DNA Methylation: Evolution


The understanding of how a biological feature has evolved is limited to the existing knowledge concerning this feature and the ability to interpret the available data. In an account of evolution of DNA methylation, similarities and differences in the structure of DNA methyltransferases should be considered, as well as the diversity of methylation patterns and the variety of biological processes that involve DNA methylation.

Keywords: DNA methyltransferases; DNA methylation patterns; DNA methylation functions

Figure 1.

DNA methyltransferase (MTase) gene structure: phylogenetic variations. All MTases contain a catalytic domain with consensus motifs I–X. Motifs I and X constitute together the methyl donor S‐adenosyl methionine (AdoMet) binding site. Motif IV with proline–cystein (PC) fully conserved dipeptide provides the SH group required for methyl transfer. Motif IX stabilizes the target recognition domain (TRD), which is located between motifs VIII and IX. Eukaryotic MTases contain also an N‐terminal domain of different lengths. Although plant and animal enzymes show structural similarities, the plant enzymes lack the cystein‐rich and TRD regions, but conserve the acidic region, which is rich in glutamine and aspartate residues. Chromomethyltransferase (CMT) MTases have a conserved chromodomain inserted between motifs II and IV of the catalytic domain. I–X: conserved motifs; PC: proline–cystein (active site); TRD: target recognition domain (variable region); a.a.: amino acid residues; GK: glutamyl‐lysyl repeats; Dnmt0: Dnmt1 transcript in oocytes; NLS: nuclear localization signal; TRF: targeting to replication forks; AR: acidic region; CD: chromodomain.



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Further Reading

Antequera F (2003) Structure, function and evolution of CpG island promoters. Cellular and Molecular Life Sciences 60: 1647–1658.

Bestor TH (2000) The DNA methyltransferases of mammals. Human Molecular Genetics 9: 2395–2402.

Bird AP (1995) Gene number, noise reduction and biological complexity. Trends in Genetics 11: 94–100.

Colot V and Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21: 402–411.

Hendrich B and Tweedie S (2003) The methyl‐CpG binding domain and the evolving role of DNA methylation in animals. Trends Genetics 19: 269–277.

Razin A, Cedar H and Riggs AD (eds) (1984) DNA Methylation: Biochemistry and Biological Significance. New York, NY: Springer‐Verlag.

Selker EU (1997) Epigenetic phenomena in filamentous fungi: useful paradigms or repeat‐induced confusion? Trends in Genetics 13: 296–301.

Weber M, Hellmann I, Stadler MB et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics 39: 457–466.

Yoder JA, Walsh CP and Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends in Genetics 13: 335–340.

Web Links

DNA (cytosine‐5‐)‐methyltransferase 3 beta (DNMT3B); LocusID: 1789. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=1789

DNA (cytosine‐5‐)‐methyltransferase 3 beta (DNMT3B); MIM number: 602900. OMIM: http://www3.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?602900

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Razin, Aharon, and Shemer, Ruth(Dec 2007) DNA Methylation: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005122.pub2]