structural and biological significance of the hairpin i-motifs formed by the C-rich strands of the insulin minisatellite.

Human type 1 diabetes and the insulin gene: principles of mapping polygenes

We review the strategy used to identify a susceptibility locus (IDDM2) for type 1 (insulin dependent) diabetes mellitus. As type 1 diabetes is becoming the paradigm for dissecting multifactorial disease genetics, the approach described provides important general guidelines for positional cloning of human disease polygenes. Main topics include: (a) historical conspectus of the mapping and identification of IDDM2--a critical survey of the work leading up to the conclusion that IDDM2 most likely corresponds to allelic variation at the insulin gene minisatellite (VNTR) locus; (b) the nature of allelic (length and sequence) variation at the VNTR locus; (c) gene interactions and disease pathogenesis; (d) mechanism of action of the INS VNTR in type 1 diabetes--insulin gene expression, parent-of-origin effects (genomic imprinting); and (e) summary and future prospects--alleles of the insulin VNTR that are protective for type 1 diabetes appear to encode susceptibility to type 2 diabetes.

Function of the human insulin promoter in primary cultured islet cells

Pancreatic islet beta cells regulate the rate of insulin gene transcription in response to a number of nutrients, the most potent of which is glucose. To test for its regulation by glucose, the promoter sequence was isolated from the human insulin gene. When linked to chloramphenicol acetyltransferase and transfected into primary islet cultures, the human insulin promoter is activated by glucose. In parallel islet transfections, glucose also activates the L-pyruvate kinase and islet amyloid chain ketoacid dehydrogenase E1a promoter, but it does not affect the beta cell glucose kinase promoter. Using deletion and substitution mutations of the proximal human insulin promoter, we mapped a metabolic response element to the E box, E1, at -100 base pairs relative to the transcription start site. Although the isolated E1 element responds to glucose, inclusion of either of two AT-rich sequences, A1 or A2/C1 on either side of E1, results in dramatic synergistic activation. Inclusion of A2/C1 also increases the response to glucose. The A2-E1-A1 region alone, however, does not explain all of the activity of the human insulin promoter in cultured islets, and other transcriptionally important elements likely to contribute to the glucose response as well.

The minisatellite in the diabetes susceptibility locus IDDM2 regulates insulin transcription

Genetic susceptibility to insulin-dependent diabetes mellitus (IDDM) is inherited as a polygenic trait. One of the loci implicated in IDDM is a polymorphic minisatellite 5' of the human insulin (INS) gene on chromosome 11. This insulin-linked polymorphic region (ILPR) is composed of tandemly repeated sequences, which fall into three size classes: IDDM is strongly associated with short ILPR alleles. We now show that the ILPR is capable of transducing a transcriptional signal in pancreatic beta-cells, with a long ILPR possessing greater activity than a short ILPR. The ILPR contains numerous high-affinity binding sites for the transcription factor Pur-1, and transcriptional activation by Pur-1 is modulated by naturally occurring sequences in the ILPR. Our results demonstrate a possible function for this unique minisatellite, which may have implications for type 1 diabetes.

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.

The third human homolog of a murine gene encoding an inhibitor of stem cell proliferation is truncated and linked to a CpG island-containing upstream sequence

The murine gene, MIP1 alpha, encodes a cytokine (macrophage inflammatory protein 1 alpha) that inhibits the proliferation of bone marrow stem cells. Two human homologs have been characterized, G0S19-1 and G0S19-2. Like MIP1 alpha, these genes contain three exons, the first of which encodes a hydrophobic signal sequence. The existence of a third human G0S19 gene, present in one in four individuals, has been predicted from restriction enzyme analyses. This paper reports that a previously identified human genomic clone containing a G0S19 sequence (G0S19-3), corresponds to the third gene. However, the first G0S19 exon is missing. The sequence differs from those of G0S19-1 and G0S19-2 upstream of a point 31 nucleotides from the junction of the first intron with the second exon. This upstream sequence contains a CpG island and is named "CpG island-containing upstream sequence," CUS. Apart from the G0S19-3-associated copy found only in individuals with the third G0S19 gene, all individuals have one DNA species hybridizing strongly to a CUS-specific probe and at least two less strongly hybridizing species. The CUS has potential binding sites for transcription factors AP-1, AP-2, AP-3, AP-4, and Sp1, a Donehower conserved repetitive element, and motifs characteristic of cytokine, oncogene, and retroviral promoters. Thus, the CUS might promote the transcription of sequences with which it became associated. We suggest that the CUS-G0S19-3 sequence was generated by recombination between a G0S19-2 gene and a member of a novel CUS-associated gene family.

