Demethylation, reactivation, and destabilization of human fragile X full-mutation alleles in mouse embryocarcinoma cells

Developmental study of fragile X syndrome using human embryonic stem cells derived from preimplantation genetically diagnosed embryos

We report on the establishment of a human embryonic stem cell (HESC) line from a preimplantation fragile X-affected embryo and demonstrate its value as an appropriate model to study developmentally regulated events that are involved in the pathogenesis of this disorder. Fragile X syndrome results from FMR1 gene inactivation due to a CGG expansion at the 5'UTR region of the gene. Early events in FMR1 silencing have not been fully characterized due to the lack of appropriate animal or cellular models. Here we show that, despite the presence of a full mutation, affected undifferentiated HESCs express FMR1 and are DNA unmethylated. However, epigenetic silencing by DNA methylation and histone modification occurs upon differentiation. Our unique cell system allows the dissection of the sequence by which these epigenetic changes are acquired and illustrates the importance of HESCs in unraveling developmentally regulated mechanisms associated with human genetic disorders.

Epigenetic analysis reveals a euchromatic configuration in the FMR1 unmethylated full mutations

Fragile X syndrome (FXS) is caused by the expansion of a CGG repeat in the 5'UTR of the FMR1 gene and the subsequent methylation of all CpG sites in the promoter region. We recently identified, in unrelated FXS families, two rare males with an unmethylated full mutation, that is, with an expanded CGG repeat (>200 triplets) lacking the typical CpG methylation in the FMR1 promoter. These individuals are not mentally retarded and do not appear to be mosaic for premutation or methylated full mutation alleles. We established lymphoblastoid and fibroblast cell lines that showed essentially normal levels of the FMR1-mRNA but reduced translational efficiency of the corresponding mRNA. Epigenetic analysis of the FMR1 gene demonstrated the lack of DNA methylation and a methylation pattern of lysines 4 and 27 on histone H3 similar to that of normal controls, in accordance with normal transcription levels and consistent with a euchromatic configuration. On the other hand, histone H3/H4 acetylation and lysine 9 methylation on histone H3 were similar to those of typical FXS cell lines, suggesting that these epigenetic changes are not sufficient for FMR1 gene inactivation. These findings demonstrate remarkable consistency and suggest a common genetic mechanism causing this rare FMR1 epigenotype. The discovery of such a mechanism may be important in view of therapeutic attempts to convert methylated into unmethylated full mutations, restoring the expression of the FMR1 gene.

Family-based linkage disequilibrium tests using general pedigrees

Linkage disequilibrium (LD) mapping has been established as a promising approach to identifying disease genes. The presence of a disease gene located near a marker locus may cause LD between the marker and the disease loci. In LD mapping, we assume that some of the affected individuals may have a common ancestor carrying the mutation and that mutation carriers are likely to share alleles at the markers loci close to the disease gene. This chapter reviews the concept of LD mapping and outlines the advantages and disadvantages of two LD mapping approaches capable of handling general pedigrees: the family-based association test (FBAT) and pseudomarker. In summary, the pseudomarker statistical approach and the FBAT approach are both expected to offer reasonable statistical power to detect genes underlying complex traits. However, when the pedigree structure is more complicated, or when the number of informative families is limited, the pseudo-marker approach is anticipated to outperform FBAT.

An origin of DNA replication in the promoter region of the human fragile X mental retardation (FMR1) gene

Fragile X syndrome, the most common form of inherited mental retardation in males, arises when the normally stable 5 to 50 CGG repeats in the 5' untranslated region of the fragile X mental retardation protein 1 (FMR1) gene expand to over 200, leading to DNA methylation and silencing of the FMR1 promoter. Although the events that trigger local CGG expansion remain unknown, the stability of trinucleotide repeat tracts is affected by their position relative to an origin of DNA replication in model systems. Origins of DNA replication in the FMR1 locus have not yet been described. Here, we report an origin of replication adjacent to the FMR1 promoter and CGG repeats that was identified by scanning a 35-kb region. Prereplication proteins Orc3p and Mcm4p bind to chromatin in the FMR1 initiation region in vivo. The position of the FMR1 origin relative to the CGG repeats is consistent with a role in repeat maintenance. The FMR1 origin is active in transformed cell lines, fibroblasts from healthy individuals, fibroblasts from patients with fragile X syndrome, and fetal cells as early as 8 weeks old. The potential role of the FMR1 origin in CGG tract instability is discussed.

