Fragile X founder chromosome effects: linkage disequilibrium or microsatellite heterogeneity?

Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Dispersal is a key factor in invasion and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of the parent-offspring distance distribution, of the western corn rootworm, Diabrotica virgifera virgifera, one of the most destructive pests of maize. This species is currently invading Europe, and the two largest invasive outbreaks, in northern Italy and Central Europe, have recently formed a secondary contact zone in northern Italy. We identified vanishing clines at 12 microsatellite loci throughout the contact zone. By analysing both the rate of change of cline slope and the spatial variation of linkage disequilibrium at these markers, we obtained two σ estimates of about 20 km/generation(1/2). Simulations indicated that these estimates were robust to changes in dispersal kernels and differences in population density between the two outbreaks, despite a systematic weak bias. These estimates are consistent with the results of direct methods for measuring dispersal applied to the same species. We conclude that secondary contact resulting from multiple introductions is very useful for the inference of dispersal parameters and should be more widely used in other species.

Microsatellites, from molecules to populations and back

Population genetics studies using microsatellites, and data on their molecular dynamics, are on the increase. But, so far, no consensus has emerged on which mutation model should be used, though this is of paramount importance for analysis of population genetic structure. However, this is not surprising given the variety of microsatellite molecular motifs. Null alleles may be disturbing for population studies, even though their presence can be detected through careful population analyses, while homoplasy seems of little concern, at least over short evolutionary scales. Interspecific studies show that microsatellites are poor markers for phylogenetic inference. However, these studies are fuelling discussions on directional mutation and the role of selection and recombination in their evolution. Nonetheless, it remains true that microsatellites may be considered as good, neutral mendelian markers.

Elevated FMR1 mRNA in premutation carriers is due to increased transcription

Carriers of premutation alleles (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene have levels of FMR1 mRNA that are elevated by as much as 10-fold in peripheral blood leukocytes and CNS tissue. The excess expanded-repeat mRNA, per se, is now believed to result in forms of clinical involvement that are largely restricted to premutation carriers, including the neurodegenerative disorder, fragile X-associated tremor/ataxia syndrome (FXTAS). Although evidence to date suggests that the elevated mRNA is not due to increased stability, the basis for the increase is not known. In the current study, we have determined the relative transcriptional activities of premutation and normal FMR1 alleles using a highly sensitive nuclear run-on assay that involves immunocapture of digoxigenin-modified run-on transcripts followed by PCR amplification of the nascent transcripts. Using the nuclear run-on approach, we demonstrate that the rate of run-on synthesis of FMR1 transcripts is increased in premutation alleles. The current run-on assay should be broadly applicable to studies of other genes with promoters of weak to moderate strength. The fraction of capped FMR1 mRNA remains unaltered for premutation transcripts, indicating that elevated message levels are not due to premature escape from the cotranscriptional capping process. We also show that, in contrast to the situation with myotonic dystrophy, there is no net nuclear sequestration of premutation FMR1 mRNA. Finally, we have demonstrated that AGG interruptions within the CGG repeat element do not influence FMR1 mRNA levels.

FMR1 CGG repeat patterns and flanking haplotypes in three Asian populations and their relationship with repeat instability

Hyper-expansion of a CGG repeat in the 5' untranslated region of the FMR1 gene followed by methylation and silencing is the predominant cause of Fragile X syndrome, the most common inherited mental retardation disorder. Most detailed studies of the FMR1 gene have focused on Caucasian populations and patients. We performed a detailed haplotype and linkage disequilibrium analysis of the FMR1 gene in a total of 454 unselected normal X chromosomes from three Asian populations, Chinese, Malay and Indian. Compared to Caucasians and African Americans, the diversity of normal FMR1 CGG repeat lengths, patterns and flanking haplotypes were lower in Asians. Strong linkage disequilibrium was observed between the CGG repeat and flanking FMR1 markers in all three Asian populations, with strong association between specific CGG repeat alleles and flanking marker alleles observed only in the Chinese and Malays. A test for randomness of distribution between FRAXA CGG repeat patterns and flanking FMR1 marker haplotypes also revealed a highly significant non-random distribution between CGG repeat patterns and flanking haplotypes in all three ethnic groups (P < 0.001). Extending previous findings in Caucasians and African Americans we present a novel statistical approach, using data from unselected population samples alone, to show an association between absence of at least one AGG interruption in any position (5', 3', or middle) and increased CGG repeat instability.

