Elsevier

Ageing Research Reviews

Volume 8, Issue 4, October 2009, Pages 314-327
Ageing Research Reviews

Review
Suicidal function of DNA methylation in age-related genome disintegration

https://doi.org/10.1016/j.arr.2009.04.005Get rights and content

Abstract

This article is dedicated to the 60th anniversary of 5-methylcytosine discovery in DNA. Cytosine methylation can affect genetic and epigenetic processes, works as a part of the genome-defense system and has mutagenic activity; however, the biological functions of this enzymatic modification are not well understood. This review will put forward the hypothesis that the host-defense role of DNA methylation in silencing and mutational destroying of retroviruses and other intragenomic parasites was extended during evolution to most host genes that have to be inactivated in differentiated somatic cells, where it acquired a new function in age-related self-destruction of the genome. The proposed model considers DNA methylation as the generator of 5mC > T transitions that induce 40–70% of all spontaneous somatic mutations of the multiple classes at CpG and CpNpG sites and flanking nucleotides in the p53, FIX, hprt, gpt human genes and some transgenes. The accumulation of 5mC-dependent mutations explains: global changes in the structure of the vertebrate genome throughout evolution; the loss of most 5mC from the DNA of various species over their lifespan and the Hayflick limit of normal cells; the polymorphism of methylation sites, including asymmetric mCpNpN sites; cyclical changes of methylation and demethylation in genes. The suicidal function of methylation may be a special genetic mechanism for increasing DNA damage and the programmed genome disintegration responsible for cell apoptosis and organism aging and death.

Introduction

Although 5-methylcytosine (5mC, mC) was discovered in DNA sixty years ago (Hotchkis, 1948, Wyatt, 1951), the biological role of this enzymatic cytosine modification in eukaryotic organisms continues to be one of the most intriguing mysteries in molecular genetics. DNA methylation affects many genetic and epigenetic processes, including regulation of gene activity and genome imprinting, by inducing chromatin remodeling (Bird, 2002, Laird, 2005). At the same time, the methylation of cytosine residues produces mutation hotspots that can lead to human genetic diseases and cancer (Cooper and Youssoufian, 1988, Rideout et al., 1990). A paradox emerges from the recognition that the genetic regulation usually requires stabile and reliable mechanisms, but methylation destabilizes structure and inactivates genes throughout the organism.

A number of other puzzling facts about DNA methylation have accrued since its discovery (Jones, 1999). For example, some eukaryotes lack DNA methyltransferase genes (MTase) (Ponger, 2005), and the 5mC content in the genome varies by more than 100-fold across species (Lyko et al., 2000, Vanyushin, 2006). Most of the genes that are methylated in vertebrates are unmethylated in lower eukaryotic species (Bird, 2002, Selker et al., 2003). The bulk of the available 5′-CpG-3′ (CG) sites are methylated in embryos (Monk et al., 1987), whereas most 5mC are lost from the genome of various species over their ontogenesis (Mazin, 1993a, Lyko et al., 2000). DNA methylation patterns are extraordinarily labile and substantial inter-individual variation has been demonstrated, even for identical twins (Fraga et al., 2005, Heijmans et al., 2007). Inactivation of the dnmt1 MTase gene causes DNA demethylation and death of homozygous mouse embryos in early development (Li et al., 1992, Takebayashi et al., 2007). However, heterozygous DNMT1-knockdown mice show increased 5mC content with aging (Yung et al., 2001), and embryonic stem (ES) cells grow normally in the absence of MTases (Li et al., 1992, Tsumura et al., 2006). About 80% of ancestral CG sites have disappeared from the human genome during evolution (Josse et al., 1961) and many spontaneous mutations result in new CG sites (Mazin, 1994a, Yang et al., 1996). The detection of asymmetrically methylated mCpNpN sites (Meyer et al., 1994, Ramsahoye et al., 2000), massive methylation of post-replicative DNA (Vanyushin, 1984) and aberrant methylation of genes (Esteller, 2005, Kobayashi et al., 2007) all contradict the mechanism of semi-conservative inheritance of methylation patterns (Holliday and Pugh, 1975, Riggs, 1975). The age-related loss of most 5mC from the genome of cultured normal cells coincides with their Hayflick limit (Mazin, 1993c, Mazin, 1995), but DNA hypermethylation is observed in cancer cells growing in vitro (Wilson and Jones, 1983, Gray et al., 1991). Conversely, a global reduction in methylation is typical for the genome of cancer cells in vivo (Gama-Sosa et al., 1983, Cadieux et al., 2006). Resolution of these paradoxes is a prerequisite for understanding the biological role of DNA methylation, but no existing hypothesis can explain all of these contradictory observations. The reasons may be hidden in the poly-functionality of methylation.

