Paul J. Hagerman

Elevated Levels of FMR1 mRNA in Carrier Males: A New Mechanism of Involvement in the Fragile-X Syndrome

Fragile-X syndrome is a trinucleotide-repeat-expansion disorder in which the clinical phenotype is believed to result from transcriptional silencing of the fragile-X mental retardation 1 (FMR1) gene as the number of CGG repeats exceeds approximately 200. For premutation alleles ( approximately 55-200 repeats), no abnormalities in FMR1-gene expression have been described, despite growing evidence of clinical involvement in premutation carriers. To address this (apparent) paradox, we have determined, for 16 carrier males (55-192 repeats), the relative levels of leukocyte FMR1 mRNA, by use of automated fluorescence-detection reverse transcriptase-PCR, and the percent of lymphocytes that are immunoreactive for FMR1 protein (FMRP). For some alleles with>100 repeats, there was a reduction in the number of FMRP-positive cells. Unexpectedly, FMR1 mRNA levels were elevated at least fivefold within this same range. No significant increase in FMR1 mRNA stability was observed in a lymphoblastoid cell line (160 repeats) derived from one of the carrier males, suggesting that the increased message levels are due to an increased rate of transcription. Current results support a mechanism of involvement in premutation carriers, in which reduced translational efficiency is at least partially compensated through increased transcriptional activity. Thus, diminished translational efficiency may be important throughout much of the premutation range, with a mechanistic switch occurring in the full-mutation range as the FMR1 gene is silenced.

Clinical involvement and protein expression in individuals with the FMR1 premutation

Most individuals with the fragile X premutation are clinically unaffected; however, some show clinical manifestations, including learning difficulties, emotional problems, or even mental retardation. The basis of clinical involvement in these individuals is unknown. Premutation alleles are reportedly associated with normal levels of mRNA and protein (FMRP). To examine this issue in more detail, we studied six individuals with a premutation. We are reporting these cases to demonstrate a spectrum of phenotypic involvement which can be seen clinically. These cases include one individual with the premutation who has no evidence of FMR1 gene dysfunction but has mental retardation from other causes. Other cases presented here show varying degrees of FMR1 gene dysfunction as assessed by FMRP and FMR1 mRNA levels and various clinical features of fragile X. In two cases we observed a significant reduction in FMRP expression and an elevated FMR1 mRNA expression level associated with moderate cognitive deficit. Thus, the utilization of FMRP measures can be helpful in understanding for which premutation patients clinical involvement is caused by dysfunction of the FMR1 gene.

Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure: II. NaCl-dependence of DNA flexibility and helical repeat

In this work, we demonstrate that it is possible to determine the molar cyclization factor jM from single ligation reactions in which both circular and linear dimer DNA species are formed concurrently from linear monomers. This approach represents a significant improvement over previous methods, in which jM is evaluated from the ratio of the rate constants for two separate processes; namely (1) the cyclization of linear DNA and (2) the association of two linear molecules to form linear dimers. Determination of jM for a 366 base-pair molecule yields 5.8 X 10(-8) M, in close agreement with the value of 5.6 X 10(-8) M determined by Shore et al. for the same molecule. Using the current approach for the determination of jM, we have investigated the dependence on NaCl concentration (0 to 162 mM-NaCl, 1 mM-MgCl2) of both the lateral and torsional flexibilities of DNA. The principal observation is that both quantities are essentially constant over the above range of NaCl concentrations, with the persistence length P approximately 450 (+/- 15) A, and the torsional elastic constant C approximately 2.0 (+/- 0.2) X 10(-19) erg cm. These observations are in accord with the previous theoretical prediction that P becomes essentially independent of NaCl concentration above 10 to 20 mM. We have examined the dependence of the helical repeat of DNA on NaCl concentration over the above range, and have found the value of 10.44 base-pairs per turn to be essentially constant over that range. This last result suggests that earlier studies have overestimated the dependence of DNA helical twist on salt concentration.