Apparently unstable normal FMR1 alleles in nine developmentally delayed patients: implications for molecular diagnosis of the fragile X syndrome

The Fragile X syndrome is a common form of X-linked mental retardation, affecting approximately 1 in 4,000 males. Since the discovery of the FMR1 gene responsible for the syndrome, molecular, rather than cytogenetic, diagnosis of Fragile X syndrome has become the gold standard. Numerous molecular diagnostic centers worldwide use PCR and Southern blotting to characterize the size of the CGG repeats within the gene, expansion of which has been shown to be associated with the vast majority of cases of Fragile X syndrome. Instability of this repeat through successive generations has been demonstrated in many patients and has been associated with numerous factors, including repeat length and molecular structure of the repeat. Nine males with normal-size alleles that exhibit repeat length instability by the presence of a second normal length distinct band by repeated PCR analysis from peripheral lymphocytes are reported. Many hypotheses addressing the reason for this apparent instability were tested without elucidating the underlying molecular causes, including cytogenetic analysis, sequence analysis of the repeat locus, and analysis of flanking dinucleotide repeat loci. All patients exhibited a normal complement of sex chromosomes by cytogenetic and molecular analysis. These results from the widely used PCR analysis illustrate an interesting molecular phenomenon and raise many questions relating to the factors and mechanisms involved in trinucleotide instability as well as having implications for the diagnostic testing of the Fragile X syndrome.

Frequency of the fragile X syndrome in Chinese mentally retarded populations is similar to that in Caucasians

Fragile X syndrome is recognized as the most common inherited cause of mental retardation in western countries. The prevalence of the fragile X syndrome in Asian populations is uncertain. We report a multi-institutional collaborative study of molecular screening for the fragile X syndrome from 1,127 Chinese mentally retarded (MR) individuals. We found that 2.8% of the Chinese MR population screened by DNA analysis had the fragile X full mutation. Our screening indicated that the fragile X syndrome prevalence was very close to that of Caucasian subjects. In addition, we found that 62.5% of fragile X chromosomes had a single haplotype for DXS548-FRAXAC1 (21-18 repeats) which was present in only 9.7% of controls. This unique distribution of microsatellite markers flanking the FMR1 CGG repeats suggests that the fragile X syndrome in Chinese populations, as in the Caucasian, may also be derived from founder chromosomes.

Possible founder effects for FRAXE alleles

To determine if FRAXE alleles may have haplotype associations with nearby microsatellites, we analyzed 149 unrelated control Caucasian X chromosomes for FRAXE GCC alleles along with five nearby microsatellites. The microsatellites included three that are new; GT25, CA4, and CA5 located approximately 24, approximately 48, and approximately 50 kb proximal to the FRAXE GCC repeat, and two that were identified previously: DXS8091 and DXS1691, located approximately 90 and approximately 5 kb distal. No significant correlations between haplotypes for the proximal microsatellites were found. Significant correlations of FRAXE GCC repeats and distal microsatellite allele sizes, DXS8091 (r = 0.24) and DXS1691 (r = -0.40), were found. One haplotype, 18-19 of DXS8091-DXS1691, was present on 57% of chromosomes with > or =22 FRAXE repeats but present on only 10% with <22 repeats. We conclude that this distal haplotype association likely reflects a FRAXE allele founder effect. The lack of association or founder effects seen for the three newly identified proximal markers, located within 50 kb of FRAXE GCC, may reflect an unusually high rate of mutation for these microsatellites or a higher rate of recombination in the proximal region.