In this review, the methodology of the systems analysis was used to compose a multicolored portrait of the mutagenic function of DNA methylation from the fractured, yet key, experimental facts accumulated over the years. Each section of the article reflects an integral part of the whole picture and discusses how this mechanism works on molecular, cellular, organismal, and evolutionary levels and over cell cycle, ontogenesis, and specific. The synthesis of these component parts into coherent model allowed the proposal of the hypothesis, which considers a role of DNA methylation in the age-related genome self-destruction as the universal genetic mechanism for programming cell's and organism's aging and death. The epigenetic function of methylation has been discussed in many recent reviews (Doerfler, 2008, Feinberg, 2008, Ooi and Bestor, 2008, Calvanese et al., 2009, Sinclair and Oberdoerffer, 2009).

Section snippets

DNA methylation induces most of spontaneous mutations of multiple classes

The mutagenic activity of cytosine methylation was studied in detail, and it is commonly accepted that CG methylation sites are hotspots for most C > T and G > A (G:C > A:T) transition mutations in human genes (Cooper and Krawczak, 1989). CG-containing restriction sites are often polymorphic and have a high frequency of 5mC > T mutations in both Esherichia coli and human DNA (Barker et al., 1984, Coulondre et al., 1985). Most single-base substitutions (BS) that are responsible for genetic diseases and

Cytosine methylation as a mutagen

Why does DNA methylation produce so many mutations? Pathways for the several of several different classes of mutations at CG sites are presented in Fig. 1. Half-methylated CG/mCG (hmCG) sites arise in newly synthesized DNA during replication (I). These sites are recognized by the “maintenance” MTase, DNMT1, which is integrated into the DNA replication enzymatic complex and restores symmetrically methylated CG sites (1). A fraction of the newly formed 5mC residues are usually deaminated during

The origin of polymorphism of methylation sites and asymmetric mCpNpN sites

One of the conclusions that follows from the model presented on the Fig. 1 is that a final product of cytosine methylation may be asymmetrically methylated TG/mCA sites (1 > 2 > 6 > 7). The unusually methylated mCpNpN (mCNN, N is A, T, C, or mC) sites have been found in the DNA of fungi, insects, plants, and animals over the last decade (Selker and Stevens, 1985, Meyer et al., 1994, Ramsahoye et al., 2000, Wada et al., 2003). It was shown that these non-palindromic sites can result from the special

Relict 5mC > T mutations at CpG sites in DNA

5mC > T transitions may occur not only in somatic cells, but also in germline cells of various species. Since these mutations are generally irreversible, owing to the lower chance of inverse substitutions (T > C > 5mC) and the fact that most are neutral, these mutations have accumulated in the genome of vertebrate germlines over millions years of evolution (Cooper and Krawczak, 1989). Thus, the observed frequency of CG sites in human DNA is only eight dinucleotides per 1000n (kbp) of DNA instead of

The genome loses most 5mC over ontogenesis in various species and the hayflick limit of normal cells

One of the most intriguing results, which follows from the model of accumulation of methylation-dependent mutations, is the possible mechanism of reduction in 5mC content in genome with age (Fig. 1). Age-related DNA demethylation was demonstrated for differentiating mammalian cells (Jost et al., 2001, Kress et al., 2001, Kress et al., 2006), normal cells cultured in vitro (Wilson and Jones, 1983, Fairweather et al., 1985, Gray et al., 1991), growing higher plants (Kirnos et al., 1983),

What are the functions of DNA methylation?

The data considered above allow us to assume that cytosine methylation is the special mutagenic mechanism, which may be implicated in various biological processes. Eukaryotic MTases may have evolved from prokaryotic methylation-restriction enzymes or tRNA methyltransferases (Bestor, 1990, Jurkowski et al., 2008) and have served diverse functions throughout genome evolution.

Evolution would be impossible without the spontaneous mutations that are a source of variability on which natural selection

DNA methylation as a mechanism of aging

Let us consider in more detail a role of DNA methylation in the age-related genome self-destruction, which may be one of the mechanisms of aging in higher eukaryotic organisms. Fifteen years ago, the hypothesis was put forward that DNA methylation is the source of the genome instability that is implicated in the aging process (Mazin, 1994b). As expected, cytosine methylation works as a special counter of cell divisions. About 50 millions new 5mC residues arise in the haploid mammalian genome (3 ×

Paradoxes of DNA methylation

The poly-functionality of DNA methylation and its crosstalk with various genetic processes might explain many of the paradoxical facts referred to in the Introduction. For example, there is a “5mC value paradox”, as the 5mC content in DNA can vary from undetectable levels to more than10 mol% across eukaryotic species. Free-living soil worms (Caenorhabditis elegans) and baker's yeast (S. cerevisiae) lack MTase genes and their genomes do not appear contain 5mC (Ponger, 2005). DNA methylation was

Conclusion

The focus of this review has been that DNA methylation is a potent endogenous generator of mutations that may induce high level of DNA damage and genome disintegration responsible for cell apoptosis and organism aging and death. The hypothesis about suicidal function of methylation is presented here as an integral model, which has been examined in detail and from a number of different perspectives. This function may be involved in various genetic processes. As a generator of mutations and a

Acknowledgements

I am grateful to P.J. Allenberg, N.E. Braudo, C.D. Jackson, and T.I. Vlasova for comments, T.I. Heifetz for proofreading the manuscript, L.A. Mazin for design of figures and web site www.DNAgeing.net and my colleagues in Moscow State University for their support.

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