Human Molecular Genetics, 2000, Vol. 9, No. 20 2929-2935
© 2000 Oxford University Press
Influence of allele lineage on the role of the insulin minisatellite in susceptibility to type 1 diabetes
Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK and 1Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2XY, UK
Received 7 August 2000; Revised and Accepted 4 October 2000.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
The insulin minisatellite or variable number of tandem repeats locus (INS VNTR) is the best candidate for the type 1 diabetes mellitus (T1DM) susceptibility locus IDDM2. Small class I alleles associate with predisposition to T1DM, whereas large class III alleles associate with dominant protection. We have analysed variant repeat distribution within the minisatellite and combined this with flanking haplotypes to define five new ancestral allele lineages. Class III alleles divide into two highly diverged lineages, IIIA and IIIB, which correspond perfectly to the previously defined Protective (PH) and Very Protective (VPH) haplotypes, respectively. Class I alleles are divided into three newly defined lineages, IC+, ID+ and ID–, by a combination of variant repeat distributions and flanking haplotypes. All class I alleles are equally predisposing to T1DM except for ID– alleles which are protective when transmitted from ID–/III heterozygous fathers. Similar results have been previously reported for alleles of 42 repeats in length (allele 814) which represent a subset of the ID– lineage. Division of class ID– alleles into those of 42 repeats and those of other sizes suggested that this protective effect was a feature of all ID– alleles, irrespective of size. ID– alleles are only clearly distinguished from all other alleles by an MspI– variant within IGF2 downstream of the minisatellite, suggesting that the apparent role of the minisatellite in susceptibility to T1DM may be modified by neighbouring haplotype and therefore that IDDM2 could have a multi-locus aetiology.
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
The insulin minisatellite or variable number of tandem repeats locus (INS VNTR) is located 596 bp upstream of the insulin gene translation initiation site. It has been associated with susceptibility to type 1 diabetes mellitus (T1DM) (1), type 2 diabetes mellitus (T2DM) (2), polycystic ovary syndrome (3), obesity (4) and birth size (5). It is composed of a variable number of variant tandem repeats of 14–15 bp in length based on the consensus sequence 5'-ACAGGGGTGTGGGG-3' (6). In white European populations, the minisatellite displays a bimodal allele size distribution with class I alleles (28–44 repeats) and class III alleles (138–159 repeats) at frequencies of
70 and 30%, respectively (7). Rare class II alleles are intermediate in size. Class I alleles generally associate with increased susceptibility to T1DM and class III alleles associate with dominant protection (7). Previous studies, which identified the insulin minisatellite as the T1DM susceptibility locus, IDDM2, classified alleles either by size or by flanking haplotype. Class III alleles of the insulin minisatellite divide by both haplotype and size into two classes which differ in their levels of associated protection against T1DM, with the Very Protective haplotype (VPH) associating with greater protection against disease than the Protective haplotype (PH) (8). Division by size also revealed heterogeneity in class I-associated predisposition to T1DM (8–11). Notably, the most common allele (allele 814; 42 repeats in length) had a protective effect but only when transmitted from I/III heterozygous fathers (9). Furthermore, in three independent populations, the homozygous 814/814 genotype did not confer risk to T1DM (9). This 814-associated protection, conferred exclusively by alleles transmitted from 814/III fathers, is similar to paramutation in lower organisms, an epigenetic effect in which one allele in the parent acts in trans to influence the activity of the other allele in a way that remains following its segregation into offspring (9,12).
The effects of the insulin-linked region on susceptibility to T1DM most likely result from variable transcriptional regulation of INS and of the neighbouring gene, insulin-like growth factor II (IGF2) (13). For example, most class III alleles associate with an increase in insulin gene transcription in the fetal thymus (14,15). Insulin and its precursors are the only known ß cell-specific proteins, so are major autoantigens in T1DM. Elevated INS expression could increase T cell tolerance to insulin peptides and so it has been proposed that this class III-associated increase in INS expression results in the observed class III-associated protection against T1DM (14,15). This transcriptional regulation may be mediated by both the composition and distribution of variant repeats within the minisatellite (10,16,17).
We have previously analysed levels of allele diversity at the insulin minisatellite by typing 876 alleles by minisatellite variant repeat mapping by PCR (MVR–PCR) (18,19). These alleles were derived from the parents of 219 T1DM affected sib pair (ASP) families, a subset of the families analysed by Bennett et al. (9). Here, we have combined MVR code with flanking haplotype to identify ancestral lineages of closely related alleles and have used these lineages to extend previous investigations into the effects of the minisatellite and its haplotypes on susceptibility to T1DM.
