Genomic imprinting in unstable DNA diseases

Epigenetics of Complex Diseases: From General Theory to Laboratory Experiments

Despite significant effort, understanding the causes and mechanisms of complex non-Mendelian diseases remains a key challenge. Although numerous molecular genetic linkage and association studies have been conducted in order to explain the heritable predisposition to complex diseases, the resulting data are quite often inconsistent and even controversial. In a similar way, identification of environmental factors causal to a disease is difficult. In this article, a new interpretation of the paradigm of "genes plus environment" is presented in which the emphasis is shifted to epigenetic misregulation as a major etiopathogenic factor. Epigenetic mechanisms are consistent with various non-Mendelian irregularities of complex diseases, such as the existence of clinically indistinguishable sporadic and familial cases, sexual dimorphism, relatively late age of onset and peaks of susceptibility to some diseases, discordance of monozygotic twins and major fluctuations on the course of disease severity. It is also suggested that a substantial portion of phenotypic variance that traditionally has been attributed to environmental effects may result from stochastic epigenetic events in the cell. It is argued that epigenetic strategies, when applied in parallel with the traditional genetic ones, may significantly advance the discovery of etiopathogenic mechanisms of complex diseases. The second part of this chapter is dedicated to a review of laboratory methods for DNA methylation analysis, which may be useful in the study of complex diseases. In this context, epigenetic microarray technologies are emphasized, as it is evident that such technologies will significantly advance epigenetic analyses in complex diseases.

Complex disease, gender and epigenetics

Gender differences in susceptibility to complex disease such as asthma, diabetes, lupus, autism and major depression, among numerous other disorders, represent one of the hallmarks of non-Mendelian biology. It has been generally accepted that endocrinological differences are involved in the sexual dimorphism of complex disease; however, specific molecular mechanisms of such hormonal effects have not been elucidated yet. This paper will review evidence that sex hormone action may be mediated via gene-specific epigenetic modifications of DNA and histones. The epigenetic modifications can explain sex effects at DNA sequence polymorphisms and haplotypes identified in gender-stratified genetic linkage and association studies. Hormone-induced DNA methylation and histone modification changes at specific gene regulatory regions may increase or reduce the risk of a disease. The epigenetic interpretation of sexual dimorphism fits well into the epigenetic theory of complex disease, which argues for the primary pathogenic role of inherited and/or acquired epigenetic misregulation rather than DNA sequence variation. The new experimental strategies, especially the high throughput microarray-based epigenetic profiling, can be used for testing the epigenetic hypothesis of gender effects in complex diseases.

5-Methylcytosine as a marker for the monitoring of DNA methylation

The extent of the DNA methylation of genomic DNA as well as the methylation pattern of many gene-regulatory areas are important aspects with regard to the state of genetic information, especially their expression. There is growing evidence that aberrant methylation is associated with many serious pathological consequences. As genetic research advances, many different approaches have been employed to determine the overall level of DNA methylation in a genome or to reveal the methylation state of particular nucleotide residues, starting from semiquantitative methods up to new and powerful techniques. In this paper, the currently employed techniques are reviewed both from the point of view of their relevance in genomic research and of their analytical application. The methods discussed include approaches based on chromatographic separation (thin-layer chromatography, high-performance liquid chromatography, affinity chromatography), separation in an electric field (capillary electrophoresis, gel electrophoresis in combination with methylation-sensitive restriction enzymes and/or specific sequencing protocols), and some other methodological procedures (mass spectrometry, methyl accepting capacity assay and immunoassays).