DNA hypomethylation and human diseases

Changes in human DNA methylation patterns are an important feature of cancer development and progression and a potential role in other conditions such as atherosclerosis and autoimmune diseases (e.g., multiple sclerosis and lupus) is being recognised. The cancer genome is frequently characterised by hypermethylation of specific genes concurrently with an overall decrease in the level of 5 methyl cytosine. This hypomethylation of the genome largely affects the intergenic and intronic regions of the DNA, particularly repeat sequences and transposable elements, and is believed to result in chromosomal instability and increased mutation events. This review examines our understanding of the patterns of cancer-associated hypomethylation, and how recent advances in understanding of chromatin biology may help elucidate the mechanisms underlying repeat sequence demethylation. It also considers how global demethylation of repeat sequences including transposable elements and the site-specific hypomethylation of certain genes might contribute to the deleterious effects that ultimately result in the initiation and progression of cancer and other diseases. The use of hypomethylation of interspersed repeat sequences and genes as potential biomarkers in the early detection of tumors and their prognostic use in monitoring disease progression are also examined.

The pedigree trimming problem

This report mathematically validates a fast algorithm for trimming irrelevant members from a pedigree. These individuals are typically dead or otherwise unavailable for study. Left in the pedigree, they slow likelihood evaluation. Of course, each pedigree of interest will have some core people who must be retained. The described algorithm retains just enough of the pedigree to maintain the proper relationships among the core people.

Spinocerebellar ataxia type 26 maps to chromosome 19p13.3 adjacent to SCA6

The dominantly inherited spinocerebellar ataxias (SCA) are a clinically and genetically heterogeneous group of neurodegenerative disorders characterized by progressive gait ataxia, upper limb incoordination, and dysarthria. We studied a six-generation kindred of Norwegian ancestry with pure cerebellar ataxia inherited in an autosomal dominant pattern. All affected family members had a slowly progressive cerebellar ataxia, with an age of onset range from 26 to 60 years. Brain magnetic resonance imaging study of 11 affected patients showed that atrophy was confined to the cerebellum. After excluding all the known SCAs using linkage analysis or direct mutation screen, we conducted a genomewide genetic linkage scan. With the aid of a novel linkage analysis strategy, we found linkage between the disease locus and marker D19S591 and D19S1034. Subsequent genetic and clinical analysis identified a critical region of 15.55cM interval on chromosome 19p13.3, flanked by markers D19S886 and D19S894, and have established a new genetic locus designated SCA26. The SCA26 locus is adjacent to the genes for Cayman ataxia and SCA6. The region consists of 3.3 million base pairs (Mb) of DNA sequences with approximately 100 known and predicted genes. Identification of the responsible gene for SCA26 ataxia will provide further insight into mechanisms of neurodegeneration.

Mega2: data-handling for facilitating genetic linkage and association analyses

Mega2, the manipulation environment for genetic analysis, transparently allows users to process genetic data for family-based or case/control studies accurately and efficiently. In addition to data validation checks, Mega2 provides analysis setup capabilities for a broad choice of commonly used genetic analysis programs, including SimWalk2, ASPEX, GeneHunter, SLINK, SIMULATE, S.A.G.E., SOLAR, Vitesse, Allegro, PREST, PAP, Loki, Merlin and MENDEL.

AVAILABILITY

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Molecular dissection of the events leading to inactivation of the FMR1 gene

The analysis of a lymphoblastoid cell line (5106), derived from a rare individual of normal intelligence with an unmethylated full mutation of the FMR1 gene, allowed us to reconstruct the chain of molecular events leading to the FMR1 inactivation and to fragile X syndrome. We found that lack of DNA methylation of the entire promoter region, including the expanded CGG repeat, correlates with methylation of lysine 4 residue on the N-tail of histone H3 (H3-K4), as in normal controls. Normal levels of FMR1 mRNA were detected by real-time fluorescent RT-PCR (0.8-1.4 times compared with a control sample), but mRNA translation was less efficient (-40%), as judged by polysome profiling, resulting in reduced levels of FMRP protein (approximately 30% of a normal control). These results underline once more that CGG repeat amplification per se does not prevent FMR1 transcription and FMRP production in the absence of DNA methylation. Surprisingly, we found by chromatin immunoprecipitation that cell line 5106 has deacetylated histones H3 and H4 as well as methylated lysine 9 on histone H3 (H3-K9), like fragile X cell lines, in both the promoter and exon 1. This indicates that these two epigenetic marks (i.e. histone deacetylation and H3-K9 methylation) can be established in the absence of DNA methylation and do not interfere with active gene transcription, contrary to expectation. Our results also suggest that the molecular pathways regulating DNA and H3-K4 methylation are independent from those regulating histone acetylation and H3-K9 methylation.