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Ancestral lineages of the insulin minisatellite
Of the 219 families investigated in this study, 128 had been previously analysed at the single nucleotide polymorphisms (SNP) –2733A/C, –2221MspI, –23HphI, +805DraIII, +1127PstI and +1428FokI and at the tyrosine hydroxylase microsatellite (HUMTH01) 9 kb 5' of INS (8). An additional SNP, +3580MspI+/–, located within intron 1 of IGF2 3' of INS (20), had been previously typed in some families (8). Analysis of +3580MspI+/– was extended to include all families allowing haplotypes to be defined over a wider area across the insulin-linked region.
MVR-PCR analysis demonstrated that almost all class III alleles of the insulin minisatellite divide by allele structure into two highly diverged lineages, IIIA and IIIB (Figs 1 and 2) (19; a full list of allele codes is available at http://www.le.ac.uk/genetics/ajj/insulin ). Integration of genotypes at each polymorphic site with the inheritance patterns defined by MVR code for each family allowed the conversion of genotypes to haplotypes. This analysis showed that lineages IIIA and IIIB correspond exactly to the PH and VPH, respectively. With only one exception, all 169 IIIA and IIIB haplotypes were +3580MspI+. Almost all class I alleles share identical haplotypes between the polymorphisms –2733A/C and +1428FokI (8), but could be divided by MVR code into two lineages, IC and ID (Fig. 1) (19). All class I haplotypes were also +3580MspI+ except for a subset of ID alleles. Combining allele structure with the presence (+) or absence (–) of +3580MspI+/– thus defined three class I subgroups: IC+, ID+ and ID– (Figs 1 and 2).
|
3' with the insulin gene to the right. Variant repeat sequences are described, with sites differing from the A-type repeat consensus underlined. Hyphens were inserted to align class I alleles and single representative examples of class IIIA and IIIB alleles are each divided over three lines due to their size. Alleles were assigned by a combination of variant repeat distribution and flanking haplotype to five groups. Allele names reflect allele group, repeat number and a further discriminator; for example allele ID42.4 is the fourth allele with a length of 42 repeats identified in group ID (for purposes of nomenclature, groups ID+ and ID– are combined since the ID+/– subdivision was based on flanking haplotype). Alleles ID40.3 and ID43.9 showed mixed haplotypes with 1/3 and 4/37 of these alleles respectively associated with the presence of the +3580MspI restriction site. A full list of allele structures is available at http://www.le.ac.uk/genetics/ajj/insulin and structural diversity is described in detail elsewhere (19).
|
To test whether the five classes of the minisatellite correspond to true lineages, we analysed linkage disequilibrium between the minisatellite and HUMTH01. HUMTH01 has five common alleles composed of 6 (allele Z-16) to 10 (allele Z) tandem repeats of a TCAT tetramer (21,22). Haplotypes of the five classes of minisatellite were each dominated by a different allele of HUMTH01 (Fig. 3), confirming that each class represented a distinct ancestral lineage that has retained linkage disequilibrium over a region of at least 9 kb. The greatest breakdown of linkage disequilibrium between the minisatellite and HUMTH01 was within the ID– lineage, where ID– haplotypes were associated with both allele Z-16 (59% of haplotypes) and allele Z (33% of haplotypes) at HUMTH01. Eighty-nine per cent of all Z/ID– haplotypes shared identical alleles of the insulin minisatellite (allele ID42.4, which represents 94% of all the alleles classified by length as allele 814) (Fig. 1). Surprisingly, these ID42.4 alleles were linked to both Z-16 and Z alleles of HUMTH01 (40 and 56% of ID42.4 alleles, respectively), indicating either a mutation event at the microsatellite or, more plausibly given the stepwise mode of microsatellite mutation, a recombination event between HUMTH01 and the insulin minisatellite, most likely between a Z-16/ID42.4 haplotype and a Z/IIIA haplotype. Reduced linkage disequilibrium on the ID– haplotype could therefore be attributed to a single ancient recombination event.
|
The insulin minisatellite and susceptibility to T1DM
To investigate the effects of each of the five lineage groups on susceptibility to T1DM, transmissions to affected offspring were analysed from I/III and I/I heterozygous parents. The parental III/III genotype was too infrequent for useful analysis.