FRAXAC1 and DXS548 polymorphisms in the Chinese population

The fragile X syndrome is the most common inherited form of mental retardation. Haplotype studies using FRAXAC1 and DXS548 polymorphic markers flanking the fragile site have demonstrated linkage disequilibrium at the FMR1 locus. We investigated the association of the FRAXAC1, DXS548 and CGG alleles between normal subjects and mentally retarded (MR) patients of unspecified cause who do have fragile X syndrome. We have evaluated the FRAXAC1 site in 390 normal subjects and 321 MR patients and the DXS548 site in 146 normal and 319 MR subjects. Both FRAXAC1 and DXS548 alleles were determined by application of the polymerase chain reaction. When compared with Caucasians, the normal Chinese population has a different FRAXAC1 allele distribution. There are more AC18 repeat alleles and fewer AC19 repeat alleles. The DXS548 allele distributions were similar between Chinese and Caucasians. The same distribution pattern of FRAXAC1 alleles was found in both normal subjects and MR patients, but there were significant differences in the distribution patterns of DXS548 alleles. The FMR1 CGG-DXS548 and FRAXAC1-DXS548 haplotype distribution between normal subjects and MR patients also differed significantly. Our results suggest a possible association between DXS548 alleles and non-FRAXA mental retardation.

Placental expression of arylamine N-acetyltransferases: evidence for linkage disequilibrium between NAT1*10 and NAT2*4 alleles of the two human arylamine N-acetyltransferase loci NAT1 and NAT2

The study of placental xenobiotic metabolism is important for the determination of foetal exposure to environmental chemicals as placental metabolism influences the nature of chemicals reaching the foetus from its mother's blood. Arylamine N-acetyltransferases are drug metabolizing enzymes which N-acetylate hydrazines and arylamines, including carcinogenic arylamines and sulphonamide drugs. The two human arylamine N-acetyltransferase isoenzymes, NAT1 and NAT2, are encoded at multi-allelic loci. Here, we have determined N-acetyltransferase (NAT) activity in term placentas from normal, uncomplicated pregnancies. Both NAT1 and NAT2 enzyme activities were detectable. Placental NAT1 activity was at least 1000 fold greater than NAT2 activity. There was a 6 fold inter-placental variation in NAT1 activity. Mean placental NAT1 specific activity was 1.42 nmoles para-aminobenzoic acid N-acetylated.min-1.mg protein-1, which is comparable to NAT1 specific activities which have been measured in adult tissues. The NAT1, but not the NAT2, protein was detectable in placentas by Western blotting. Maternal and foetal NAT genotypes were determined from placenta, using placental blood clots and cord blood respectively, allowing NAT haplotype determination. There appeared to be linkage disequilbrium between NAT1* and NAT2* alleles such that the combination NAT1*10/NAT2*4 was found 3.5 times more frequently than would be expected.

Reduced penetrance of the Huntington's disease mutation

Controversy persists concerning the significance of Huntington disease (HD) alleles in the 36-39 repeat range. Although some clinically affected persons have been documented with repeats in this range, elderly unaffected individuals have also been reported. We examined 10 paternal transmissions of HD alleles of 37-39 repeats in collateral branches of families with de novo HD. All 10 descendants, including many who are elderly, are without symptoms of HD. Forty percent of the transmissions were unstable, although none varied by more than one repeat. The observation that individuals with alleles of 37-39 repeats may survive unaffected beyond common life expectancy supports the presence of reduced penetrance for HD among some persons with repeat sizes which overlap the clinical range. Non-penetrance may be increased in the collateral branches of de novo mutation families when compared to penetrance estimates from patient series. There was no CAA-->CAG mutation for the penultimate glutamine in either a de novo expanded 42 repeat allele or the corresponding non-penetrant 38 repeat allele in a family with fresh mutation to HD.