Minisatellite variant repeat mapping: application to DNA typing and mutation analysis

Most DNA typing systems assay allele length variation at tandemly repeated loci such as minisatellites and microsatellites. Allele length measurements are approximate, which impedes the use of such loci in forensic analysis and in studies of allelic variability at hypervariable loci. We now review progress in the development of alternative DNA typing systems based on allelic variation in the interspersion patterns of variant repeat units along minisatellite alleles. Minisatellite variant repeat mapping by PCR (MVR-PCR) not only provides a powerful new digital approach to DNA typing, but also for the first time allows investigation of the true level of allelic variability at minisatellite loci and of the mutational mechanisms that generate ultravariability.

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.

Detection of single and multiple polymorphic loci by synthetic tandem repeats of short oligonucleotides

Loci containing tandem repeats of short sequences are sometimes associated with a high level of polymorphism due to variations in the number of repeats. The different variants can be easily characterized by Southern blotting when the repeats span a range from a few hundred bases to a few kilobases, and probes derived from such tandem repeats constitute convenient genetic markers. These structures, usually called minisatellites, are best documented in the human genome, where their number has been estimated to be at least 1500. However, their role and mode of evolution are poorly understood. We are developing tools to evaluate the number of such redundant sequences in a genome and to gain access to new polymorphic loci. Our strategy is based on the use of polymers of oligonucleotides as DNA probes for hybridization on Southern blots. In a previous report, we made polymers with random units of 14 bp and showed that they detect multiple polymorphic loci on human genomic DNA. At present, we are testing the effect of an increase in the complexity of the polymer, as obtained by the use of a longer random unit, and the effect of slight sequence modifications to a particular tandem repeat sequence. In addition, some of these synthetic probes can detect a single polymorphic locus and directly provide new genetic markers.

Coronary artery disease and apolipoprotein A-I/C-III gene polymorphism: a study of Saudi Arabians

The infrequent band of 3.2-kb of the apolipoprotein A-I/C-III polymorphic region has previously been found to be associated with coronary artery disease and with hypertriglyceridaemia in Caucasians. We studied the apolipoprotein A-I/C-III gene cluster polymorphism in 97 Saudi Arabians in relation to coronary artery disease. Patients were categorized as being with or without coronary artery disease on the basis of coronary angiography. Genomic blotting of Sac I-digested chromosomal DNA with the use of an apolipoprotein A-I gene probe revealed 4.2-kb and 3.2-kb hybridization bands. The genotype frequency of patients with and without coronary artery disease was not different. The frequency of the 3.2-kb allele occurred in 16% of patients with coronary artery disease and in 21% of patients with normal coronary arteries (non-significant). In conclusion, we have not been able to confirm in Saudi Arabians associations previously reported in Caucasians of the 3.2-kb band and coronary artery disease.

Polymorphism in 5' flanking region of human insulin gene. Relationships with atherosclerosis, lipid levels, and age in three samples from Denmark

Variations in the DNA sequence flanking the 5' region of the human insulin gene (U- and L-alleles) were studied in relation to atherosclerosis, lipid levels, and age in three groups of atherosclerotic individuals and in nonatherosclerotic controls. The atherosclerotic groups comprised a postmyocardial infarction group with a mean age of 48 years, a group of individuals operated on for carotid stenosis with a mean age of 62 years, and a group of 85-year-olds with clinical coronary disease, peripheral arterial disease, or both. All 331 individuals were unrelated Caucasians of Danish ancestry. There were no significant differences (p greater than 0.05) in genotype distribution or allele frequencies between atherosclerotic and nonatherosclerotic individuals, but in the 85-year-olds, there was evidence (p less than 0.10) for a lower U-allele frequency in nonatherosclerotic women compared to atherosclerotic women. In nonatherosclerotic women, there was a significant decrease in U-allele frequency with age (60 to 85 years). This decrease does not prove conclusively, but is compatible with, the hypothesis that the U-allele predisposes to, or the L-allele protects against, atherosclerosis. The possible effect of the U-allele on the development of atherosclerosis does not seem to be mediated through conventional risk factors.