Genome-wide demethylation destabilizes CTG.CAG trinucleotide repeats in mammalian cells

Many neurological diseases, including myotonic dystrophy, Huntington's disease and several spinocerebellar ataxias, result from intergenerational increases in the length of a CTG.CAG repeat tract. Although the basis for intergenerational repeat expansion is unclear, repeat tracts are especially unstable during germline development and production of gametes. Mammalian development is characterized by waves of genome-wide demethylation and remethylation. To test whether changes in methylation status might contribute to trinucleotide repeat instability, we examined the effects of DNA methyltransferase inhibitors on trinucleotide repeat stability in mammalian cells. Using a selectable genetic system for detection of repeat contractions in CHO cells, we showed that the rate of contractions increased >1000-fold upon treatment with the DNA methyltransferase inhibitor 5-aza-deoxycytidine (5-aza-CdR). The link between DNA demethylation and repeat instability was strengthened by similar results obtained with hydralazine treatment, which inhibits expression of DNA methyltransferase. In human cells from myotonic dystrophy patients, treatment with 5-aza-CdR strongly destabilized repeat tracts in the DMPK gene, with a clear bias toward expansion. The bias toward expansion events and changes in repeat length that occur in jumps, rather than by accumulation of small changes, are reminiscent of the intergenerational repeat instability observed in human patients. The dramatic destabilizing effect of DNA methyltransferase inhibitors supports the hypothesis that changes in methylation patterns during epigenetic reprogramming may trigger the intergenerational repeat expansions that lead to disease.

Loss of FMR1 hypermethylation in somatic cell heterokaryons

Fragile X syndrome is associated with a trinucleotide (CGG) repeat expansion in the 5'-untranslated region of the FMR1 gene and hypermethylation of the FMR1 promoter. Rare cases of clinically normal males (HFM) have been identified with an expanded CGG repeat; however, here, the FMR1 promoter is not methylated. Using classical complementation (cell fusion) studies, we analyzed if possible differences in the genetic background between HFM and cells from individuals with fragile X syndrome (FX cells) could have an influence on the methylation status of the FMR1 promoter. We observed that demethylation of the hypermethylated FMR1 promoter can occur when FX cells are complemented (by cell fusion) with cells from HFM as well as with cells from control individuals. The observed demethylation is specific and can happen without DNA replication. In contrast, demethylation was not observed when cells from unrelated individuals with fragile X syndrome were fused, indicating that FX cells have lost the necessary factor(s) to demethylate the aberrantly methylated FMR1 promoter.

Microcell-mediated chromosome transfer (MMCT): small cells with huge potential

Microcell-mediated chromosome transfer (MMCT) is a technique that has been in use since the 1970s for the fusion of microcells, containing single or a small number of chromosomes, with whole cells, and the subsequent selection of the hybrids. MMCT can be carried out with somatic cells, embryonic carcinoma (EC) or embryonic stem (ES) cell recipients, to study in vitro or in vivo effects of the transferred genetic material. These effects may be unpredictable--do the transferred genes function normally while in the regulatory milieu of the host cell? Will epigenetic effects become apparent, and how will these alter gene expression? What happens to the host cell phenotype? Here, we present a review of MMCT in which we argue that, although this is an old technique, its adaptability and efficiency make it an excellent method for the dissection of gene function and dysfunction in a very wide range of current systems.