The role of size, sequence and haplotype in the stability of FRAXA and FRAXE alleles during transmission

Factors involved in the stability of trinucleotide repeats during transmission were studied in 139 families in which a full mutation, premutation or intermediate allele at either FRAXA or FRAXE was segregating. The transmission of alleles at FRAXA, FRAXE and four microsatellite loci were recorded for all individuals. Instability within the minimal and common ranges (0-40 repeats for FRAXA, 0-30 repeats for FRAXE) was extremely rare; only one example was observed, an increased in size at FRAXA from 29 to 39 repeats. Four FRAXA and three FRAXE alleles in the intermediate range (41-60) repeats for FRAXA, 31-60 for FRAXE) were unstably transmitted. Instability was more frequent for FRAXA intermediate alleles that had a tract of pure CGG greater than 37 although instability only occurred in two of 13 such transmissions: the changes observed were limited to only one or two repeats. Premutation FRAXA alleles over 100 repeats expanded to a full mutation during female transmission in 100% of cases, in agreement with other published series. There was no clear correlation between haplotype and probability of expansion of FRAXA premutations. Instability at FRAXA or FRAXE was more often observed in conjunction with a second instability at an independent locus suggesting genomic instability as a possible mechanism by which at least some FRAXA and FRAXE mutations arise.

Fragile X "gray zone" alleles: AGG patterns, expansion risks, and associated haplotypes

The risk for fragile X "gray-zone" alleles to expand appears to depend on the absence of stabilizing AGGs, which interrupt the CGG repeat region. To characterize such alleles better, we analyzed a series of 101 chromosomes with triplet repeat lengths ranging from 35 to 59 for variations in their AGG interspersion patterns. Among these, 11.9% had 3 AGGs, 59.3% had 2, 24.8% had 1, and 4.0% had 0. An inverse relationship between FMR1 repeat length and the number of interrupting AGGs was observed. Within the range of 35-44 repeats, 98.7% of alleles were found to have a pure CGG repeat length (PCGG) of less than 33. However, among alleles with 45-59 repeats, 50% were found to have 0 or 1 AGG and a PCGG of more than 33. Thus, gray-zone alleles with 45-59 repeats frequently have a long stretch of pure CGGs and thus are more likely to be unstably inherited than alleles with 35-44 repeats. We found length associations of PCGG with 2 flanking microsatellites, DXS548 and FRAXAC1: a PCGG < or = 20 was strongly associated with haplotype 20-19, whereas a PCGG > 20 was more strongly associated with the haplotype 25-21. This result could reflect a founder effect or a generalized instability of CGGs and microsatellites.

A survey of FRAXE allele sizes in three populations

FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) were analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA.

Fragile X founder chromosomes in Italy: a few initial events and possible explanation for their heterogeneity

A total of 137 fragile X and 235 control chromosomes from various regions of Italy were haplotyped by analyzing two neighbouring marker microsatellites, FRAXAC1 and DXS548. The number of CGG repeats at the 5' end of the FMR1 gene was also assessed in 141 control chromosomes and correlated with their haplotypes. Significant linkage disequilibrium between some "major" haplotypes and fragile X was observed, while other "minor" haplotypes may have originated by subsequent mutation at the marker microsatellite loci and/or recombination between them. Recent evidence suggests that the initial mechanism leading to CGG instability might consist of rare (10 (-6/-7)) CGG repeat slippage events and/or loss of a stabilizing AGG via A-to-C transversion. Also, the apparently high variety of fragile X chromosomes may be partly due to the relatively high mutation rate (10 (-4/-5)) of the microsatellite markers used in haplotyping. Our fragile X sample also showed a higher than expected heterozygosity when compared to the control sample and we suggest that this might be explained by the chance occurrence of the few founding events on different chromosomes, irrespective of their actual frequency in the population. Alternatively, a local mechanism could enhance the microsatellite mutation rate only on fragile X chromosomes, or fragile X mutations might occur more frequently on certain background haplotypes.

