Trends in Biochemical Sciences
Genomic DNA methylation: the mark and its mediators
Introduction
DNA methylation is found in the genomes of diverse organisms including both prokaryotes and eukaryotes. In prokaryotes, DNA methylation occurs on both cytosine and adenine bases and encompasses part of the host restriction system (reviewed in Ref. [1]). In multicellular eukaryotes, however, methylation seems to be confined to cytosine bases and is associated with a repressed chromatin state and inhibition of gene expression [2]. DNA methylation is essential for viability in mice, because targeted disruption of the DNA methyltransferase enzymes results in lethality 3, 4.
There are two general mechanisms by which DNA methylation inhibits gene expression: first, modification of cytosine bases can inhibit the association of some DNA-binding factors with their cognate DNA recognition sequences [5]; and second, proteins that recognize methyl-CpG can elicit the repressive potential of methylated DNA 6, 7. Methyl-CpG-binding proteins (MBPs) use transcriptional co-repressor molecules to silence transcription and to modify surrounding chromatin, providing a link between DNA methylation and chromatin remodelling and modification 8, 9, 10, 11, 12, 13.
In this review, we focus on recent advances in our understanding of the mechanisms by which DNA methylation is targeted for transcriptional repression and the role of MBPs in interpreting the methyl-CpG signal and silencing gene expression. We emphasize examples from mammalian systems, including studies on animal models, because several recent reviews have covered topics of DNA methylation and silencing in plants and fungi 14, 15, 16, 17, 18.
Section snippets
DNA methyltransferases
Mammalian cytosine DNA methyltransferase enzymes fit into two general classes based on their preferred DNA substrate. The de novo methyltransferases DNMT3a and DNMT3b are mainly responsible for introducing cytosine methylation at previously unmethylated CpG sites, whereas the maintenance methyltransferase DNMT1 copies pre-existing methylation patterns onto the new DNA strand during DNA replication. A fourth DNA methyltransferase, DNMT2, shows weak DNA methyltransferase activity in vitro [19],
Coupling epigenetic modification of DNA to gene expression silencing
DNA methylation is linked with transcriptional silencing of associated genes 6, 40, 41, 42, and much effort has been invested in studying the mechanisms that underpin this relationship. Two basic models have evolved: in the first, DNA methylation can directly repress transcription by blocking transcriptional activators from binding to cognate DNA sequences [5]; in the second, MBPs recognize methylated DNA and recruit co-repressors to silence gene expression directly 9, 43 (Figure 2a,b). For
A family of methyl-CpG-binding proteins
Biochemical activities that specifically recognize methyl-CpG were identified more than a decade ago 58, 59. Characterization of the methyl-CpG-binding domain (MBD) – the protein motif responsible for binding to methylated CpG dinucleotides – facilitated bioinformatic identification of a family of proteins that share this domain [7] (Figure 3). With the exception of MBD3, which contains amino acid substitutions that prevent binding to methyl-CpG, the mammalian MBD proteins (named MBD1–MBD4) and
Concluding remarks
The absolute requirement for an intact system for DNA methylation in mice suggests that this epigenetic modification has a vital role in development; however, studies aimed at understanding the scope of the impact that DNA methylation has on development have barely scratched the surface. The molecular characterization of enzymes and proteins involved in placing and interpreting the DNA methylation signals and, more recently, the availability of mouse knockout lines for these components have
Acknowledgements
Work in the Bird laboratory is supported by the Wellcome Trust, the Rett Syndrome Research Foundation, Rett Syndrome UK (Jeans for Genes) and Cancer Research UK. R.J.K. is a Wellcome Trust Prize Student.
References (91)
- et al.
Methylation-induced repression – belts, braces, and chromatin
Cell
(1999) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
Cell
(1992)DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
Cell
(1999)- et al.
DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein
Cell
(1991) - et al.
Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly
Mol. Cell
(2004) Gardening the genome: DNA methylation in Arabidopsis thaliana
Nat. Rev. Genet.
(2005)- et al.
Controlling DNA methylation: many roads to one modification
Curr. Opin. Genet. Dev.
(2005) - et al.
The methyl-CpG binding domain and the evolving role of DNA methylation in animals
Trends Genet.
(2003) The human Dnmt2 has residual DNA-(cytosine-C5) methyltransferase activity
J. Biol. Chem.
(2003)DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction
J. Biol. Chem.
(2004)