Transcription of the FMR1 gene in individuals with fragile X syndrome

Fragile X syndrome generally arises as a consequence of a large expansion of a CGG trinucleotide repeat element that is located in the GC-rich promoter region of the fragile X mental retardation gene (FMR1). In the conventional model for fragile X, clinical involvement arises as a consequence of silencing of the FMR1 gene, with the attendant loss of FMR1 protein (FMRP). However, it has recently been demonstrated that most males with large premutation alleles (100-200 repeats), or with unmethylated full mutation alleles, have FMR1 mRNA levels that are higher than normal, despite reduced levels of FMRP. In the current work, we extend and confirm these observations using quantitative (fluorescent) reverse transcription polymerase chain reaction on larger sample populations, establishing that even for smaller premutation alleles (55-100 repeats) the mRNA levels are significantly elevated (mean 2.1-fold elevation; P = 3.9 x 10(-3)), relative to normal controls. Thus, an abnormal molecular phenotype is established close to the upper end of the normal range. We also demonstrate that the levels of FMR1 mRNA are elevated in females with premutation alleles; however, the mRNA levels are more varied than in the males, and are attenuated in a manner that is consistent with the fraction of normal alleles that are active in any given individual. Finally, we demonstrate that in lymphoblastoid cells derived from a patient with a severe form of fragile X caused by a point mutation in the second KH domain of the gene, but with a normal CGG element (25 repeats), the FMR1 mRNA level is normal. Thus, although models in which FMRP level (or level of function) modulates transcriptional activity remain viable, other explanations for the elevated message levels, including direct (cis) effects of the CGG element on transcription, must also be considered.

Intranuclear inclusions in neural cells with premutation alleles in fragile X associated tremor/ataxia syndrome

Fragile X syndrome is generally considered to be a non-progressive neurodevelopmental disorder in which carriers of premutation alleles (~55 to 200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene are largely unaffected. However, we have recently identified a new syndrome among male carriers, characterised by tremor and/or ataxia, cognitive deficits, parkinsonism, and autonomic dysfunction.1,5,6,8,10 Neuroradiological findings include moderate to severe cortical atrophy (cerebral and cerebellar cortical volume loss) and characteristic hyperintensities on T2-weighted MR imaging of the deep cerebellar white matter and middle cerebellar peduncles.2,8 The disorder, termed fragile X associated tremor/ataxia syndrome,8 has been observed thus far almost exclusively in older adult male premutation carriers of more than 50 years of age. Eosinophilic intranuclear inclusions are broadly distributed in both neurones and astrocytes throughout the cerebrum and brain stem of all persons with fragile X associated tremor/ataxia syndrome (FXTAS) examined to date (8/8),5,7 with the greatest numbers of neuronal inclusions found in the hippocampus. No inclusions were detected in the Purkinje cells, although axonal degeneration and Purkinje cell loss were prominent findings in the cerebellum.5 Premutation carriers generally have elevated FMR1 mRNA levels, suggesting that FXTAS could result from a toxic gain of function of the FMR1 mRNA.5,6,8 To determine whether inclusion formation and clinical involvement are associated with allelic mosaicism, we defined the size of the CGG expansion and the relative expression levels of the FMR1 gene in various regions of the brain of a male premutation carrier who died with neurological symptoms consistent with FXTAS, and whose neural cells possessed numerous intranuclear inclusions. Analysis of multiple brain regions was undertaken to demonstrate that premutation alleles were directly associated with inclusion formation, and that full mutation alleles, even if present at …

Gel electrophoretic analysis of the geometry of a DNA four-way junction

Branched DNA molecules (Holliday structures) are believed to be key intermediates in the process of homologous genetic recombination. However, despite the importance of such structures, their transient nature makes it difficult to analyze their physical properties. In an effort to evaluate several models for the geometry of such branched molecules, a stable, synthetic DNA four-way junction has been constructed. The geometry of the synthetic junction has been probed by gel electrophoresis, utilizing the fact that bent DNA molecules demonstrate reduced mobilities on polyacrylamide gels to an extent that varies with the degree of the bend angle. From the synthetic four-way junction, we have produced a set of molecules in which all combinations of two junction arms have been extended by 105 base-pairs. The electrophoretic mobilities of the extended junctions differ in a manner which indicates that the junction is not a completely flexible structure; nor is it tetrahedral or planar-tetragonal. Instead, the four strands that comprise the DNA four-way junction are structurally non-equivalent. The significance of these observations with regard to previous models for four-way junction geometry is discussed.