Apolipoprotein A-I/C-III gene cluster polymorphism in Saudi Arabians, Filipinos and Caucasians

We studied the polymorphic locus in the A-I/C-III gene cluster on the long arm of chromosome 11 in 147 Saudi Arabian, in 84 Filipino and in 69 Caucasian blood donors. Digestion of DNA yielded two fragments 4.2 kb and 3.2 kb long. The genotype distribution was the same in Arabs and Filipinos, but both were significantly different from Caucasians (p = 0.005 and 0.0005). The 3.2-kb allele occurred in 18% of the Saudi Arabians, in 23% of the Filipinos and in 4% of Caucasians. The frequency of the 3.2-kb allele was significantly higher in Arabs and Filipinos compared to Caucasians (p = 0.0005).

Hypervariable region 5'-flanking [Leu A3]insulin gene of insulin Tochigi is different from those of insulin Wakayama I,II

Three families with abnormal insulinemia have been reported in Japan and sequencing analysis revealed that they had the same point mutation in one allele of the insulin genes causing [Leu A3]insulin. To estimate whether or not this same mutation came from a common ancestor we determined the sequence of the hypervariable region 5'-flanking the third [Leu A3]insulin allele (insulin Tochigi). This region is composed of 42 tandem repeating oligonucleotides, is 599 base pairs long and the sequence is 5' cdi jfa faa aba baa aaa fab aaa caa aac aca cba aaf ccb 3' (abbreviated as a = ACAGGGGTGTGGGG; b = ACAGGGGTCTGGGG; c = ACAGGGGTCCTGGGG; d = ACAGGGGTCCGGGG; f = ACAGGGGTCCCGGGG; i = ACAGGGTCCTGGGG; j = ACAGGGGTGTGAGG). The length of this region is different from those of the first and second [Leu A3]insulin alleles (insulin Wakayama I,II). This difference suggests either that insulin Tochigi and insulin Wakayama I,II are not of the same origin, or that three cases of [Leu A3]insulin in Japan have the same ancestor but recombination has occurred in this region at some point in the past.

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.

Coronary artery disease, HDL cholesterol, and insulin-gene flanking sequences

The relationship between coronary artery disease, HDL cholesterol, and the hypervariable region flanking the human insulin gene was studied in Saudi Arabian non-diabetic subjects (n = 68) and in patients with Type 2 diabetes (n = 35). A locus of insulin-gene-linked DNA polymorphism with three average size classes of alleles was found: a small class 1, a rare medium size class 2, and a large class 3 allele. In the total group of subjects (n = 103), those with the class 3 allele had a lower plasma HDL cholesterol concentration than those without the class 3 allele (0.93 +/- 0.26 vs 1.12 +/- 0.30 mmol l-1, 2p less than 0.003). No difference in genotype and allelic frequency was found between patients with and without coronary artery disease in the combined group of subjects, with and without diabetes. Similarly the genotype distribution was not different between non-diabetic subjects and patients with Type 2 diabetes in the combined group of subjects, both with and without coronary artery disease. In conclusion, the study did not confirm a previous study showing an association between the class 3 allele and atherosclerosis in a Caucasian population. However, the class 3 allele was associated with a low plasma HDL cholesterol concentration.

Nucleotide sequence of the rat gamma-crystallin gene region and comparison with an orthologous human region

The sequences of a 51-kb region containing the cluster of five rat gamma-crystallin-coding genes (CRYG) and of a 7-kb region surrounding the sixth rat CRYG gene were determined. Approximately 78% of the total sequence represents intergenic DNA. We also sequenced 22 kb of DNA from the human CRYG gene cluster. All CRYG genes are associated with CpG-rich regions. The sequence similarity between the human and rat gene regions drops sharply (to 65%) in intronic and 3'-flanking regions but decreases only gradually in the 5'-flanking region. Highly conserved regions (greater than 80%) are found as far upstream as 1.5 kb. Overall intergenic distances are conserved. The human region contains much more repetitive DNA (24% vs. 10%) but less simple-sequence (sps) DNA (0.7% vs. 4%) than the rat region. Almost all repeats and spsDNA elements are located in the intergenic region. The location of repetitive and spsDNA differs between the orthologous regions and these elements were probably inserted after the evolutionary separation of rat and man. The Alu repeats in man and the B3 repeats in the rat are close copies of their respective consensus sequences and bordered by virtually perfect repeats. In contrast, the B1 and B2 repeats in the rat have diverged considerably from the consensus sequence and the surrounding direct repeats are usually imperfect. Thus the dispersion of the B1 and B2 repeats in the rat probably preceded that of the B3 repeats. Within the rat genomic region the spacing of Z-DNA elements is surprisingly regular, they are located about 12 kb apart. A search for putative matrix-associated regions suggests that the rat CRYG gene cluster is organized into two chromosomal domains.