Transmissions from I/III heterozygous parents
Bennett et al. (9) found class I alleles to be more predisposing to T1DM when transmitted from I/III heterozygous mothers compared with fathers due to the protective effects of allele 814 (42 repeats) when transmitted from 814/III fathers. In this study, we analysed a subset of the ASP families previously investigated by Bennett et al. (9). As expected, analysis of transmissions using the transmission/disequilibrium test (TDT) (23) found that, whereas class I alleles were transmitted to affected offspring from I/III heterozygous mothers at a frequency significantly greater than 50%, they were not significantly predisposing when transmitted from I/III heterozygous fathers (Table 1). Surprisingly, analysis of the same transmissions by identity by descent (IBD) did identify linkage of the minisatellite with susceptibility to T1DM for transmissions from both I/III heterozygous mothers (P < 0.002) and fathers (P < 0.02) (Table 1). IBD considers co-transmission of any allele to ASPs, whereas TDT considers transmission of specific allele classes to affected offspring. This finding of significant linkage of the minisatellite with susceptibility to T1DM when analysed by IBD but not TDT therefore suggests that for transmissions from I/III heterozygous fathers either some paternally transmitted class I alleles are more protective than class III alleles or the aetiological variant which associates with disease is linked to, but not in linkage disequilibrium with, the insulin minisatellite. To clarify the nature of this difference between maternal and paternal transmissions, the same transmissions were re-analysed following division of either class I or class III alleles into the lineages defined by a combination of minisatellite variant repeat distribution and flanking haplotype.
|
Subdivision of class III alleles
Three groups have identified subclasses of class III alleles that can be recognized by size and by flanking haplotype (8,24,25) and are differentially associated with levels of protection against T1DM, the PH and the VPH. In this study we failed to detect any differences between the levels of protection associated with these classes (data not shown). Since these families are a subset of those used by Bennett et al. (8), this was presumably due to our smaller sample size. Due to the absence in this subset of families of any detectable heterogeneity between class III allele subgroups, class III alleles in subsequent analyses were treated as a single homogeneous group.
Single alleles of the insulin minisatellite have been previously characterized from both the PH and VPH, with marked differences in the composition and distribution of variant repeats demonstrated between the PH and VPH (24,26,27). We have extended these studies to demonstrate that the level of allele diversity within both IIIA (PH) and IIIB (VPH) lineages is low (19). However, the relationship between the variant repeat composition of alleles and their levels of associated protection against T1DM remains ambiguous.
Subdivision of class I alleles
Class I alleles were divided by a combination of variant repeat distribution and haplotype into the three newly defined ancestral lineages, IC+, ID+ and ID– (Fig. 1). Variant repeat distribution at the INS VNTR is very similar for ID+ and ID– alleles but differs substantially from IC+ alleles. ID– alleles are the only alleles associated with the absence of the +3580MspI+/– polymorphic restriction site within IGF2, >4 kb downstream of the VNTR. Transmission frequencies of each of the three lineages were analysed from I/III heterozygous parents by the transmission asymmetry test (TAT) (28,29) (Table 2). Previous studies of these families have demonstrated that protection against T1DM associates with class I alleles of 42 repeats in length (allele 814), but only when transmitted from 814/III heterozygous fathers (8,9). In the present study, 195/196 alleles of 42 repeats in length were within the ID– lineage and it was anticipated that ID– alleles were likely to be protective when transmitted from ID–/III fathers. No difference was observed between class I allele transmissions from either IC+/III or ID+/III heterozygous mothers and fathers from whom class I alleles were transmitted to affected offspring at frequencies of 61–67%. Similarly, ID– alleles were transmitted from ID–/III mothers at a frequency of 73% and were significantly predisposing to disease (TDT; 
2 = 9.1, 1df, P < 0.005). In contrast, ID– alleles were not predisposing from ID–/III fathers, being transmitted at a frequency of 41%, significantly lower than the maternal transmission frequency (2 x 2 contingency table; 2 = 6.6, 1 df, P < 0.02). Whereas the transmission frequency of 41% is not significantly different from 50%, it does raise the possibility that ID– alleles may be more protective against T1DM than class III alleles transmitted from ID–/III heterozygous fathers. This in turn could contribute to the significant linkage by IBD but not TDT observed for transmissions from all I/III fathers (Table 1).
|
To test whether the protective effect of the ID– lineage was a property specifically of allele 814, all ID– alleles were divided into those of 42 repeats (814) and those of other sizes (non-814) and transmissions analysed from ID–/III fathers. Both 814 and non-814 alleles were transmitted to diabetic offspring at frequencies of <50% (45 and 30%, respectively) (data not shown). These transmission frequencies were significantly lower than the mean transmission frequency of 67% seen for class I alleles from all other I/III heterozygous parents (exact P = 0.031 and P = 0.019 for 814 and non-814 alleles, respectively). Although these results are based on a small sample size and must therefore be treated with caution, the data suggest that the protective effect previously associated with allele 814 (9) may not be a property exclusively of allele 814 but instead of all alleles in the ID– lineage irrespective of size.
Levels of protection associated with ID– alleles were indistinguishable between ID–/IIIA and ID–/IIIB fathers (data not shown), indicating that the ID– effect is not significantly modulated by differences between the lineages of the untransmitted class III allele.