Recombination-induced CAG trinucleotide repeat expansions in yeast involve the MRE11-RAD50-XRS2 complex

Recombination induced by double-strand breaks (DSBs) in yeast leads to a higher proportion of expansions to contractions than does replication-associated tract length changes. Expansions are apparently dependent on the property of the repeat array to form hairpins, since DSB repair of a CAA(87) repeat induces only contractions of the repeat sequence. DSB-repair efficiency is reduced by 40% when DNA synthesis must traverse a CAG(98) array, as compared with a CAA(87) array. These data indicate that repair- associated DNA synthesis is inhibited by secondary structures formed by CAG(98) and that these structures promote repeat expansions during DSB repair. Overexpression of Mre11p or Rad50p suppresses the inhibition of DSB repair by CAG(98) and significantly increases the average size of expansions found at the recipient locus. Both effects are dependent on the integrity of the Mre11p-Rad50p-Xrs2p complex. The Mre11 complex thus appears to be directly involved in removing CAG or CTG hairpins that arise frequently during DNA synthesis accompanying gene conversion of these trinucleotide repeats.

Alzheimer's disease and down syndrome: from meiosis to dementia

Several molecular and clinical similarities have been detected in Alzheimer's disease (AD) and Down syndrome (DS). The most remarkable feature is abnormal accumulation of beta-amyloid in the brains of both individuals affected with AD and aging DS patients followed by dementia. In addition, AD patients exhibit dermatoglyphic patterns similar to those in DS, and late maternal age is a risk factor in both diseases. AD and DS could be related genetically because AD families exhibit a higher rate of DS cases and vice versa. Although numerous discoveries have been made in the elucidation of the etiopathogenic factors in AD and DS, little progress has been achieved in understanding the origin of the common features of the two diseases. This article reviews clinical and molecular similarities in DS and AD and also chromosome 21 studies in both diseases. A new hypothesis explaining the association between AD and DS is suggested, and this hypothesis is based on the poorly understood molecular phenomenon of aberrant meiotic recombination. Aberration in meiotic recombination has been consistently detected in chromosomal diseases including trisomy 21 and sex chromosomes. There are no studies dedicated to meiotic recombination in genetic diseases; however, evidence for disturbed recombination has been documented in several neurological diseases such as Huntington's disease, myotonic dystrophy, and fragile X syndrome. Interestingly, the rate of trisomic XXY children born to mothers transmitting fragile X mutation is higher than expected. This finding suggests that AD could be associated with DS in a similar way to which fragile X syndrome is related to trisomy of sex chromosomes. Based on analogy with fragile X syndrome, it can be predicted that AD should demonstrate aberrant meiotic recombination in chromosome 21, most likely in the region D21S1/S11-D21S16 which is linked to early onset familial AD. Based on the same rationale, different patterns of meiotic recombination in the nondisjunct chromosome 21 within DS patients grouped according to the concomitant disease are predicted.

DNA binding discrimination of the murine DNA cytosine-C5 methyltransferase

Mammalian DNA cytosine-C5 methyltransferase modifies the CpG dinucleotide in the context of many different genomic sequences. A rigorous DNA binding assay was developed for the murine enzyme and used to define how sequences flanking the CpG dinucleotide affect the stability of the enzyme:DNA complex. Oligonucleotides containing a single CpG site form reversible 1:1 complexes with the enzyme that are sequence-specific. A guanine/cytosine-rich 30 base-pair sequence, a mimic of the GC-box cis-element, bound threefold more tightly than an adenine/thymine-rich sequence, a mimic of the cyclic AMP responsive element. However, the binding discrimination between hemi- and unmethylated forms of these DNA substrates was small, as we previously observed at the K(m)DNA level (Biochemistry, 35, 7308-7315 (1996)). Single-stranded substrates are bound much more weakly than double-stranded DNA forms. An in vitro screening method was used to select for CpG flanking sequence preferences of the DNA methyltransferase from a large, divergent population of DNA substrates. After five iterative rounds of increasing selective pressure, guanosine/cytosine-rich sequences were abundant and contributed to binding stabilization for at least 12 base-pairs on either side of a central CpG. Our results suggest a read-out of sequence-dependent conformational features, such as helical flexibility, minor groove dimensions and critical phosphate orientation and mobility, rather than interactions with specific bases over the course of two complete helical turns. Thus, both studies reveal a preference for guanosine/cytosine deoxynucleotides flanking the cognate CpG. The enzyme specificity for similar sequences in the genome may contribute to the in vivo functions of this vital enzyme.