Tissue-specific expression of transfected human insulin genes in pluripotent clonal rat insulinoma lines induced during passage in vivo

The pluripotent rat islet tumor cell line MSL-G2 expresses primarily glucagon or cholecystokinin and not insulin in vitro but changes phenotype completely after prolonged in vivo cultivation to yield small-sized hypoglycemic tumors composed almost entirely of insulin-producing beta cells. When a genomic DNA fragment containing the coding and upstream regulatory regions of the human insulin gene was stably transfected into MSL-G2 cells no measurable amounts of insulin or insulin mRNA were detected in vitro. However, successive transplantation of two transfected clones resulted in hypoglycemic tumors that efficiently coexpressed human and rat insulin as determined by human C-peptide-specific immunoreagents. These results demonstrate that cis-acting tissue-specific insulin gene enhancer elements are conserved between rat and human insulin genes. We propose that the in vivo differentiation of MSL-G2 cells and transfected subclones into insulin-producing cells reflects processes of natural beta-cell ontogeny leading to insulin gene expression.

The human factor VII gene is polymorphic due to variation in repeat copy number in a minisatellite

The gene coding for human factor VII, a vitamin K-dependent coagulation factor, contains five minisatellite imperfect tandem repeats with monomer element lengths ranging from 14 to 37 bp, and copy numbers ranging from 6 to 52. Three of these repeats are entirely within introns, one is entirely in an untranslated portion of an exon, and one spans an exon-intron border and contains coding sequence. A consensus sequence derived from a comparison of the monomers is similar to a core sequence found in other minisatellites. All of the minisatellites display higher-order periodicities. At least one of these minisatellites is polymorphic. A variation in repeat copy number has been observed in a tandem-repeat region in the seventh factor-VII intron.

Assessment of small polymorphisms in defined human collagen gene segments

Restriction fragment length polymorphisms (RFLPs) greater than 1.5 kb in size have been identified in all but one of the human fibrillar collagen genes. However, the number of informative RFLPs for these genes is still limited. Here we present the conjunct use of two techniques for the assessment of small length variations within defined segments of the genome. This strategy has the potential to be used for the allelic exclusion of cloned genomic fragments prior to sequencing. Moreover it can be a useful and sensitive tool to determine if genetic linkage exists between abnormal phenotypes and loci where conventional Southern blotting analysis has failed to detect informative RFLPs.

Diabetes mellitus, atherosclerosis, and the 5' flanking polymorphism of the human insulin gene

On the 5' side of the human insulin gene is a highly polymorphic locus containing 2 major size classes of DNA restriction fragments which segregate in families as stable genetic elements. Fragments with an average size of about 600 base-pairs (bp) (the 'L-allele') seem to be a weak genetic marker for type 1 (insulin-dependent) diabetes mellitus, whereas fragments of an average size of about 2500 bp (the 'U-allele') have hitherto been associated with type 2 (non-insulin-dependent) diabetes mellitus and diabetic hypertriglyceridaemia. Recent evidence does not confirm the association between the U-allele and type 2 diabetes. Our own studies suggest that the U-allele is a fairly strong marker for the development of atherosclerosis with a relative risk for U-carriers of 3.36. The U-allele has not been associated with conventional cardiovascular risk factors such as body weight, blood pressure, or levels of blood glucose, triglycerides or lipoproteins. The putative functions of the polymorphic region in the aetiology of type 1 diabetes and atherosclerosis, and the relation of this region to other genetic markers for these disorders are not known.

Insulin-gene flanking sequences, diabetes mellitus and atherosclerosis: a review

A highly polymorphic locus flanking the human insulin gene contains two major size classes of DNA restriction fragments, which segregate in families as stable genetic elements. The L-allele, i.e. fragments with an average size of about 600 base-pairs seems to be a weak genetic marker for Type 1 (insulin-dependent) diabetes mellitus, whereas the U-allele, i.e. fragments of an average size of about 2500 base-pairs hitherto has been associated with Type 2 (non-insulin-dependent) diabetes mellitus and diabetic hypertriglyceridaemia. The most recent reports on this subject do not confirm an association between the U-allele and Type 2 diabetes. Our own studies indicate that the U-allele is a fairly strong marker for the development of atherosclerosis (relative risk for U-carriers 3.36). The putative functions of the polymorphic region in atherogenesis and the relation of this region to other genetic markers for atherosclerosis are not known.