Transmissions from I/I heterozygous parents
Analysis of transmission from I/I heterozygous parents by TDT found no heterogeneity between maternal and paternal transmissions from each genotype (Table 3). Furthermore, there was no evidence for linkage of the minisatellite with disease for transmissions from these parents when analysed by IBD (data not shown), suggesting that all class I alleles transmitted from I/I parents are equally predisposing to T1DM as indicated by previous studies (9). Only one parental genotype showed any evidence for deviation from 50% transmission, although this was of borderline significance (P = 0.04). This paternal IC+/ID– genotype displayed over-transmission of ID– alleles to diabetic offspring. Therefore, in contrast to transmissions from ID–/III fathers, ID– alleles are not protective when inherited from I/I parents and may even be relatively predisposing on transmission from IC+/ID– fathers, consistent with predisposition being modified by the untransmitted paternal allele (9).
|
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
Analysis of variant repeat distribution at the insulin minisatellite combined with flanking haplotype divided the insulin-linked region into five newly defined ancestral lineages: IC+, ID+, ID–, IIIA and IIIB. In general, class I alleles were equally predisposing to T1DM with the exception of ID– alleles transmitted exclusively from ID–/III heterozygous fathers. ID– alleles are typically larger than either ID+ or IC+ alleles (Fig. 2). A very tight size threshold may therefore exist above which class I alleles transmitted from I/III fathers are protective. Alternatively, protection could be due to variant repeat distribution within the insulin minisatellite. Typically, the protective ID– alleles differ from the predisposing ID+ alleles by the presence of an ABA motif 10 repeats upstream of the end of ID– alleles (Fig. 1). However, this motif is also present in all IC+ alleles which are predisposing to T1DM. While ID– alleles can be distinguished from IC+ by the presence of a 5' CAC block, a central FAC block and a 3' F repeat, these motifs are also present in most ID+ alleles which, in contrast to ID–, are predisposing to disease. There is therefore no consistent difference between repeat type distributions in the protective ID– lineages and both the IC+ and ID+ lineages, suggesting that ID– protection is not mediated by variant repeat composition or distribution.
A strong aetiological candidate for ID– protection is therefore the flanking haplotype. All ID– alleles lack the +3580MspI+/– polymorphic site within the first intron of IGF2 >4 kb downstream of the minisatellite, which is present in 99.6% of all other haplotypes. When considered in isolation, this SNP cannot be a candidate for all the effects associated with IDDM2, as in these families the +3580MspI– allele was transmitted from heterozygous parents to affected offspring at a frequency of 54% (P = 0.2) (for families where only one parent is heterozygous) compared with 60% transmission for class I alleles (P < 0.0001). However, all heterogeneity in the effects associated with class I allele susceptibility to T1DM observed in this study could be associated with this single polymorphic site, or to any other polymorphism in linkage disequilibrium with the ID– haplotype, as opposed to variation within the minisatellite itself. This in turn suggests that IDDM2 may have a multi-locus aetiological basis, with the putative effects of the secondary polymorphism depending on both parental genotype and gender.
The deep divergence between the ancestral class I, IIIA and IIIB lineages more generally raises the possibility that multiple and potentially aetiological lineage-restricted polymorphisms have accumulated within the insulin-linked region. However, the insulin minisatellite does remain the strongest candidate for the primary aetiological locus of IDDM2 and differences in repeat-type distribution (Fig. 1) and composition (Table 4) may account for the different effects of the three major lineages (classes I, IIIA and IIIB) on susceptibility to disease. For example, the H-type repeat may protect against disease by increasing insulin gene transcription through the binding of the Pur-1 transcription factor (17), although its presence in IIIA (PH) but not IIIB (VPH) alleles excludes it as the sole determinant of protection. A-type repeats encourage the formation in vitro of G-quartet structures that may elevate in vivo insulin gene transcription by facilitating denaturation at the insulin gene promoter (16). This functional role for A-type repeats is not supported by the higher frequency and copy number of A-type repeats found in IIIA (PH) alleles compared with the more protective IIIB (VPH) alleles. However, in IIIB alleles 5/6 repeats closest to the insulin gene were A-type compared with 0/6 in IIIA alleles (Fig. 1), so repeat distribution may be a more important factor than absolute composition. Methylation within the minisatellite may result in protection against T1DM (10) and imprinting is an obvious mechanism to account for the parent-of-origin effects observed at IDDM2. F-type repeats were the only variant repeats detected in this study which contained potential methylation sites. We found no correlation between the number of F-type repeats within each lineage and levels of protection against disease; for example there was no detectable difference between the effects associated with IC+ (two F repeats) and ID+ (four F repeats) alleles. However, some o-type repeats (repeats not amplified by MVR–PCR due to the presence of unknown repeat unit sequence variants) may contain CpG sites and so in the absence of detailed information on methylation within the minisatellite, a general correlation between levels of methylation and protection against T1DM cannot be excluded.