Fragile X males with unmethylated, full mutation trinucleotide repeat expansions have elevated levels of FMR1 messenger RNA

Fragile X syndrome normally arises as a consequence of large expansions (n >200) of a (CGG)(n) trinucleotide repeat in the promoter region of the FMR1 gene. The clinical phenotype is thought to result from hypermethylation of the repeat and adjacent upstream elements, with consequent down-regulation of transcription (transcriptional silencing). However, the relationship between repeat expansion and transcription has not been defined in the full mutation range. Using the method of quantitative (fluorescence) reverse transcriptase polymerase chain reaction, we demonstrated previously that FMR1 mRNA levels are substantially elevated in premutation (55 </= n < 200) male carriers. In the current work, we report that in fragile X males with unmethylated alleles in the full mutation range (n > 200), FMR1 mRNA levels remain significantly elevated (mean 3.5-fold elevation; P = 6.7 x 10(-3)) relative to normal controls, even for alleles exceeding 300 repeats. This conclusion is independent of any assumption regarding the transcriptional activity of methylated alleles. However, if it were assumed that all methylated alleles were transcriptionally silent, the FMR1 mRNA levels for cells with unmethylated alleles would be even higher (mean 4.5-fold elevation; P = 2.1 x 10(-4)). These observations show that the full-mutation CGG expansion per se is not a strong impediment to transcription and that the apparent up-regulation of the FMR1 locus remains active in at least some cells with full-mutation alleles.

Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. I. Computational analysis

The tendency for relatively short (less than 500 base-pair) DNA molecules to circularize in the presence of DNA ligase is a sensitive function of both the lateral and torsional flexibilities of the molecules being studied. This tendency is reflected in a quantity known as the j-factor, which is determined experimentally by measuring the relative rates of circle and linear dimer formation at a specified concentration of linear monomer. Shimada & Yamakawa have provided an analytical representation of j that takes account of DNA molecules whose ends are not torsionally aligned. Their approach, however, assumes that contributions from helix writhe are small. Using a Monte Carlo approach for the determination of j, thereby avoiding any assumptions regarding writhe, we demonstrate that the computed, torsion angle-averaged quantity, [j], is exactly reproduced by the corresponding Shimada & Yamakawa quantity for all lengths examined. However, for DNA molecules having lengths that are substantially greater than the persistence length, P, the analysis of experimental ring-closure data using j (Shimada & Yamakawa) may lead to underestimates for the torsional elastic constant C. We demonstrate that no single set of values for P, C and the helical repeat (hR) can produce a reasonable fit of the computed j curve to the experimental values of Shore et al. This observation suggests that P, C and/or hR vary within the set of DNA molecules studied by those authors. The current computational analysis considers the effects on j of single or multiple bends in the helix axis. For single, centrally located bends, the shift in the distribution of end-to-end separations to smaller values is nearly offset by the less favorable polar alignment of the ends of the chain; the net effect being a modest change in j that is not a monotonic function of the bend angle. In contrast, polar alignment, and hence j, can be enhanced dramatically for molecules containing multiple, phased bends. However, for studies of the distribution of circle sizes formed from ligation of bend-containing DNA oligomers, the DNA lengths giving rise to maximal j values are smaller than predicted on the basis of the number of bends and the per-bend angle. This last result suggests that such studies may yield apparent bend angles that are too large.

Straightening out the bends in curved DNA

Polymeric DNA molecules possess a certain degree of intrinsic flexibility (Refs. 1-3; reviewed in Ref. 4), which affords their organization into various compact structures such as chromatin and viral capsids. Viewed from afar, at the level of hundreds of base pairs, such flexibility has generally been regarded as being isotropic, although recent theoretical studies [5-8] suggest that a strong local (base pair level) directionality exists for the transient deflections of the helix axis. Work over the past decade (recent reviews include

A majority of fragile X males with methylated, full mutation alleles have significant levels of FMR1 messenger RNA

FMR1 mRNA levels were determined in peripheral blood leucocytes for 48 fragile X males with methylated, full mutation alleles that are resistant to cleavage by methylation sensitive enzymes. Using quantitative (fluorescence) RT-PCR, we observed that more than half of these males produceFMR1 mRNA, with some mRNA levels approaching those found in normal subjects. In none of the samples analysed was there any evidence of premutation alleles. These results suggest that the assumed relationship between enzyme resistance andFMR1 gene silencing may not be generally valid. Despite the presence of FMR1 mRNA in some subjects, no FMRP production was detected by either immunocytochemistry or western blotting. The low/absent FMRP levels are probably a reflection of a post-trancriptional effect such as a defect in translation.