Fragile X founder effects and new mutations in Finland

The apparent associations between fragile X mutations and nearby microsatellites may reflect both founder effects and microsatellite instability. To gain further insight into their relative contributions, we typed a sample of 56 unrelated control and 37 fragile X chromosomes from an eastern Finnish population for FMR1 CGG repeat lengths, AGG interspersion patterns, DXS548, FRAXAC1, FRAXE and a new polymorphic locus, Alu-L. In the controls, the most common FMR1 allele was 30 repeats with a range of 20 to 47 and a calculated heterozygosity of 88%. A strong founder effect was observed for locus DXS548 with 95% of fragile X chromosomes having the 21 CA repeat (196 bp) allele compared to 17% of controls, while none of the fragile X but 69% of controls had the 20 repeat allele. Although the FRAXAC1 locus is much closer than DXS548 to FMR1 (7 kb vs. 150 kb), there was no significant difference between fragile X and control FRAXAC1 allele distributions. The FRAXE repeat, located 600 kb distal to FMR1, was found to show strong linkage disequilibrium as well. A newly defined polymorphism, Alu-L, located at approximately 40 kb distal to the FMR1 repeat, showed very low polymorphism in the Finnish samples. Analysis of the combined loci DXS548-FRAXAC1-FRAXE showed three founder haplotypes. Haplotype 21-19-16 was found on 27 (75%) of fragile X chromosomes but on none of controls. Three (8.4%) fragile X chromosomes had haplotypes 21-19-15, 21-19-20, and 21-19-25 differing from the common fragile X haplotype only in FRAXE. These could have arisen by recombination or from mutations of FRAXE. A second haplotype 21-18-17 was found in four (11.1%) fragile X chromosomes but only one (1.9%) control. This may represent a more recent founder mutation. A third haplotype 25-21-15, seen in two fragile X chromosomes (5.6%) and one (1.9%) control, was even less common and thus may represent an even more recent mutation or admixture of immigrant types. Analysis of the AGG interspersions within the FMR1 CGG repeat showed that 7/8 premutation chromosomes lacked an AGG whereas all controls had at least one AGG. This supports the hypothesis that the mutation of AGG to CGG leads to repeat instability and mutational expansion.

Evolutionary dynamics of the FMR1 locus

Rare haplotypes for close flanking markers are associated with increased allele size and frequency of the fragile X mutation. Exceptional founder haplotypes can be identified, but many haplotypes with rare alleles contribute to full mutations. A transition matrix constructed from the data predicts that a population with reduced variability will manifest a slowly increasing frequency of premutations and full mutations, reach a distribution close to the observed one after a few hundred generations, and then slowly be depleted of these alleles. This prediction is opposite to less well supported inference of increasing frequency of progressive amplification, but the data are inadequate to reach any firm conclusions. Factors that may determine the evolution of these systems, but cannot now be evaluated, are discussed.

Distribution of FMR-1 and associated microsatellite alleles in a normal Chinese population

The CGG repeat size distribution of the fragile X mental retardation gene (FMR-1) was studied in a population of normal Chinese X chromosomes along with that of two proximal microsatellite polymorphic markers: FRAXAC1 and DXS548. The most common CGG repeat allele was 29 (47.2%) with 30 being second most common (26%). This distribution was different from that seen in Caucasian controls, where the most common allele was 30 repeats. Other differences with Caucasian controls included a secondary modal peak at 36 repeats and the absence of peaks at 20 or 23 repeats. There were only two FRAXAC1 and five DXS548 alleles found in the Chinese sample. A striking linkage disequilibrium of FMR-1 alleles with FRAXAC1 alleles was observed, in that 90% of the 29 CGG repeat alleles but only 41% of the 30 CGG repeat alleles had the FRAXAC1 152 bp allele (18 AC repeats). This disequilibrium suggests that slippage between the closely spaced normal CGG repeat alleles, 29 and 30, and between 152 and 154 FRAXAC1 alleles is very rare. This study lays the groundwork for an understanding of founder chromosome effects in comparing Asian and Caucasian populations.