|
Finally, analysis of allele structures by MVR–PCR allowed the identification of individuals homozygous at the insulin minisatellite for both allele size and structure. More T1DM ASP families in this study had at least one homozygous parent (36/219 families) than families with at least one homozygous offspring (21/219 families) (
2 test against an expected 1:1 ratio; 2 = 3.95, P < 0.05). The expected number of families with true homozygous parents, derived by Hardy–Weinberg equilibrium from the allele frequency distribution in this cohort, is intermediate between that observed for parents and children (30.6/219 families; data not shown). This result is consistent with previous studies which demonstrated that the homozygous 814/814 genotype was under-represented in three T1DM populations compared with controls due to the protective effect of the common allele 814 (a subset of our ID– lineage) transmitted from 814/III fathers (9). However, if the difference in parent–offspring homozygosity observed in this study was entirely due to the protective effects of the ID–/ID– genotype, only this genotype would be expected to be under-represented in offspring. In contrast, the proportion of all true homozygotes that had the ID–/ID– genotype was indistinguishable between parents and independent offspring (67% in each generation), suggesting that true homozygosity may protect against T1DM, irrespective of genotype. Alternatively, it has been shown that the I/I genotype associates with reduced infant birth size (5). It is possible that true homozygosity may elevate fetal lethality, resulting in the lower frequency of homozygotes in the offspring. However, we cannot exclude the possibility that parental homozygosity may actually predispose to T1DM in offspring, as opposed to homozygosity in offspring being protective against T1DM. Bennett et al. (9) suggested that the protective effects of allele 814 transmitted from 814/III heterozygous fathers were due to the absence of ‘silencing’ of 814-associated gene expression in the fetal thymus (14,15) and that this might be mediated by a paramutagenic interaction between the 814 and class III alleles in the father. Evidence for interaction between alleles has since been found at Ins2, the mouse homologue of the human insulin-linked region (30). If gene ‘silencing’ in the offspring was the result of changes in methylation state or chromatin conformation due to DNA–DNA interactions in the parent (12), this model would predict that elevated parental homozygosity might promote such DNA–DNA interactions, resulting in increased gene ‘silencing’ and thus susceptibility to T1DM in offspring, potentially accounting for the elevated frequency of true homozygous parents compared with offspring observed in this study. Furthermore, the protective effects of ID– alleles transmitted from ID–/III fathers could relate to heterozygosity specifically in this genotype both at the insulin minisatellite and at the +3580MspI+/– variant, or at any other variant in linkage disequilibrium with +3580MspI+/–. The restriction of ID– protection to transmissions from fathers could be due to gender-specific differences in the identity of the regions involved in DNA–DNA interactions. However, this parent-of-origin effect has not been replicated in an independent family data set and until this is achieved its existence and properties remain speculative.
In summary, deeply divergent ancestral lineages of the insulin-linked region underlie the differential associations of alleles of the insulin minisatellite with susceptibility to T1DM and there is evidence that variation in the flanking haplotype contributes to the overall effects of IDDM2. The very high level of minisatellite lineage divergence raises the possibility that additional lineage-restricted polymorphisms have accumulated in linkage disequilibrium with the minisatellite and may contribute to IDDM2 aetiology. The identification of specific aetiological variants may prove difficult in white populations due to strong linkage disequilibrium and may therefore require the characterization of diversity in the insulin-linked region in additional populations.
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
DNA source
The families investigated in this study were a subset of those analysed by Bennett et al. (9).
Analysis of inheritance patterns
Allele sizes and MVR–PCR codes were determined as described elsewhere (19). In the majority of families, allele transmission could be analysed by allele size. Inheritance patterns from parents with alleles homozygous by size but heterozygous by MVR code were determined by MVR–PCR analysis of alleles from both parents and offspring. Where one allele was transmitted to both offspring, the identity of the untransmitted allele was defined by MVR code subtraction (18).