The contribution of cis-elements to disease-associated repeat instability: clinical and experimental evidence

Alterations in the length (instability) of gene-specific microsatellites and minisatellites are associated with at least 35 human diseases. This review will discuss the various cis-elements that contribute to repeat instability, primarily through examination of the most abundant disease-associated repetitive element, trinucleotide repeats. For the purpose of this review, we define cis-elements to include the sequence of the repeat units, the length and purity of the repeat tracts, the sequences flanking the repeat, as well as the surrounding epigenetic environment, including DNA methylation and chromatin structure. Gender-, tissue-, developmental- and locus-specific cis-elements in conjunction with trans-factors may facilitate instability through the processes of DNA replication, repair and/or recombination. Here we review the available human data that supports the involvement of cis-elements in repeat instability with limited reference to model systems. In diverse tissues at different developmental times and at specific loci, repetitive elements display variable levels of instability, suggesting vastly different mechanisms may be responsible for repeat instability amongst the disease loci and between various tissues.

A distinct neurocognitive phenotype in female fragile-X premutation carriers assessed with visual attention tasks

Premature ovarian failure (POF) and underlying hormonal changes are recognized as a distinct phenotype in female fragile-X premutation carriers. Neurocognitive deficits, in particular mental retardation, are associated with the full mutation in males and females. In female full mutation carriers this neurocognitive phenotype is expressed more mildly than in males. Research on whether the fragile-X premutation is associated with a particular neurocognitive phenotype or not has been equivocal. By means of the Sonneville Visual Attentions Tasks (SVAT) computer-based battery of neurocognitive tasks, we assessed reaction time on different tasks in three groups of subjects: female premutation carriers, female full mutation carriers, and female control subjects. The results show that a fraction of the female premutation carriers perform poorly on several selective attention tasks, but not on other tasks. Their neurocognitive profile is different from that of control subjects and of the majority of female premutation carriers. It may also be different from the phenotype of female full mutation carriers, though in that respect this study remains inconclusive. These findings support earlier findings that the fragile-X premutation may affect neurocognitive functioning, in particular aspects of attention.

CpG methylation modifies the genetic stability of cloned repeat sequences

The genetic stability of tandemly repeated DNAs is affected by repeat sequence, tract length, tract purity, and replication direction. Alterations in DNA methylation status are thought to influence many processes of mutagenesis. By use of bacterial and primate cell systems, we have determined the effect of CpG methylation on the genetic stability of cloned di-, tri-, penta- and minisatellite repeated DNA sequences. Depending on the repeat sequence, methylation can significantly enhance or reduce its genetic stability. This effect was evident when repeat tracts were replicated from either direction. Unexpectedly, methylation of adjacent sequences altered the stability of contiguous repeat sequences void of methylatable sites. Of the seven repeat sequences investigated, methylation stabilized five, destabilized one, and had no effect on another. Thus, although methylation generally stabilized repeat tracts, its influence depended on the sequence of the repeat. The current results lend support to the notion that the biological consequences of CpG methylation may be affected through local alterations of DNA structure as well as through direct protein-DNA interactions. In vivo CpG methylation in bacteria may have technical applications for the isolation and stable propagation of DNA sequences that have been recalcitrant to isolation and/or analyses because of their extreme instability.

Advances in understanding of fragile X pathogenesis and FMRP function, and in identification of X linked mental retardation genes

The fragile X mental retardation syndrome is caused by large methylated expansions of a CGG repeat in the FMR1 gene that lead to the loss of expression of FMRP, an RNA-binding protein. FMRP is proposed to act as a regulator of mRNA transport or translation that plays a role in synaptic maturation and function. The recent observations of unexpected phenotypes in some carriers of fragile X premutations suggest a pathological role, in these individuals, of an abnormal FMR1 mRNA. FMRP was recently shown to interact preferentially with mRNAs containing a G quartet structure. Mouse and Drosophila models are used to decipher the function of FMRP, which was found to inhibit translation of some mRNA targets, but may be stimulatory in other cases. Proteins interacting with FMRP have been identified, and suggest a link with the Rac1 GTPase pathway that is important in neuronal maturation. Recent advances also include identification of other genes implicated in X-linked mental retardation.

The fragile X gene and its function

The fragile X syndrome represents the most common inherited cause of mental retardation worldwide. It is caused by a stretch of CGG repeats within the fragile X gene, which increases in length as it is transmitted from generation to generation. Once the repeat exceeds a threshold length, no protein is produced resulting in the fragile X phenotype. Ten years after the discovery of the gene, much has been learned about the function of the fragile X protein. Knowledge has been collected about the mutation mechanism, although still not all players that allow the destabilization of the CGG repeat are known.