Haplotyping
The identity of the –23HphI flanking site was determined by allele-specific PCR across the minisatellite using universal primer INS-1296 and allele-specific primers INS-23+ and INS-23– as described elsewhere (19). Polymorphisms at sites –2733A/C, –2221MspI, +805DraIII, +1127PstI, +1428FokI and HUMTH01 were analysed as described elsewhere (8). To type the +3580MspI+/– polymorphic site (20), a 188 bp region containing the polymorphism was amplified using primers 3580-A (5'-CCCCAGGTCACCCCATGTGA-3') and 3580-B (5'-GGGCTGGAGGCAGCTGAGTG-3') in 10 µl PCR reactions on an MJ Tetrad thermal cycler (MJ Research, Waltham, MA), with 75 mM Tris–HCl pH 8.8, 20 mM (NH4)2SO4, 0.1% (v/v) Tween 20, 2 mM MgCl2, 0.2 mM of each dNTP, 0.4 µM of each primer and 0.05 U/µl Taq polymerase (Advanced Biotechnologies, Leatherland, UK). Genomic DNA (10 ng) was amplified at 96°C for 40 s, 58°C for 30 s, 70°C for 1 min for 31 cycles and digested with 2 U of MspI (Gibco BRL, Paisley, UK) in REact 1 buffer (Gibco BRL) for 2 h at 37°C. Samples were electrophoresed for 2 h at 5 V/cm through 4% Metaphor (FMC Bioproducts, Rockland, ME) agarose gels in 0.5x TBE buffer (44.5 mM Tris–borate pH 8.3, 1 mM EDTA) supplemented with 0.5 µg/ml ethidium bromide.
|
ACKNOWLEDGEMENTS |
|---|
We are grateful to Yuri Dubrova, Sarah Nutland and colleagues for helpful discussions. This work was supported in part by the British Diabetic Association and Wellcome Trust, in part by an International Research Scholars Award to A.J.J. from the Howard Hughes Medical Institute and in part by grants to A.J.J. from the Wellcome Trust, Medical Research Council and Royal Society.
|
FOOTNOTES |
|---|
+ To whom correspondence should be addressed. Tel: +44 116 252 3413; Fax: +44 116 252 3378; Email: jdhs1@le.ac.uk
§ Present address: Institut de Biologie, CNRS UPR 1142, 4 Boulevard Henri IV, 34060 Montpellier, France
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONRESULTSDISCUSSIONMATERIALS AND METHODSREFERENCES |
|---|
1 Bennett, S.T. and Todd, J.A. (1996) Human type 1 diabetes and the insulin gene: principles of mapping polygenes. Annu. Rev. Genet., 30, 343–370.[Web of Science][Medline]
2 Huxtable, S.J., Saker, P.J., Haddad, L., Walker, M., Frayling, T.M., Levy, J.C., Hitman, G.A., O’Rahilly, S., Hattersley, A.T. and McCarthy, M.I. (2000) Analysis of parent–offspring trios provides evidence for linkage and association between the insulin gene and type 2 diabetes mediated exclusively through paternally transmitted class III variable number tandem repeat alleles. Diabetes, 49, 126–130.[Abstract]
3 Waterworth, D.M., Bennett, S.T., Gharani, N., McCarthy, M.I., Hague, S., Batty, S., Conway, G.S., White, D., Todd, J.A., Franks, S. et al. (1997) Linkage and association of insulin gene VNTR regulatory polymorphism with polycystic ovary syndrome. Lancet, 349, 986–990.[Web of Science][Medline]
4 O’Dell, S.D., Bujac, S.R., Miller, G.J. and Day, I.N. (1999) Associations of IGF2 ApaI RFLP and INS VNTR class I allele size with obesity. Eur. J. Hum. Genet., 7, 821–827.[Web of Science][Medline]
5 Dunger, D.B., Ong, K.K., Huxtable, S.J., Sherriff, A., Woods, K.A., Ahmed, M.L., Golding, J., Pembrey, M.E., Ring, S., Bennett, S.T. et al. (1998) Association of the INS VNTR with size at birth. Nature Genet., 19, 98–100.[Web of Science][Medline]
6 Bell, G.I., Selby, M.J. and Rutter, W.J. (1982) The highly polymorphic region near the human insulin gene is composed of simple tandemly repeating sequences. Nature, 295, 31–35.[Medline]
7 Bell, G.I., Horita, S. and Karam, J.H. (1984) A polymorphic locus near the human insulin gene is associated with insulin-dependent diabetes mellitus. Diabetes, 33, 176–183.[Abstract]
8 Bennett, S.T., Lucassen, A.M., Gough, S.C., Powell, E.E., Undlien, D.E., Pritchard, L.E., Merriman, M.E., Kawaguchi, Y., Dronsfield, M.J., Pociot, F. et al. (1995) Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nature Genet., 9, 284–292.[Web of Science][Medline]
9 Bennett, S.T., Wilson, A.J., Esposito, L., Bouzekri, N., Undlien, D.E., Cucca, F., Nistico, L., Buzzetti, R., Bosi, E., Pociot, F. et al. (1997) Insulin VNTR allele-specific effect in type 1 diabetes depends on identity of untransmitted paternal allele. Nature Genet., 17, 350–352.[Web of Science][Medline]
10 Awata, T., Kurihara, S., Kikuchi, C., Takei, S., Inoue, I., Ishii, C., Takahashi, K., Negishi, K., Yoshida, Y., Hagura, R. et al. (1997) Evidence for association between the class I subset of the insulin gene minisatellite (IDDM2 locus) and IDDM in the Japanese population. Diabetes, 46, 1637–1642.[Abstract]
11 Urrutia, I., Calvo, B., Bilbao, J.R. and Castano, L. (1998) Anomalous behaviour of the 5' insulin gene polymorphism allele 814: lack of association with type I diabetes in Basques. Diabetologia, 41, 1121–1123.[Web of Science][Medline]
12 Wolffe, A.P. and Matzke, M.A. (1999) Epigenetics: regulation through repression. Science, 286, 481–486.
13 Paquette, J., Giannoukakis, N., Polychronakos, C., Vafiadis, P. and Deal, C. (1998) The INS 5' variable number of tandem repeats is associated with IGF2 expression in humans. J. Biol. Chem., 273, 14158–14164.
14 Vafiadis, P., Bennett, S.T., Todd, J.A., Nadeau, J., Grabs, R., Goodyer, C.G., Wickramasinghe, S., Colle, E. and Polychronakos, C. (1997) Insulin expression in human thymus is modulated by INS VNTR alleles at the IDDM2 locus. Nature Genet., 15, 289–292.[Web of Science][Medline]
15 Pugliese, A., Zeller, M., Fernandez Jr, A., Zalcberg, L.J., Bartlett, R.J., Ricordi, C., Pietropaolo, M., Eisenbarth, G.S., Bennett, S.T. and Patel, D.D. (1997) The insulin gene is transcribed in the human thymus and transcription levels correlated with allelic variation at the INS VNTR-IDDM2 susceptibility locus for type 1 diabetes. Nature Genet., 15, 293–297.[Web of Science][Medline]
16 Catasti, P., Chen, X., Moyzis, R.K., Bradbury, E.M. and Gupta, G. (1996) Structure–function correlations of the insulin-linked polymorphic region. J. Mol. Biol., 264, 534–545.[Web of Science][Medline]
17 Kennedy, G.C., German, M.S. and Rutter, W.J. (1995) The minisatellite in the diabetes susceptibility locus IDDM2 regulates insulin transcription. Nature Genet., 9, 293–298.[Web of Science][Medline]
18 Jeffreys, A.J., MacLeod, A., Tamaki, K., Neil, D.L. and Monckton, D.G. (1991) Minisatellite repeat coding as a digital approach to DNA typing. Nature, 354, 204–209.[Medline]
19 Stead, J.D. and Jeffreys, A.J. (2000) Allele diversity and germline mutation at the insulin minisatellite. Hum. Mol. Genet., 9, 713–723.
20 Lucassen, A.M., Julier, C., Beressi, J.P., Boitard, C., Froguel, P., Lathrop, M. and Bell, J.I. (1993) Susceptibility to insulin dependent diabetes mellitus maps to a 4.1 kb segment of DNA spanning the insulin gene and associated VNTR. Nature Genet., 4, 305–310.[Web of Science][Medline]
21 O’Malley, K.L. and Rotwein, P. (1988) Human tyrosine hydroxylase and insulin genes are contiguous on chromosome 11. Nucleic Acids Res., 16, 4437–4446.
22 Polymeropoulos, M.H., Xiao, H., Rath, D.S. and Merril, C.R. (1991) Tetranucleotide repeat polymorphism at the human tyrosine hydroxylase gene (TH). Nucleic Acids Res., 19, 3753.
23 Spielman, R.S., McGinnis, R.E. and Ewens, W.J. (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet., 52, 506–516.[Web of Science][Medline]
24 Owerbach, D. and Gabbay, K.H. (1993) Localization of a type I diabetes susceptibility locus to the variable tandem repeat region flanking the insulin gene. Diabetes, 42, 1708–1714.[Abstract]
25 Undlien, D.E., Bennett, S.T., Todd, J.A., Akselsen, H.E., Ikaheimo, I., Reijonen, H., Knip, M., Thorsby, E. and Ronningen, K.S. (1995) Insulin gene region-encoded susceptibility to IDDM maps upstream of the insulin gene. Diabetes, 44, 620–625.[Abstract]
26 Owerbach, D. and Aagaard, L. (1984) Analysis of a 1963 bp polymorphic region flanking the human insulin gene. Gene, 32, 475–479.[Web of Science][Medline]
27 Owerbach, D. and Gabbay, K.H. (1996) The search for IDDM susceptibility genes: the next generation. Diabetes, 45, 544–551.[Abstract]
28 Weinberg, C.R., Wilcox, A.J. and Lie, R.T. (1998) A log-linear approach to case-parent-triad data: assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting. Am. J. Hum. Genet., 62, 969–978.[Web of Science][Medline]
29 Weinberg, C.R. (1999) Methods for detection of parent-of-origin effects in genetic studies of case-parents triads. Am. J. Hum. Genet., 65, 229–235.[Web of Science][Medline]
30 Duvillie, B., Bucchini, D., Tang, T., Jami, J. and Paldi, A. (1998) Imprinting at the mouse Ins2 locus: evidence for cis- and trans-allelic interactions. Genomics, 47, 52–57.[Web of Science][Medline]
31 Eaves, I.A., Bennett, S.T., Forster, P., Ferber, K.M., Ehrmann, D., Wilson, A.J., Bhattacharyya, S., Ziegler, A.G., Brinkmann, B. and Todd, J.A. (1999) Transmission ratio distortion at the INS-IGF2 VNTR. Nature Genet., 22, 324–325.[Web of Science][Medline]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. Awata, E. Kawasaki, H. Ikegami, T. Kobayashi, T. Maruyama, K. Nakanishi, A. Shimada, H. Iizuka, S. Kurihara, M. Osaki, et al. Insulin Gene/IDDM2 Locus in Japanese Type 1 Diabetes: Contribution of Class I Alleles and Influence of Class I Subdivision in Susceptibility to Type 1 Diabetes J. Clin. Endocrinol. Metab., May 1, 2007; 92(5): 1791 - 1795. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. N. M. Day, S. Rodriguez, J. Kralovicova, P. J. Wood, I. Vorechovsky, and T. R. Gaunt Questioning INS VNTR role in obesity and diabetes: subclasses tag IGF2-INS-TH haplotypes; and -23HphI as a STEP (splicing and translational efficiency polymorphism) Physiol Genomics, December 13, 2006; 28(1): 113 - 113. [Full Text] [PDF]
|
|
|
|
 |
|
 M. Desai, E. Zeggini, V. A. Horton, K. R. Owen, A. T. Hattersley, J. C. Levy, G. A. Hitman, M. Walker, R. R. Holman, M. I. McCarthy, et al. The Variable Number of Tandem Repeats Upstream of the Insulin Gene Is a Susceptibility Locus for Latent Autoimmune Diabetes in Adults Diabetes, June 1, 2006; 55(6): 1890 - 1894. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Le Fur, C. Auffray, F. Letourneur, C. Cruaud, C. Le Stunff, and P. Bougneres Heterogeneity of class I INS VNTR allele association with insulin secretion in obese children Physiol Genomics, May 16, 2006; 25(3): 480 - 484. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Durinovic-Bello, E. Jelinek, M. Schlosser, T. Eiermann, B. O. Boehm, W. Karges, L. Marchand, and C. Polychronakos Class III Alleles at the Insulin VNTR Polymorphism Are Associated With Regulatory T-Cell Responses to Proinsulin Epitopes in HLA-DR4, DQ8 Individuals Diabetes, December 1, 2005; 54(suppl_2): S18 - S24. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. N. M. Day, X.-h. Chen, T. R. Gaunt, T. H. T. King, A. Voropanov, S. Ye, S. Rodriguez, H. E. Syddall, A. A. Sayer, E. M. Dennison, et al. Late Life Metabolic Syndrome, Early Growth, and Common Polymorphism in the Growth Hormone and Placental Lactogen Gene Cluster J. Clin. Endocrinol. Metab., November 1, 2004; 89(11): 5569 - 5576. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Rodriguez, T. R. Gaunt, S. D. O'Dell, X.-h. Chen, D. Gu, E. Hawe, G. J. Miller, S. E. Humphries, and I. N.M. Day Haplotypic analyses of the IGF2-INS-TH gene cluster in relation to cardiovascular risk traits Hum. Mol. Genet., April 1, 2004; 13(7): 715 - 725. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. D.H. Stead, M. E. Hurles, and A. J. Jeffreys Global Haplotype Diversity in the Human Insulin Gene Region Genome Res., September 1, 2003; 13(9): 2101 - 2111. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Langdon and J. A.L. Armour Evolution and population genetics of the H-ras minisatellite and cancer predisposition Hum. Mol. Genet., April 15, 2003; 12(8): 891 - 900. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M A Kelly, M L Rayner, C H Mijovic, and A H Barnett Molecular aspects of type 1 diabetes Mol. Pathol., February 1, 2003; 56(1): 1 - 10. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||